ARTICLE | doi:10.20944/preprints202005.0463.v3
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2; genome-wide mutations; transition; transversion; nonsynonymous and synonymous mutations; microevolution
Online: 5 October 2020 (10:56:36 CEST)
To understand SARS-CoV-2 microevolution, this study explored the genome-wide frequency, gene-wise distribution, and molecular nature of all point-mutations detected across its 71,703 RNA-genomes deposited in the GISAID repository, till 21 August 2020. Globally, nsp1/nsp2/nsp3/ nsp11 and orf7a/orf3a/S were the most mutation-ridden non-structural and structural genes respectively. Phylogeny based on 4,618 spatiotemporally-representative genomes revealed that entities belonging to the early lineages are mostly spread over Asian countries (including India, the biggest hotspot of the pandemic) whereas the recently-derived lineages are more globally distributed. Of the total 16,602 polymorphism-bearing sites in the pan-genome, 11,037 and 4,965 involved transitions and transversions, which in turn were predominated by cytidine-to-uridine and guanosine-to-uridine conversions, respectively. Positive selection of nonsynonymous mutations (dN/dS >1) in most of the structural, but not non-structural, genes indicated that SARS-CoV-2 has already harmonized its replication/transcription machineries with the host’s metabolic system, while it is still redefining virulence/transmissibility strategies at the molecular level.
ARTICLE | doi:10.20944/preprints202004.0281.v1
Online: 16 April 2020 (15:30:56 CEST)
Spike protein of Coronaviruses help in receptor binding and virus entry into the host cells. While spike protein helps in receptor mediated virus entry, it is also extremely important as an immunogen as it is the most accessible part of the viral architecture. SARS-CoV2 or COVID 19 has four different structural proteins, N (nucleocapsid), M (membrane), E (envelope) and S (spike). Although all these proteins are the part of virus structure, only E, M and S are exposed towards the outer surface of the virus particle. S protein forms a knob like structure protruding outwards beyond the other structural proteins. It forms homotrimers containing an S1 and S2 as monomers and together they form the viral spikes. Mutations in structural proteins of virus play crucial role in viral virulence by determining generation of antibody escape variants and cellular tropism. In this paper we have performed in depth analyses of spike protein sequence from various parts of the world and tried to correlate the data with the current situation of virulent nature of this virus in certain parts of the world much more as compared to others. Here, we have focussed on the isolates from the North America and have pointed out three major hot spots of mutations in the S1 subunit.
REVIEW | doi:10.20944/preprints202308.1235.v2
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Meningioma; NF2 mutations; biomarker; miRNA; proteomics
Online: 3 November 2023 (16:28:48 CET)
Meningiomas are the most prevalent primary intracranial tumors. The majority are benign but can undergo dedifferentiation into advanced grades classified by World Health Organization (WHO) into Grades 1 to 3. Meningiomas tremendous variability in tumor behavior and slow growth rates complicate their diagnosis and treatment. A deeper comprehension of the molecular pathways and cellular microenvironment factors implicated in meningioma survival and pathology is needed. This review summarizes the known genetic and epigenetic aberrations involved in meningioma, with a focus on Neurofibromatosis type 2 (NF2) and non-NF2 mutations. Novel potential biomarkers for meningioma diagnosis and prognosis are also discussed, including epigenetic-, RNA-, metabolomics, and protein-based markers. Finally, the landscape of available meningioma-specific animal models is overviewed. Use of these animal models can enable planning of adjuvant treatment, potentially assisting in preoperative and postoperative decision-making. Discovery of novel biomarkers will allow, in combination with WHO grading, more precise meningioma grading, including meningioma identification, subtype determination, and prediction of metastasis, recurrence, and response to therapy. Moreover, these biomarkers may be exploited in the development of personalized targeted therapies that can distinguish between the 15 diverse meningioma subtypes.
ARTICLE | doi:10.20944/preprints202304.0083.v3
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: drug-resistant TB; heteroresistance; mutations; spoligotyping
Online: 9 June 2023 (15:36:21 CEST)
Drug-resistant tuberculosis (DR-TB) is still a major public health concern in South Africa. Mutations in M. tuberculosis can cause varying levels of phenotypic resistance to anti-TB medications. There have been no prior studies on gene mutations and the genotyping of DR-TB in the rural Eastern Cape Province; hence we aimed to identify DR-TB mutations, genetic diversity and allocated lineages among patients in this area. Using Xpert® MTB/RIF, we assessed the rifampin-resistance of sputum samples collected from 1157 patients suspected of having tuberculosis. GenoType MTBDR plus VER 2.0 was used for the detection of mutations causing resistance to anti-TB medications. The next step was to spotlight type 441 isolates. The most prevalent rifampin resistance-conferring mutations were in rpoB codon S531L, in INH-resistant strains, katG gene at codon S315TB and the inhA gene at codon C-15TB had highest mutations; 54.5% and 24.7%, respectively. In addition, 24.6% of strains showed mutations in both the rpoB and inhA genes, while 69.9% of strains showed mutations in both the katG and rpoB genes. Heteroresistance was seen in 17.9% of all cases in the study. According to spoligotyping analysis, Beijing families predominated. Investigating the evolutionary lineages of M. tuberculosis isolates can be done using the information provided by the study's diversity of mutations. In locations where these mutations have been discovered, decision-making regarding standardization of treatment regimens or individualized treatment may be aided by the detection frequency of rpoB, katG, and inhA mutations in various study areas.
ARTICLE | doi:10.20944/preprints202006.0024.v1
Online: 4 June 2020 (05:50:09 CEST)
COVID-19 pandemic has caused a large-scale havoc in almost every country across the globe, putting major challenges for the healthcare system in many parts of the world. Several of the laboratories are running in the race with undying efforts for developing potential vaccine, drugs or therapeutics to treat or prevent the infection. However, with the limited time window and high rate of infection, the task is very big for humanity to find a cure. With hundreds of genomic data of SARS-CoV-2 virus isolates from humans are being submitted almost every day, it is coming into knowledge that virus is mutating, slower in countries with sporadic cases, but higher in countries experiencing large outbreak. These types of mutations in virus may bring challenges in vaccine or therapeutic development for use in each and every country, as each hotspot region may have their own pattern of mutations in virus with ongoing outbreak. In our current study, we retrieved non-synonymous mutation data of around 12,225 SARS-CoV-2 virus samples isolated from humans globally, and discovered all mutations that are collectively happening in antibody epitope regions of the virus country-wise. We found a few numbers of epitope regions in SARS-CoV-2 that are highly conserved collectively in all variants and may be used for epitope-based vaccine development for whole world. We also found epitope regions that are conserved collectively in SARS-CoV-2 variants country-wise and can be used for customized epitope-based vaccine development in each different country.
INTERESTING IMAGES | doi:10.20944/preprints202309.1918.v1
Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: multidrug-resistant tuberculosis; genetic mutations; clinical cases.
Online: 28 September 2023 (08:02:58 CEST)
The emergence of M. tuberculosis strains resistant to Isoniazid (INH) and Rifampicin (RIF), the two most potent drugs of first-line anti-TB therapy is termed multidrug drug-resistant TB (MDR-TB). Multidrug-resistant tuberculosis has been a serious medical and epidemic problem all over the world. We present here a series of clinical cases consist of two patients diagnosed with isoniazid resistant tuberculosis. Histopathological examination supports the diagnosis of tuberculous granulomas. And the pathology molecular examination revealed the presence of Isoniazid-resistant Mycobacterium tuberculosis1,2 via the following mutation c.947G>A; p.Gly316Asp. Isoniazid-resistance is associated with mutations in the furA-katG and fabG1-inhA operons, as well as mutations in the ahpC gene. 64% of the isoniazid-resistance phenotypes were associated with the katG315 mutation worldwide. The second most common mutation is inhA-15, and it has been reported in 19% of the Isoniazid-resistant isolates. The significant association between the two mutations, inhA c-15 and katG 315 respectively, and the high-level resistance is of interest in the interpretation of current and future molecular diagnostic testing, as an early prediction of the level of Isoniazid-resistance is essential to decide the benefit of high-dose Isoniazid use.
ARTICLE | doi:10.20944/preprints202309.1910.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: Data Structures; Concurrency; Graph Processing; Graph Mutations
Online: 27 September 2023 (15:10:25 CEST)
The graph model enables a broad range of analysis, thus graph processing is an invaluable tool in data analytics. At the heart of every graph processing system lies a concurrent graph data structure that stores the graph. Such a data structure needs to be highly efficient for both graph algorithms and queries. Due to the continuous evolution, the sparsity, and the scale-free nature of real-world graphs, graph processing systems face the challenge of providing an appropriate graph data structure that enables both fast analytical workloads and low-memory fast graph mutations. Existing graph structures offer a hard tradeoff between read-only performance, update friendliness, and memory consumption upon updates. In this paper, we introduce CSR++, a new graph data structure that removes these tradeoffs and enables both fast read-only analytics and quick and memory-friendly mutations. CSR++ combines ideas from CSR, the fastest read-only data structure, and adjacency lists to achieve the best of both worlds. We compare CSR++ to CSR, adjacency lists from the Boost Graph Library, as well as state-of-the-art update-friendly graph structures: LLAMA, STINGER, GraphOne, and Teseo. In our evaluation, which is based on popular graph processing algorithms executed over real-world graphs, we show that CSR++ remains close to CSR in read-only concurrent performance (within 10% on average), while significantly outperforming CSR (by an order of magnitude) and LLAMA (by almost 2×) with frequent updates. We also show that both CSR++’s update throughput and analytics performance exceed that of several state-of-the-art graph structures, while maintaining low memory consumption when the workload includes updates.
ARTICLE | doi:10.20944/preprints202212.0359.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: tuberculosis; spatial analysis; mutations; spoligotypes; heteroresistance; cluster
Online: 20 December 2022 (08:10:25 CET)
Tuberculosis (TB), an infectious airborne disease caused by Mycobacterium tuberculosis (Mtb), is a serious public health threat reported as the leading cause of morbidity and mortality worldwide. South Africa is a high TB burden country with TB being the highest infectious disease killer. The study investigated the distribution and clustering of Mtb mutations and spoligotypes in rural Eastern Cape Province. The Mtb isolates included were 1,157 from DR-TB patients and analysed by LPA followed by spoligotyping of 441 isolates, of these, 36 were whole genome sequenced. Distribution of mutations and spoligotypes was done by spatial analysis and clustering analysis was done by Bayesian model-based clustering of allele frequencies at heterozygous sites, using Mclust package in R. The rpoB gene had highest number of mutations. The distribution of rpoB and katG mutations was more prevalent in four health care facilities, inhA mutations were more prevalent in three healthcare facilities and heteroresistant isolates were more prevalent in five healthcare facilities. The Mtb was genetically diverse with Beijing more prevalent and largely distributed. Spatial analysis and mapping of gene mutations and spoligotypes revealed better picture of distribution. Clustering of isolates indicates that there is transmission of mixed infection in this area.
COMMUNICATION | doi:10.20944/preprints202107.0302.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Aedes aegypti; Insecticides resistance; kdr mutations; Nigeria
Online: 13 July 2021 (11:26:32 CEST)
The outbreak of yellow fever transmitted by Aedes aegypti has been of major concern in Nigeria, this mosquito also transmits several other arboviruses globally. The control of many of the Aedes aegypti borne diseases relies heavily on the use of insecticides. Therefore, constant monitoring of insecticide resistance status and associated mechanisms in crucial within the local population. Here, we determined the resistance profile of adult Aedes aegypti from Ikorodu Local Government Area of Lagos State, Nigeria to different classes of insecticides using WHO procedures. The presence of kdr mutations F1534C, S989P and V1016G were also determined among resistant populations using molecular methods. High level of resistance to DDT and pyrethroid was rec-orded in Aedes aegypti in this study, though possible resistance to deltamethrin was reported in one of the locations. Resistance to bendiocarb was recorded in Majidun community while Aedes aegypti in both locations were susceptible to malathion. The presence of F1534C mutation associated with resistance in Aedes aegypti was detected for the first time in Nigeria, and the presence of S989P mutation was detected singly and in co-occurrence with F1534C for the first time in Africa. The role of these mutations in resistance phenotype expressed in Aedes aegypti in this study area need to established.
ARTICLE | doi:10.20944/preprints202008.0562.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: mutations; exon; p53; regulation; DNA; tumour suppressor
Online: 26 August 2020 (09:10:14 CEST)
Introduction: The tumour suppressor protein p53 commonly referred to as guardian of the genome plays important role in preserving the genome through the regulation of programmed cell death, DNA repair, energy metabolism, cell cycle entry or exit and senescence. Mutations in p53 can either result to a loss of tumour suppressor function or gain of oncogenic properties. Hence, mutations in p53 are the most frequent genetic mutational alteration in human cancers, associated with worse prognosis and more aggressive disease outcome. Methods: To assess the mutational hotspots and conserved regions of p53, I analyzed 76 complete p53 protein sequences covering whole exons from the NCBI GenBank database. Multiple sequence alignment (MSA) was done using ClustalX version 2.1. Results: Thirty-five (19) mutations were identified with more frequent mutations in amino acid (aa) position 72 and 79 (Exon 4), amino acid deletion in codon 112-122 (Exon 4), codon 213 (Exon 6), codon 248 (Exon 7), codon 273 (Exon 8) and codon 278 (Exon 8). Mutations at amino acid position 79, 248, 278 located in the DNA-binding domain exhibited more than one alteration in same position. Conclusions: Findings from this study revealed the prevalence of mutations in the DNA binding domain of p53 and the structure-function effect of the mutations. Assessing the pattern and frequency of p53 alterations, and analyzing it thoroughly for each carrier, could help in identifying correlations between p53 status and outcome and possible candidate for gene therapy.
REVIEW | doi:10.20944/preprints201812.0273.v3
Subject: Biology And Life Sciences, Biophysics Keywords: mutations; disease-causing mutations; polymorphism; folding free energy change; binding free energy change; drug discovery; in silico screening
Online: 28 January 2019 (11:39:23 CET)
Structural information of biological macromolecules is crucial and necessary to deliver predictions about the effects of mutations—whether polymorphic or deleterious (i.e., disease causing), wherein, thermodynamic parameters, namely, folding and binding free energies potentially serve as effective biomarkers. It may be emphasized that the effect of a mutation depends on various factors, including the type of protein (globular, membrane or intrinsically disordered protein) and the structural context to which it occurs. Such information may positively aid drug-design. Furthermore, due to the intrinsic plasticity of proteins, even mutations involving radical change of the structural and physico-chemical properties of the amino acids (native vs. mutant) can still have minimal effects of protein thermodynamics. However, if a mutation causes significant perturbation of either folding or binding free energies, it is quite likely to be deleterious. Mitigating such effects is a promising alternative to the traditional approaches of designing inhibitors. This can be done by structure-based in silico screening of small molecules for which binding to the dysfunctional protein restores its wild type thermodynamics. In this review we emphasize on the effects of mutations on two important biophysical characteristics, stability and binding affinity, and how structures can be used for structure-based drug design to mitigate the effects of disease-causing variants on the above biophysical characteristics.
REVIEW | doi:10.20944/preprints202309.0120.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: Melanoma; BRAF mutations; BRAF inhibitors; MEK inhibitors; Immunotherapy
Online: 4 September 2023 (15:46:20 CEST)
Skin cancer is a prevalent and heterogenous disease with several subtypes, such as melanoma, basal cell carcinoma, and squamous cell carcinoma. Among them, melanoma is the most aggressive subtype, with a higher propensity to spread compared to most solid tumors. The application of OMICS approaches has revolutionized the field of melanoma research by providing comprehensive insights into the molecular alterations and biological processes underlying melanoma development and progression. This review aims to offer an overview of melanoma biology, covering its transition from primary to malignant melanoma, as well as the key genes and pathways involved in the initiation and progression of this disease. Utilizing online databases, we extensively explored the general expression profile of genes, identified the most frequently altered genes, and gene mutations, and examined genetic alterations responsible for drug resistance. Additionally, we studied the mechanisms responsible for immune checkpoint inhibitors resistance in melanoma.
ARTICLE | doi:10.20944/preprints202307.1814.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; virus; transmission; mutations; Delta strain
Online: 27 July 2023 (09:36:12 CEST)
The rapid changes in the coronavirus genomes are creating new strains over time after the first variation found in Wuhan in 2019. SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) genotypes need periodically undergo whole genome sequencing. Genome sequencing has been extremely helpful in combating this virus because so many diagnoses, treatments, and vaccinations have been developed against it. To achieve this, we generated 17 high-quality whole-genome sequence data from 48 SARS-CoV-2 genotypes of COVID-19 patients who tested positive by PCR in the Tashkent city of Uzbekistan. We identified nucleotide polymorphisms, including nonsynonymous (missense) and synonymous mutations in the coding regions of the sequenced sample genomes. All whole genome sequences were categorized by phylogenetic analysis into the G clade (or GK sub-clade). A total of 134 mutations were identified, consisting of 65 shared and 69 unique mutations. Collectively, nucleotide changes represented one frameshift mutation, one conservative and disruptive insertion deletion, four upstream region mutations, four downstream region mutations, 39 synonymous mutations, and 84 missense mutations. Furthermore, bioinformatics web tools were used to analyze amino acid changes in virus genomes. Several amino acid mutations were found, which were not found in previously published Delta strain sequences.
ARTICLE | doi:10.20944/preprints202308.1895.v1
Subject: Public Health And Healthcare, Primary Health Care Keywords: keyword multidrug-resistant tuberculosis; gene mutations; heteroresistance; Beijing variants
Online: 29 August 2023 (03:33:51 CEST)
Multidrug-resistant tuberculosis emerged as a serious challenge to tuberculosis management and control. In the Eastern Cape, the Beijing variants are prevalent and a driving force of multidrug-resistant tuberculosis; hence, we investigated the distribution of gene mutations in Beijing strains compared to non-Beijing strains. Multidrug-resistant tuberculosis and heteroresistant isolates were identified in 412 sputum cultures by drug susceptibility testing. The isolates were analyzed for mutations in three genes associated with resistance to antituberculosis first-line drugs: katG and inhA promoters for isoniazid and rpoB for rifampicin. All isolates were genotyped by spoligotyping. There were more males than females and a more economically active age group in the study. The most prevalent mutations in rpoB resistance were in S531L, katG in S315Tb, and inhA in c-15tb. Heteroresistance was found in 18 isolates. Beijing variants were predominant. Most of the heteroresistant isolates were INH, with heteroresistance occurring more in the inhA gene mutation region c-15tb. Beijing and LAM variants were found more frequently in INH heteroresistant isolates. Mutations in katG S315Tb and rpoB S531L were higher in Beijing variants. The Beijing family is a major contributor to the epidemiological picture and accounts for most of the multidrug-resistant tuberculosis in the study area.
CASE REPORT | doi:10.20944/preprints202307.0290.v1
Subject: Medicine And Pharmacology, Surgery Keywords: vascular EDS; bowel perforation; case report; collagen; gene mutations
Online: 5 July 2023 (11:48:13 CEST)
Introduction: Ehlers-Danlos syndromes (EDS) constitute a rare entity of genetic disorders, affecting the collagen of all types all. Herein, we describe a case of vascular type of EDS, with coexisting segmental absence of intestinal musculature, while performing simultaneously a narrative review of the existing literature. Case Presentation: A 23-year-old male patient with a history of multiple abdominal operations due to recurrent bowel perforations and the presence of high-output enterocutaneous fistula was admitted to our surgical department for further evaluation and treatment. After detailed diagnostic testing, the diagnosis of vascular type of EDS (vEDS) was made and a conservative therapeutic approach was adopted. In addition, a comprehensive review of the international literature was carried out by applying the appropriate search terms. Results: The diagnosis of vEDS was molecularly confirmed by means of genetic testing. The patient was treated conservatively, with parenteral nutrition and supportive methods. Thirty-four cases of bowel perforation in vEDS have been reported so far. Interestingly, this case is the second one ever to report with co-existence of vEDS with Segmental Absence of Intestinal Musculature. Conclusions: Establishing the diagnosis of vEDS promptly is of vital significance in order to ensure that patients receive appropriate treatment. Due to initial non-specific clinical presentation, EDS should always be included in the differential diagnoses of young patients with unexplained perforations of the gastrointestinal tract.
ARTICLE | doi:10.20944/preprints202301.0050.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: Plasmodium falciparum chloroquine resistance; mutations; CVINT; malaria; allele frequency
Online: 4 January 2023 (03:04:50 CET)
The replacement of chloroquine with artemisinin-based combination therapies (ACTs) for over a decade has had varying impacts on the ability of malaria parasite to sustain its chloroquine resistance prowess in different malaria-endemic regions. We evaluated the frequency of Plasmodium falciparum chloroquine resistance transporter (PfCRT) mutations in an endemic area of southwest Nigeria 17 years after replacement of chloroquine with ACTs for malaria treatment. Genomic DNA was isolated from dried blood spot samples obtained from 129 patients (aged 1-35 years) with microscopically confirmed P. falciparum infection. PfCRT fragments covering codons 72-76, CVMNK (wildtype) and A220 were amplified and sequenced. Two mutant PfCRT haplotypes on residues 72-76 (CVIET and CVINT) were identified with a prevalence of 18.6% and 2.3%, respectively. Interestingly, the CVINT haplotype was identified for the first time in this region. A220S changes were found in 16.3% of samples occurring concurrently with the CVIET haplotype, while a Q271E mutation occurred in a wildtype isolate. The reduced prevalence of the PfCRT mutant alleles in this study may suggest a gradual disappearance of chloroquine-resistant malaria parasites following reduced drug pressure. It may also be an indicator of the ability of malaria parasites to develop resistance gradually against the current first-line regimen.
BRIEF REPORT | doi:10.20944/preprints202208.0025.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: glioblastoma; extracellular vesicles; Next Generation Sequencing; pathogenic mutations; NF1
Online: 1 August 2022 (15:07:04 CEST)
The biological heterogeneity of glioblastoma (GBM), the most aggressive type of brain cancer, is a critical hallmark, caused by changes in the genomic mutational asset and influencing the clinical progression over the time. The understanding and monitoring of the mutational profile is important not only to reveal novel therapeutic targets in this set of patients, but also to ameliorate the clinical stratification of subjects and the prognostic significance. As neurosurgery represents the primary technique to manage GBM, it is of outmost importance to optimize alternative and less invasive methods to monitor the dynamic mutation profile of these patients. Extracellular vesicles (EV) are included in the liquid biopsy analysis and have emerged as the biological mirror of escaping and surviving mechanisms by many tumors as well as glioblastoma. Very few studies have investigated the technical feasibility to detect and analyze the genomic profile by Next Generation Sequencing (NGS) in circulating EV of patients with grade IV glioblastoma. Here, we attempted to characterize and to compare with the corresponding matched tissue samples, potential variants with pathogenic significance of the DNA contained in peripheral blood derived EV. The NGS analysis has revealed that patients with grade IV glioblastoma, exhibited lesser DNA content in EV than controls and that both in EV and matched cancer tissues, the NF1 gene was consistently mutated in all patients with the c.2568C>G as the most common pathogenic variant expressed. This study supports the clinical utility of the circulating EV in glioblastoma and as eligible tool for personalized medicine.
ARTICLE | doi:10.20944/preprints202009.0375.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: co-infection; SARS-CoV-2; pike glycoprotein; stop mutations
Online: 17 September 2020 (05:33:59 CEST)
There is a rising global concern for the ongoing outbreak of SARS-CoV-2 due to its high transmission rate and unavailability of treatment. Through the binding of its spike glycoprotein with angiotensin type 2 (ACE2), SARS-CoV-2 can efficiently get in the cells of patients and start its pandemic cycle. Herein, the biological diversity of SARS-CoV-2 infection was assessed in Babylon province of Iraq by investigating the possible genetic variations of the spike glycoprotein. A specific coding region of 795 bp within the viral spike (S) gene was amplified from 19 patients who suffered from obvious symptoms of SARS-CoV-2 infection. Sequencing results identified fifteen novel nucleic acid variations with a variety of distributions within the investigated samples. The electropherograms of all the identified variations showed obvious co-infections with at least two different viral strains per sample. Within these co-infections, the majority of samples exhibited three nonsense single nucleotide polymorphism (SNP)s, p.301Cdel, p.380Ydel, and p.436del, which yielded three truncated SARS-CoV-2 spike glycoproteins of 301, 380, and 436 amino acids length, respectively. The network and phylogenetic analyses indicated that for all viral infections were derived from multi-ancestral origins. Results inferred from the specific clade-based tree entailed that some viral strains were derived from European G-clade sequences. In conclusion, our data demonstrated the absence of any single strain infection among all investigated viral samples in the studied area, which may entail a higher risk of SARS-CoV-2 in this country. Through the identified high frequency of truncated spike proteins, we suggest that defective SARS-CoV-2 may depend on helper strains having intact spikes in its infection. Alternatively, another putative ACE2-independent route of viral infection way also suggested. To the best of our knowledge, this is the first report to describe the co-infection of multiple strains of SARS-CoV-2 in patients with COVID-19.
ARTICLE | doi:10.20944/preprints202006.0072.v1
Subject: Biology And Life Sciences, Virology Keywords: Envelope protein; SARS-CoV2; COVID-19; Non-synonymous mutations
Online: 7 June 2020 (09:20:25 CEST)
In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617. The envelope protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane domain and (C)-terminus in 0.414\% of these 3617 genomes. The C-terminus motif DLLV has been changed to DFLV and YLLV in the proteins QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) respectively, which might affect the binding of this motif with the host protein PALS1.
ARTICLE | doi:10.20944/preprints202004.0137.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; genomes; nucleotide; amino-acid; mutations; replacements
Online: 9 April 2020 (05:56:35 CEST)
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionarily divergent RNA virus etiological agent of COVID-19, is responsible for present devastating pandemic respiratory illness. To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,407 nucleotide-level mutations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide deletion analysis found nine deletions throughout the genome, including in polyprotein (n=6), ORF10 (n=1) and 3´-UTR (n=2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n=722), making the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) having crucial interactions with angiotensin-converting enzyme 2 (ACE2), and cross-reacting neutralizing antibody were found to be conserved among the analyzed SARS-CoV-2 strains, except for replacement of Lysine with Arginine at 378 position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Our method of genome annotation is a promising tool for monitoring and tracking the epidemic, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategy.
REVIEW | doi:10.20944/preprints201906.0231.v1
Subject: Physical Sciences, Radiation And Radiography Keywords: bystander effect, genomic instability, lethal mutations,radiotherapy, diagnostic radiology
Online: 24 June 2019 (08:34:26 CEST)
Non-targeted effects (NTE) such as bystander effects or genomic instability have been known for many years but their significance for radiotherapy or medical diagnostic radiology are far from clear. Central to the issue are reported differences in response of normal and tumour tissues to signals from directly irradiated cells. This review will discuss possible mechanisms and implications of these different responses and will then discuss possible new therapeutic avenues suggested by the analysis. Finally, the importance of NTE for diagnostic radiology and nuclear medicine which stems from the dominance of NTE in the low dose region of the dose response curve will be presented. Areas such as second cancer induction and microenvironment plasticity will be discussed.
ARTICLE | doi:10.20944/preprints202311.0196.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Vulvovaginal Candidiasis; qPCR; Candida species, antifungal susceptibility, resistance-related mutations
Online: 3 November 2023 (04:02:59 CET)
Vulvovaginal candidiasis (VVC) is a prevalent condition affecting women worldwide. This study aimed to develop a rapid qPCR assay for accurate identification of VVC etiological agents and reduced azole susceptibility. One hundred and twenty nine vaginal samples from an outpatient clinic (Bilbao-Spain) were analyzed using culture-based methods and multiplex qPCR targeting fungal species, Candida albicans being the predominant species. Antifungal susceptibility tests revealed reduced azole susceptibility in three (3,48%) isolates. Molecular analysis identified several mutations in genes associated with azole resistance and novel mutations in TAC1 and MRR1 genes were also identified, which could contribute to drug resistance.
REVIEW | doi:10.20944/preprints202310.0345.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Prostate cancer, SPOP mutations, Androgen Receptor, disease characterization, therapeutic targets
Online: 6 October 2023 (11:29:08 CEST)
Background: Prostate cancer is a global health concern, necessitating ongoing research to enhance our comprehension of its molecular foundations and develop more efficacious therapeutic approaches. Among the emerging protagonists in this arena is Speckle-type POZ (pox virus and zinc finger protein) (SPOP), an E3 ubiquitin ligase substrate adaptor protein. SPOP's recent ascent to prominence in prostate cancer research is attributed to its crucial role in regulating the Androgen Receptor (AR) signaling pathway. This systematic review aims to provide a comprehensive synthesis of existing knowledge concerning SPOP mutations in prostate cancer. It seeks to elucidate their significance in characterizing the disease and their potential as therapeutic targets. Methods: A systematic literature search was conducted in multiple databases, including PubMed, Web of science, Scopus and google scholar to identify relevant studies published up to September 2023. Eligible studies included investigations of SPOP mutations in prostate cancer and their implications. Data extraction, quality assessment, and synthesis were performed in conformity to the PRISMA guidelines. Results: The review revealed that SPOP mutations are recurrent events in prostate cancer, with a notable prevalence in specific molecular subtypes. These mutations primarily affect the MATH domain of SPOP, disrupting its substrate recognition function. Notably, SPOP mutations have profound consequences on the AR signaling pathway, leading to increased AR protein stability and transcriptional activity. The clinical implications of SPOP mutations remain diverse, with varying associations with prognostic outcomes. Conclusion: SPOP mutations represent a significant facet of prostate cancer biology, influencing disease heterogeneity and clinical behavior. While their precise prognostic significance is evolving, their functional impact on the AR pathway highlights their potential as therapeutic targets. This systematic review provides a comprehensive overview of SPOP mutations in prostate cancer, contributing to our understanding of the disease's molecular landscape and therapeutic avenues.
REVIEW | doi:10.20944/preprints202309.0507.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; COVID-19; vaccine; immunity; immune escape; mutations
Online: 7 September 2023 (10:45:47 CEST)
The newly emerged variants of SARS-CoV-2 created a potential threat among societies and highlighted one of the significant concerns in facing the pandemic. SARS-CoV-2 variants harboring mutations in the structural protein, especially in the RBD domain of spike protein, have raised concern about potential immune escape. The spike protein of SARS-CoV-2 play a vital role in infection and is an important target for neutralizing antibodies. The mutations that occur in the structural proteins, especially in the spike protein, lead to changes in the virus attributes of transmissibility, an increase in disease severity, a notable reduction in neutralizing antibodies generated, and thus a decreased response to vaccines and therapy. The immune response against SARS-CoV-2 has been reported mainly through innate immune responses rather than adaptive immune responses. SARS-CoV-2 invades the host's innate immunity, possibly through inducing cytokine storm, impairing type I IFN responses, and suppressing antigens presentation to T cells. Therefore, the adaptive immune response is required to combat SARS-CoV-2 infection. The SARS-CoV-2 infections activated both arms of adaptive immunity; humoral and cell-mediated immunity. The observed multiple mutations in the RBD domain of the spike protein compromised the adaptive immune response and showed immune escape because it increases the affinity of spike protein binding with the ACE-2 receptor of host cells and increases resistance to neutralizing antibodies. Cytotoxic T-cell responses are crucial in controlling SARS-CoV-2 infections from the infected tissues and clearing them from circulation. CD8+cytotoxic T cells identify and directly kill the infected cells by releasing soluble mediators perforin and granzymes. The functional exhaustion of cytotoxic T cells may increase the severity of the disease. The expression of activation markers of T cells could indicate hyperactivation or functional exhaustion; the exact implication is not yet understood in SARS-CoV-2 infections. These mutations at critical residues influence the antigenic profile of SARS-CoV-2, which may evade the immune responses and thus reduce the immunogenicity and efficacy of vaccines. Therefore, the spike protein may be recognized as a primary target for vaccines and drugs. This review article summarizes the impact of mutations in the spike protein of SARS-CoV-2, especially mutations of RBD, on immunogenicity, immune escape, and vaccine-induced immunity, which could potentially contribute to future studies focusing on vaccine design and immunotherapy.
REVIEW | doi:10.20944/preprints202308.0465.v1
Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: lleles; Brain; Disease; Genes; Gastrointestinal Tract; Mutations; Epigenetics; Evolution; Phenotypes
Online: 4 August 2023 (19:17:21 CEST)
Complex interactions between gene variants and environmental risk factors underlie the pathophysiological pathways in major psychiatric disorders. Autism Spectrum Disorder is a psychiatric condition in which susceptible alleles along with epigenetic memories contribute to the mutational landscape of the ailing brain. The present work reviews recent evolutionary, molecular, and epigenetic mechanisms potentially linked to the etiology of autism. First, we present a clinical vignette to describe clusters of maladaptive behaviors frequently diagnosed in autistic patients. Next, we microdissect brain regions pertinent to the nosology of autism as well as cell networks from the bilateral body plan. Lastly, we catalog a number of pathogenic environments associated with disease risk factors. This set of perspectives provides emerging insights into the dynamic interplay between epigenetic and environmental variation in the development of Autism Spectrum Disorders.
CASE REPORT | doi:10.20944/preprints201911.0200.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: BRCA1; BRCA2; biliary tract cancers; ereditary BRCA cancer; somatic mutations
Online: 17 November 2019 (10:44:44 CET)
BRCA-associated hereditary breast and ovarian cancer syndrome (HBOC) implies increased absolute risk also for other malignancies such as cholangiocarcinoma (CCA). However, even if somatic mutations in CCA have been reported, there are no data on its utilization as predisposing genetic factor in a family. For the first time, we utilized CCA somatic BRCA mutation to individualize a family with HBOC. A 47-year-old woman (daughter of a patient died for CCA) accessed to our Genetic Councelling to evaluate her personal cancer risk. We performed a somatic BRCA1/2 NGS analysis on DNA extracted from formalin-fixed, paraffin-embedded CCA-tissue of her mother. After demonstration of pathogenic variant c.6468_6469delTC in BRCA2 gene mutation, the same germline pathogenic variant was found in DNA blood of one of two daugthers. So far, CCA tissue can be utilized, in addition to patient’s selection to specific therapeutic strategies, also to individualize families belonging to HBOC syndrome.
REVIEW | doi:10.20944/preprints202311.0716.v1
Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: borderline ovarian tumors; molecular features; mutations; genetic mutations; BRAF; KRAS; NRAS; ARID1A; CADM1; PIK3CA; CHEK2; CLAUDIN-1; ERBB2; loss of heterozygosity; PTEN; microsatellite instability
Online: 13 November 2023 (08:32:29 CET)
Borderline ovarian tumors (BOTs) show intriguing characteristics distinguishing them from other ovarian tumors. This unique type of non-invasive neoplasms is characterized by atypical growth of epithelial cells, nuclear atypia, and a moderate-level mitotic activity that places BOTs between benign tumors and invasive cancers. Similar to invasive carcinomas, BOTs can be categorized into six histological subtypes based on the type of epithelial cells present. The most prevalent subtypes are serous and mucinous BOTs, whereas endometrioid, clear cell, seromucinous, and borderline Brenner tumors are diagnosed less often. Noticeably, molecular changes found in BOTs can vary on a case-by-case basis, which warrants further research on the molecular landscape of these tumors. Identifying carcinogenic mutations through molecular analysis and developing targeted therapies represent significant advancements in the diagnosis and treatment of ovarian malignancies. A growing body of evidence indicates that BOTs often remain clinically dormant for extended periods before a molecular trigger initiates increased cell replication, potentially leading to carcinoma development or recurrence. Continued research in this area is crucial for improving risk assessment and developing personalized treatment approaches. While molecular studies have contributed significantly to our understanding of BOT pathogenesis, substantial research is still required to elucidate the relationship between ovarian neoplasms and extraneous disease, identify accurate prognostic indicators, and develop targeted therapeutic approaches. The aim of the present systematic review was to analyze the spectrum of molecular changes found in BOTs and discuss their significance in the context of the overall therapeutic approach.
ARTICLE | doi:10.20944/preprints202305.1361.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Omicron Variant of Concern; Mutations; Lineages
Online: 19 May 2023 (03:00:56 CEST)
The emergence of the SARS-CoV-2 Variant of Concern (VOC) Omicron has been characterized by an explosive number of cases in almost every part of the world. The dissemination of different sub-lineages and recombinant genomes also led to several posterior waves in many countries. The circulation of this VOC and its major sub-lineages (BA.1 to BA.5) was monitored in community cases and in international travelers returning to Venezuela, by a rapid partial sequencing method. The specific sub-lineage assignment was performed by complete genome sequencing. Epidemic waves of SARS-CoV-2 cases were observed among international travelers during 2022, a situation not seen before December 2021. The succession of the Omicron VOC sub-lineages BA.1 to BA.5 occurred sequentially, except for BA.3, which was almost not detected. However, the sub-lineages generally circulated two months earlier in international travelers than in community cases. The diversity of Omicron sub-lineages found in international travelers was related to the one found in the USA, consistent with the most frequent destination of international travel from Venezuela this year. These differences are compatible with the delay observed in Latin American countries in the circulation of the different lineages of the Omicron VOC.
REVIEW | doi:10.20944/preprints202304.1236.v1
Subject: Medicine And Pharmacology, Hematology Keywords: FLT3 mutations; resistant/relapsed acute myeloid leukemia; tyrosine kinase inhibitors; gilteritinib
Online: 29 April 2023 (10:55:21 CEST)
The traditionally dismal outcome of acute myeloid leukemia (AML) patients carrying the FMS-related tyrosine kinase 3 (FLT3) mutations has been mitigated by the recent introduction into the clinics of tyrosine kinase inhibitors (TKI) such as midostaurin and gilteritinib. The present work summarizes the clinical data that led to the use of gilteritinib in clinical practice. Gilteritinib is a 2nd generation TKI with deeper single-agent activity than 1st generation drugs against both FLT3-ITD and TKD mutations, in human studies. Moreover, the phase I/II dose-escalation, dose-expansion Chrysalis trial showed an acceptable safety profile of gilteritinib (diarrhea, elevated aspartate aminotransferase, febrile neutropenia, anemia, thrombocytopenia, sepsis, and pneumonia) and a 49% overall response rate (ORR) in 191 FLT3-mutated relapsed/refractory (R/R) AML patients. In 2019, the pivotal ADMIRAL trial showed that the median overall survival was significantly longer in patients treated with gilteritinib than among those receiving chemotherapy (9.3 vs 5.6 months, respectively) and the ORR to gilteritinib was 67.6%, outperforming the 25.8% for chemotherapy arm and leading to the license for its clinical use by the US Food and Drug Administration. Since then, several real-world experiences confirmed the positive results in the R/R AML setting. Finally, gilterinib based combinations currently under investigation with several compounds (venetoclax, azacitidine, conventional chemotherapy, etc.) and some practical tips (maintenance after allogeneic transplantation, interaction with antifungal drugs, extramedullary disease, and onset of resistance) will be analyzed in detail in the review.
ARTICLE | doi:10.20944/preprints202205.0247.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Variants of Concern; Rapid screening; Mutations
Online: 19 May 2022 (03:31:36 CEST)
Some of the lineages of SARS-CoV-2, the new coronavirus responsible for COVID-19, exhibit higher transmissibility or partial resistance to antibody mediated neutralization and were des-ignated by WHO as Variants of Interests (VOIs) or Concern (VOCs). The aim of this study was to monitor the dissemination of VOIs and VOCs in Venezuela during a year. A 614 nt genomic fragment was sequenced for the detection of some relevant mutations of these variants. Their presence was confirmed by complete genome sequencing, with a correlation higher than 99% between both methodologies. After the previously reported introduction of the Gamma VOC since the beginning of the year 2021, the variants Alpha VOC and Lambda VOI were detected as early as March 2021, at a very low frequency. In contrast, the Mu VOI, detected in May 2021, was able to circulate throughout the country. After the detection of Delta VOC in June 2021, it be-came the predominant circulating variant. With the arrival of the Omicron VOC in December, this variant was able to displace the Delta one in less than one month. This succession of variants was accompanied by a reduction in the Cycle threshold (Ct) values, in agreement with the in-crease in transmissibility described for these variants.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: oxidative stress; calcification; signal transduction; vitamin D; cancer mutations; quantum phenomena
Online: 27 May 2021 (14:06:00 CEST)
The leading cause of illness in aging is a group known as Noncommunicable Diseases. There should be some meeting points that modify the cells homeostasis and impaired the cell physiology developing different diseases. Quantum physics studied the atomic and subatomic particles and revolutionized the reality perception with paradoxical and weird concepts. Heisenberg's uncertainty principle established that it is not possible to determine the two characteristic properties of particles with accuracy. Subatomic particles have a wave-particle duality. Two subatomic particles are entangled, something happening over here can have an instantaneous effect over there, no matter how far away there are. All these concepts have tried to apply to biology and life sciences, quantum biology is behind photosynthesis, mitochondrial respiration, enzyme activity, the sense of smell, animal migration, heredity's fidelity, and consciousness. We can apply all these concepts to diseases pathogeny. So, we describe quantum phenomena in oxidative stress, calcification, signal transduction, vitamin D production and cancer mutations. Aging diseases also could be explained by applying quantum physics concepts. It is a new, hard to believe, and an incredible path to be built, but we need to open the treatment options to our patients with new perspectives.
COMMUNICATION | doi:10.20944/preprints202008.0665.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; envelop protein; mutations; transmembrane domain; triple cysteine motif
Online: 30 August 2020 (11:50:59 CEST)
The ongoing mutations in the structural proteins of SARS-CoV-2 is the major impediment for prevention and control of the COVID-19 disease. The envelope (E) protein of SARS-CoV-2 is a structural protein existing in both monomeric and homopentameric forms, associated with a multitude of functions including virus assembly, replication, dissemination, release of virions, infection, pathogenesis, and immune response stimulation. In the present study, 81,818 high quality E protein sequences retrieving from the GISAID were subjected to mutational analyses. Our analysis revealed that only 0.012 % (982/81818) stains possessed amino acid (aa) substitutions in 63 sites of the genome while 58.77% mutations in the primary structure of nucleotides in 134 sites. We found the V25A mutation in the transmembrane domain which is a key factor for the homopentameric conformation of E protein. We also observed a triple cysteine motif harboring mutations (L39M, A41S, A41V, C43F, C43R, C43S, C44Y, N45R) which may hinder the binding of E protein with spike glycoprotein. These results therefore suggest the continuous monitoring of each structural protein of SARS-CoV-2 since the number of genome sequences from across the world are continuously increasing.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; 4521 lines; mutations; MAF (minor allele frequency); deamination
Online: 19 April 2020 (07:05:58 CEST)
Aims: The sequencing data of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) are rapidly emerging. The mutation profile across SARS-CoV-2 populations is an important inference of the evolution of coronaviruses. Materials & Methods: With 4,521 lines of SARS-CoV-2, we obtained 3,169 unique point mutation sites in the SARS-CoV-2 genome. We counted the numbers and calculated the MAF (minor allele frequency) of each mutation type. Results: Nearly half of the point mutations are C-T mismatches and 20% are A-G mismatches. The MAF of C-T and A-G mismatches is significantly higher than MAF of other mutation types. Conclusions: The excessive C-T mismatches do not resemble the random mutation profile, and are likely to be explained by the cytosine-to-uridine deamination system in hosts. Not only the population analyses in previous studies are questionable, but also the 17% divergence between SARS-CoV-2 and RaTG13 could be erroneous due to the deamination.
REVIEW | doi:10.20944/preprints202311.1517.v1
Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: Benign recurrent intrahepatic cholestasis; mutations; elevated conjugated bilirubin; normal gamma-glutamyl transferase
Online: 23 November 2023 (11:12:32 CET)
Benign recurrent intrahepatic cholestasis (BRIC) is a rare genetic cause of cholestasis. It is considered as part of inherited intrahepatic cholestasis syndromes, such as progressive familial intrahepatic cholestasis (PFIC), and intrahepatic cholestasis of pregnancy. BRIC is presented in infancy or in early adulthood. It is characterized by exacerbations and remissions of jaundice with accompanying intense itching, lasting from weeks to years throughout lifetime. Normal gamma-glutamyl transferase (GGT) is a characteristic laboratory finding. Contrary to PFIC, which may progress to cirrhosis, BRIC does not progress to chronic liver disease or cirrhosis. However, incessant episodes of cholestasis result in marked reduction in quality of life and distinct mutations increase the risk of hepatobiliary malignancy. In intervals between the exacerbations, the histological findings of centrilobular cholestasis together with the abnormal laboratory parameters return to normal. In this context, liver biopsy might be avoided. In this review, we will focus on the genetic aspects of BRIC, its pathophysiology, clinical presentation, and prognosis of this autosomal recessive genetically determined cholestatic disorder. Moreover, triggering factors as well as treatment options will be further elucidated.
ARTICLE | doi:10.20944/preprints202310.1792.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: RRAS2; Somatic mutations; 3'-untranslated region; Chronic Lymphocytic Leukemia (CLL); Clinical implications
Online: 27 October 2023 (12:17:15 CEST)
Chronic lymphocytic leukemia (CLL) is a hematologic malignancy characterized by progressive accumulation of a rare population of CD5+ B lymphocytes in peripheral blood, bone marrow and lymphoid tissues. CLL exhibits remarkable clinical heterogeneity, with some patients presenting with indolent disease and others progressing rapidly to aggressive CLL. The significant heterogeneity of CLL underscores the importance of identifying novel prognostic markers. Recently, the RAS-related gene RRAS2 has emerged as both a driver oncogene and a potential marker for CLL progression, with higher RRAS2 expression associated with poorer disease prognosis. Although missense somatic mutations in the coding sequence of RRAS2 have not been described in CLL, this study reports the frequent detection of three somatic mutations in the 3' untranslated region (3'UTR) affecting positions +26, +53, and +180 downstream of the stop codon in the mRNA. An inverse relationship was observed between these three somatic mutations and RRAS2 mRNA expression, which correlated with lower blood lymphocytosis and better prognosis. These findings highlight the importance of RRAS2 overexpression in CLL development and prognosis and point to somatic mutations in its 3'UTR as novel mechanistic clues. Our results may contribute to the development of targeted therapeutic strategies and improved risk stratification for CLL patients.
ARTICLE | doi:10.20944/preprints202309.0467.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: pan-cancer analysis; RKIP; YY1; gene expression; mutations; immune infiltration; drug resistance
Online: 7 September 2023 (13:33:14 CEST)
Recent studies suggest that PEBP1/RKIP and YY1, despite having distinct molecular functions, may interact and mutually influence one another's activity. They exhibit reciprocal control over each other's expression through regulatory loops, prompting the hypothesis that their interplay could be pivotal in cancer advancement and resistance to drugs. To delve into this interplay's functional characteristics, we conducted a comprehensive analysis using bioinformatics tools across a range of cancers. Our results confirm the association between elevated YY1 mRNA levels and varying survival outcomes in diverse tumors. Furthermore, we observed differing degrees of inhibitory or stimulatory effects of these two genes in various cancer pathways, along with correlations between their mRNA expression and immune infiltration. Additionally, YY1/PEBP1 expression (or methylation) displayed connections with genomic alterations across cancer types. Notably, we uncovered links between YY1/PEBP1 and different indicators of immunosuppression, such as immune checkpoint blockade response, and T-cell dysfunction/exclusion levels, across different patient groups. Overall, our findings underscore the significant role of the interplay between YY1 and PEBP1 in cancer progression, influencing genomic changes, tumor immunity or the tumor microenvironment. Additionally, these two gene products appear to impact the sensitivity of anticancer drugs, opening new avenues for cancer therapy.
ARTICLE | doi:10.20944/preprints202306.0199.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: mutations; folding free energy change; binding free energy change; single nucleotide variant
Online: 2 June 2023 (11:58:21 CEST)
Development of methods and algorithms to predict the effect of mutations on protein stability, protein-protein, and protein-DNA/RNA binding is necessitated by the needs of protein engineering and for understanding the molecular mechanism of disease-causing variants. The vast majority of the leading methods are either methods with adjustable parameters or machine learning algorithms, both requiring a database of experimentally measured folding and binding free energy changes. These databases are collections of experimental data taken from scientific investigations typically aimed at probing the role of particular residue on the above-mentioned thermodynamics characteristics, i.e., the mutations are not introduced at random and do not necessarily represent mutations originating from single nucleotide variant (SNV). Thus, the reported performance of the leading algorithms assessed on these databases or other limited cases, may not be applicable for predicting the effect of SNVs seen in the human population. Indeed, we demonstrate that the SNVs and non-SNVs are not equally presented in the corresponding databases and the distribution of the free energy changes are not the same. Furthermore, the Pearson correlation coefficients (PCCs) obtained on cases involving SNVs are less impressive than for non-SNVs, indicating that caution should be used in applying them to reveal the effect of human SNVs. All methods are found to underestimate the energy changes by roughly a factor of 2.
ARTICLE | doi:10.20944/preprints202107.0554.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; ORF10; Co-mutations; Intrinsic Protein Disorder; Ubiquitin Ligase Complex
Online: 26 July 2021 (09:07:38 CEST)
The devastating impact of the ongoing coronavirus disease 2019 (COVID-19) on public health, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has made fighting of the COVID-19 pandemic is a top priority in medical research and pharmaceutical development. Surveillance of SARS-CoV-2 mutations is essential for the comprehension of SARS-CoV-2 variant diversity and their impact on virulence and pathogenicity. The SARS-CoV-2 open reading frame 10 (ORF10) protein interacts with multiple human proteins CUL2, ELOB, ELOC, MAP7D1, PPT1, RBX1, THTPA, TIMM8B, and ZYG11B expressed in the lung tissues. Mutations and co-mutations in the emerging SARS-CoV-2 ORF10 variants are expected to impact the severity of the virus and its associated consequences. In this article, We highlight 128 single mutations and 35 co-mutations in the unique SARS-CoV-2 ORF10 variants in this article. The possible predicted effects of these mutations and co-mutations on the secondary structure of ORF10 variants and host protein interactomes are presented. The findings highlight the possible effects of mutations and co-mutations on the emerging 140 ORF10 unique variants from secondary structure and intrinsic protein disorder perspectives.
ARTICLE | doi:10.20944/preprints202106.0472.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; Mutations; Furin Cleavage Site (FCS); Evenly-uneven; Invariant regions
Online: 18 June 2021 (09:22:08 CEST)
Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no hypothesis has managed to identify the origin, and the issue has resurfaced. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins across different continents comprising 24 geo-locations. The results showed an evenly uneven distribution of unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across the 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations we have considered. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and to be prepared to meet the challenges of potential future pandemics.
ARTICLE | doi:10.20944/preprints201910.0154.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: papillary thyroid cancer; germline mutations; whole genome sequencing; predisposition markers; pathway analysis
Online: 13 October 2019 (17:07:34 CEST)
Evidence of familial inheritance in non-medullary thyroid cancer (NMTC) has accumulated over the last few decades. However, known variants account for a very small percentage of the genetic burden. Here, we focused on the identification of common pathways and networks enriched in NMTC families to better understand its pathogenesis with the final aim of identifying one novel high/moderate-penetrance germline predisposition variant segregating with the disease in each studied family. We performed whole genome sequencing on 23 affected and 3 unaffected family members from five NMTC-prone families and prioritized the identified variants using our Familial Cancer Variant Prioritization Pipeline (FCVPPv2). In total, 31 coding variants and 39 variants located in upstream, downstream, 5′ or 3′ untranslated regions passed FCVPPv2 filtering. Altogether, 210 genes affected by variants that passed the first three steps of the FCVPPv2 were analyzed using Ingenuity Pathway Analysis software. These genes were enriched in tumorigenic signaling pathways mediated by receptor tyrosine kinases and G-protein coupled receptors, implicating a central role of PI3K/AKT and MAPK/ERK signaling in familial NMTC. Our approach can facilitate the identification and functional validation of causal variants in each family as well as the screening and genetic counseling of other individuals at risk of developing NMTC.
ARTICLE | doi:10.20944/preprints201807.0085.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: CagA; phosphatidylserine; phosphatidylserine mutations; conservation N-terminal CagA; homology modeling; molecular docking
Online: 5 July 2018 (08:34:40 CEST)
Helicobacter pylori cytotoxin-associated gene A protein (CagA) has been associated with the increase in virulence and risk of cancer. It has been demonstrated that CagA's translocation is dependent on its interaction with phosphatidylserine. We evaluated the variability of the N-terminal CagA in 127 sequences reported in NCBI, by referring to molecular interaction forces with the Phosphatidylserine and the docking of 3 mutations chosen from variations in specific positions. The major sites of conservation of the residues involved in CagA-Phosphatidylserine interaction were 617, 621 and 626 which had no amino acid variation. Position 636 had the lowest conservation score, so mutations in this position were evaluated to observe the differences in intermolecular forces of the CagA-Phosphatidylserine complex. We evaluated the docking of 3 mutations: K636A, K636R and K636N. The models of the crystal and mutations presented a ΔG of −8.919907, −8.665261, −8.701923, −8.515097 Kcal/mol, respectively, while mutations K636A, K636R, K636N and the crystal structure presented 0, 3, 4 and 1 H-bonds, respectively. Likewise, the bulk effect of the ΔG and amount of H-bonds was estimated in all of the docking models. The type of mutation affected both the ΔG (χ2(1) = 93.82, p-value < 2.2 × 10−16) and the H-bonds (χ2(1) = 91.93, p-value < 2.2 × 10−16). In all the data, 76.9% of the strains that exhibit the K636N mutation produced a severe pathology. The average H-bond count diminished when comparing the mutations with the crystal structure of all the docking models, which means that other molecular forces are involved in the CagA-Phosphatidylserine complex interaction.
ARTICLE | doi:10.20944/preprints201712.0024.v1
Subject: Biology And Life Sciences, Virology Keywords: HIV-1; quasispecies; minority resistance mutations; HAART; drug resistance; undetectable viral load
Online: 4 December 2017 (09:34:16 CET)
Increased access to highly active antiretroviral therapy (HAART) by HIV+ individuals has become a reality worldwide. In Brazil, ART currently reaches over half of the HIV-infected subjects. In the context of a remarkable HIV-1 genetic variability, highly related variants, called quasispecies, are generated. HIV quasispecies generated during infection can influence virus persistence and pathogenicity, representing a challenge to treatment. However, the clinical relevance of minority quasispecies is still uncertain. For this study, we have determined the archived proviral sequences, viral subtype and drug resistance mutations from a cohort of HIV+ patients with undetectable viral load undergoing HAART as first-line therapy using next-generation sequencing for near full-length virus genome (NFLG) assembly. HIV-1 consensus sequences representing NFLG were obtained for eleven patients, while for another twelve varying genome coverage rates were obtained. Phylogenetic analysis showed the predominance of subtype B (83%; 19/23). Considering the minority variants, 18 patients carried archived virus harboring at least one mutation conferring antiretroviral resistance; for six patients, the mutations correlated with the current ARVs used. These data highlight the importance of monitoring HIV minority drug resistant variants and their clinical impact, to guide future regimen switches and improve HIV treatment success.
REVIEW | doi:10.20944/preprints202206.0022.v1
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Omicron; bioinformatics; immune escape; RBD mutations; vaccine development
Online: 1 June 2022 (14:12:36 CEST)
The evolution and the emergence of new mutations of viruses affect their transmissibility and/or pathogenicity features, depending on different evolutionary scenarios of virus adaptation to the host. A typical trade-off scenario of SARS-CoV-2 evolution has been proposed, which leads to the appearance of an Omicron strain with lowered lethality, yet enhanced transmissibility. This direction of evolution might be partly explained by virus adaptation to therapeutic agents and enhanced escape from vaccine-induced and natural immunity formed by other SARS-CoV-2 strains. Omicron’s high mutation rate in the Spike protein, as well as its previously described high genome mutation rate (Kandeel et al., 2021), revealed a gap between it and other SARS-CoV-2 strains, indicating the absence of a transitional evolutionary form to the Omicron strain. Therefore, Omicron has emerged as a new serotype and divergent from the evolutionary lineage of other SARS-CoV-2 strains. Omicron is a rapidly evolving variant of high concern, whose new subvariants continue to manifest. Its further understanding and the further monitoring of key mutations that provide virus immune escape and/or high affinity towards the receptor could be useful for vaccine and therapeutic development in order to control the evolutionary direction of the COVID-19 pandemic.
REVIEW | doi:10.20944/preprints201907.0286.v1
Subject: Biology And Life Sciences, Virology Keywords: HIV-1 Gag; Gag inhibitors; Protease; Protease inhibitors; drug resistance mutations; drug design
Online: 25 July 2019 (10:05:03 CEST)
HIV treatment strategies against viral enzymes are continuously hampered by viral drug resistance. Recent findings show that viral substrate Gag contributes to HIV-1 Protease Inhibitor (PI) resistance, leading to demands for new strategies in HIV treatment where Gag is recognized as a drug target. To successfully target Gag, there is a need of in-depth understanding of the Gag polyprotein and the effects of Gag mutations. Here, we propose new strategies in designing novel Gag inhibitors against existing and novel emerging Gag mutations via a structural understanding of the Gag-Protease relationship in PI resistance. In this review, we discuss the role of both novel and previously reported mutations, revealing insights to how they aid in PI resistance, and how new Gag inhibitors can be designed.
ARTICLE | doi:10.20944/preprints202302.0237.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: esterases; phthalate esters; rational design of proteins; distal mutations; molecular dynamics simulation; toxicity; allostery
Online: 14 February 2023 (06:22:31 CET)
Phthalate esters (PAEs) are a ubiquitous kind of environmental endocrine-disrupting chemicals, causing environmental and health issues. EstJ6 is an effective phthalate-degrading hydrolase, and its mutant with a combination of three non-conservative distal mutations has an improved activity against PAEs with unknown molecular mechanisms. Herein, we attempt to fill the significant gap between distal mutations and the activity of this enzyme using computational approaches. We find mutations result in a redistribution of enzyme’s preexisting conformational states and dynamics changes of key functional regions, especially the lid over the active site. The outward motion of the lid upon mutations should make it easier for substrates or products to enter or exit. Additionally, the stronger substrate binding affinity and conformational rearrangements of catalytic reaction-associated residues in mutant, accompanied by the strengthened communication within the protein, might contribute to the elevated catalytic efficiency. Finally, an attempt has been done to improve the thermostability of EstJ6 upon introducing a distal disulfide bond between residues A23 and A29, and the simulation results are as expected. Together, our work explored the allosteric effects caused by distal mutations, which could provide insights into the rational design of esterases for industrial applications in the future.
ARTICLE | doi:10.20944/preprints202207.0018.v1
Subject: Biology And Life Sciences, Virology Keywords: hepatocellular carcinoma (HCC); hepatitis B virus (HBV); mutations; HBV/HIV co-infection; Botswana; Africa
Online: 1 July 2022 (16:31:00 CEST)
Mutations within the hepatitis B virus (HBV) genome have been associated with rapid progres-sion to hepatocellular carcinoma (HCC); however, there is limited information regarding the prevalence and impact of these mutations in most of sub-Saharan Africa, including Botswana. We aimed to determine the prevalence of HBV mutations known to be associated with progression to HCC using a retrospective, cross-sectional analysis of 48 previously generated HBV sequences from adults with concomitant HBV/HIV initiating HIV antiretroviral therapy in Botswana. The sequences were aligned with reference sequences, and HCC-associated mutations were manually identified using BioEdit. Sixteen (33.3 %) of 48 participant samples had 20 HCC-associated mu-tations. Seven HCC mutations were present in the core region, 4 in the preCore region, 7 in the X region, and one mutation in the surface region, as well as deletions within the preSurface 1 region. Seven of the 16 participants (43.8%) had multiple HCC-associated mutations. There were also previously uncharacterized mutations at positions with known HCC-associated mutations. HCC-associated mutations were common in this cohort; hence, some participants may require close clinical monitoring as they might be more prone to rapid disease progression. Other functionally uncharacterized polymorphisms were also detected and require characterization in future studies.
ARTICLE | doi:10.20944/preprints202204.0312.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Tensional homeostasis; Traction microscopy; Gastric cancer cells; E-cadherin mutations; Extra-cellular matrix proteins
Online: 30 April 2022 (05:18:13 CEST)
In epithelia, breakdown of tensional homeostasis is closely associated with E-cadherin dysfunction and disruption of tissue function and integrity. In this study, we investigated the effect of E-cadherin mutations affecting distinct protein domains on tensional homeostasis of gastric cancer cells. We used micropattern traction microscopy to measure temporal fluctuations of cellular traction forces in AGS cells transfected with the wild-type E-cadherin or with variants affecting the extracellular, the juxtamembrane, and the intracellular domains of the protein. We focused on the dynamic aspect of tensional homeostasis, namely the ability of cells to maintain a consistent level of tension, with low temporal variability around a set point. Cells were cultured on hydrogels micropatterned with different extracellular matrix (ECM) proteins to test whether the ECM adhesion impacts cell behavior. A combination of Fibronectin and Vitronectin was used as a substrate that promotes the adhesive ability of E-cadherin dysfunctional cells, whereas Collagen VI was used to test an unfavorable ECM condition. Our results showed that mutations affecting distinct E-cadherin domains influenced differently cell tensional homeostasis, and pinpointed the juxtamembrane and intracellular regions of E-cadherin as the key players in this process. Furthermore, Fibronectin and Vitronectin might modulate cancer cell behavior towards tensional homeostasis.
REVIEW | doi:10.20944/preprints202108.0321.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: cancer; mutations; cancer drivers; precision medicine; protein structure; personalized medicine; cancer therapies; genetic signatures
Online: 16 August 2021 (11:15:11 CEST)
Cancer is fundamentally a disease of perturbed genes. Although many mutations can be marked in the genome of a cancer or transformed cell, the initiation and progression were shown to be driven by only a few mutational events viz. driver mutations that progressively govern and execute the functional impacts. The driver mutations are thus believed to dictate and dysregulate the subsequent cellular proliferative function/decisions thereby producing a cancerous state. Therefore, identifying the driver events from the genomic alterations in a patient’s cancer cell gained large attention recently for designing better targeting therapies towards paving way for the precision cancer medicine. With rolling advancements in high-throughput omics technologies, analysis of genetic variations and gene expression profiles for cancer patients has become a routine clinical practice. However, it is anticipated that protein structural alterations resulting from such driver mutations can provide more direct and clinically relevant evidence of disease states than genetic signatures alone. This review comprehensively discusses various aspects and approaches that have been developed for the prediction of cancer drivers using genetic signatures and protein structures, and their potential application in developing precision cancer therapies.Keywords:
REVIEW | doi:10.20944/preprints202308.1547.v1
Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: Main Protease Inhibitors; SARS-CoV-2; COVID-19; mutations; vaccines; therapeutics; drug repurposing; management strategies
Online: 22 August 2023 (09:31:05 CEST)
Worldwide, the COVID-19 pandemic, which was brought on by the brand-new coronavirus SARS-CoV-2, has claimed a sizable number of lives. Despite the urgency, COVID-19 does not have any particular antiviral treatments at this time. As a result, scientists are concentrating on repurposing already existing antiviral medications or creating brand-new ones. The SARS-CoV-2 main protease, which is necessary for viral replication, has been identified as a possible target for a family of medicines called main protease inhibitors (MPIs). Studies of the major proteases from SARS-CoV and MERS-CoV, which have remarkably similar structures and functions to SARS-CoV-2, have provided insight for the creation of MPIs. By analyzing the MPI trials for SARS-CoV and MERS-CoV, this review sheds light on the possible therapeutic uses of MPIs for COVID-19. The review talks about how MPIs work, how effective they are against SARS-CoV and MERS-CoV, and how safe they are. The paper also emphasizes current developments in the creation of MPIs for SARS-CoV-2, including as computational studies, in vitro and in vivo research, and clinical trials. According to the review, there is a lot of hope for MPIs in the treatment of COVID-19, and numerous medications are in the works. Although more research is needed to assess their safety and effectiveness in clinical settings, these medications may offer patients with COVID-19 a much-needed therapeutic option. The review also emphasizes the importance of ongoing research into the structure and function of the SARS-CoV-2 main protease, as this information will be critical for the development of effective MPIs and other antiviral drugs in the future.
ARTICLE | doi:10.20944/preprints202306.1845.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: (luminal) breast cancer; breast cancer biology; mutations; primary tumor; de novo - stage IV; tumor microenvironment
Online: 27 June 2023 (04:47:03 CEST)
Background. The molecular mechanisms underlying de novo metastasis of luminal breast cancer (dnMBC) remain largely unknown. Materials & Methods. Newly diagnosed dnMBC patients (grade 2/3, ER+, PR+/-, HER2-), with available core needle biopsy (CNB), collected from the primary tumor, were selected from our clinical-pathological database. Tumors from dnMBC patients were 1:1 pairwise matched (n=32) to tumors from newly diagnosed patients who had no distant metastases at baseline (eBC group). RNA was extracted from 5 x 10µm sections of FFPE CNBs. RNA sequencing was performed using the Illumina platform. Differentially expressed genes (DEG)s were assessed using EdgeR, deconvolution was performed using CIBERSORTx to assess immune cell fractions. Paired Wilcoxon test was used to compare dnMBC and eBC groups, and corrected for false discovery rate (FDR). Results. Many regulatory DEGs were significantly downregulated in dnMBC compared to eBC. Also, immune-related and hypoxia-related signatures were significantly upregulated. Paired Wilcoxon analysis showed that CCL17 and neutrophils fraction were significantly upregulated, whereas the memory B-cell fraction was significantly downregulated in the dnMBC group. Conclusion. Primary luminal tumors of dnMBC patients display significant transcriptomic and immunological differences compared to comparable tumors from eBC patients.
REVIEW | doi:10.20944/preprints202208.0220.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Molecular switches; oncolytic vectors; patient-specific ubiquitous mutations; targeted therapy; multi-region sequencing; molecular biology
Online: 11 August 2022 (11:50:12 CEST)
Most existing cancer therapies negatively affect normal tissue as well as cancerous tissue. A potentially effective strategy for treating cancer that precludes off-target damage and could be an option for most patients would involve targeting one or more mutations that are ubiquitous in the given patient’s tumor(s). To effect this strategy, one would employ multi-region sequencing of a patient’s primary tumor and metastases to seek out mutations that are shared between all or at least most regions. Once the target or targets are known, one would ideally rapidly generate a molecular switch for at least one of said ubiquitous mutations that can distinguish the mutated DNA, RNA, or protein from the wild-type version and subsequently trigger a therapeutic response. I propose that the therapeutic response involve the replication of an oncolytic virus or intracellular bacterium, as any mutation can theoretically be detected by a vector that enters the cell - and automatic propagation could be very helpful. Moreover, the mutation “signal” can be easily enhanced through transcriptional and translational (if the target is an intracellular protein) enhancement. Importantly, RNA may make the best target for the molecular switches in terms of amplification of the signal and ease of targeting.
REVIEW | doi:10.20944/preprints202203.0376.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; Mutations; Omicron; Delta; Variants of Concern; Variants of Interest; Immunity Escape; Mechanisms
Online: 29 March 2022 (08:44:09 CEST)
With the emergence of COVID-19 pandemic in 2019, the world saw a humungous loss of human life and economic resources globally but also the rapid appearance of SARS-CoV-2 variants which have exhibited a higher transmissibility and/or virulence and which also evade immune system to such an extent that it raises a big question mark on the efficacy of current diagnostics, vaccines and convalescent plasma and mAb therapies. This has been attributed to the emergence of huge spectrum of mutations, especially in the virus’s spike (S) protein, occurring in regions harboring high concentration of B cell epitopes thus allowing neutralizing antibody escape. The mutations resulting in ACE 2 receptor recognition failure (T19R), unfavorable electrostatic interactions (E484K), structural change (∆69-70), disruption of hydrogen bonds, salt bridges or hydrophobic interactions (K417N, N501Y, ∆Y145) and change in orientation (N501Y) cause strong immune evasion by these variants. Further, the recent emergence of Omicron with more than 30 mutations in the S protein VOC allows it to escape and fail diagnosis as well as immune system and the protection generated by different vaccination regimes. Yet Omicron may not be the end of the story. This review presents an insight of the immunity escape and its mechanisms followed by different SARS-CoV-2 variant of concerns.
ARTICLE | doi:10.20944/preprints202105.0492.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Drug resistance; nsp12; protein design; fitness; RNA-dependent RNA polymerase; resistance mutations; SARS-CoV-2.
Online: 20 May 2021 (13:18:14 CEST)
Favipiravir is a broad-spectrum inhibitor of viral RNA-dependent RNA polymerase (RdRp) currently being used to manage COVID-19 in several countries. By acting as a substrate for RdRp, favipiravir gets incorporated into the nascent viral RNA and prevents strand extension. A high mutation rate of SARS-CoV-2 RdRp may facilitate antigenic drift as an answer to the host immune response, thereby generating resistance of virus to favipiravir. Therefore, it is extremely crucial to predict potential mutational sites in the RdRp and the emergence of structural modifications contributing to drug resistance. Here, we used high-throughput interface-based protein design to generate >100,000 designs and identify mutation hotspot residues in the favipiravir-binding site of RdRp. Several mutants had lower binding affinities to favipiravir, out of which hotspot residues with a high propensity to undergo positive selection were identified. The results showed that the designs retained an average of 97 to 98% sequence identity, suggesting that SARS-CoV-2 can develop favipiravir resistance with just a few mutations. Notably, we observed that out of 134 mutations predicted designs, 63 specific mutations were already present in the CoV-GLUE database, thus attaining ~47% correlation match with the clinical sequencing data. The findings improve our understanding of the potential signatures of adaptation in SARS-CoV-2 against favipiravir and management of COVID-19. Furthermore, they can help develop exhaustive strategies for robust antiviral design and discovery.
REVIEW | doi:10.20944/preprints202008.0007.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: spatial genome architecture; 3D chromatin organization; DNA loops; noncoding mutations; enhancer; blood cancer; hematopoietic malignancies
Online: 2 August 2020 (09:33:40 CEST)
Associations between blood cancer and genetic predisposition, including both inherited variants and acquired mutations and epimutations, have been well characterized. However, the majority of these variants affect noncoding regions, making their mechanisms difficult to hypothesize and hindering the translation of these insights into patient benefits. Fueled by unprecedented progress in next-generation sequencing and computational integrative analysis, studies have started applying combinations of epigenetic, genome architecture and functional assays to bridge the gap between noncoding variants and blood cancer. These complementary tools have not only allowed us to understand the potential malignant role of these variants but also to differentiate key variants, cell types and conditions from misleading ones. Here, we briefly review recent studies that have provided fundamental insights into our understanding of how noncoding mutations at enhancers predispose and promote blood malignancies in the context of spatial genome architecture.
ARTICLE | doi:10.20944/preprints202311.1585.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: prime editing; CRISPR/Cas9; gene editing; gene therapy; RYR1-related diseases; neuromuscular diseases; RYR1 gene; mutations
Online: 24 November 2023 (08:51:01 CET)
We report the first correction by Prime editing of a mutation in the RYR1 gene, paving the way to gene therapies for RYR1-related myopathies. The RYR1 gene codes for a calcium channel named Ryanodine receptor 1, which is expressed in skeletal muscle fibers. The failure of this channel causes muscle weakness in patients, which degenerates into motor disabilities. Currently, there are no effective treatments for these diseases, which are mainly caused by point mutations. Prime editing allows the modification of precise nucleotides in the DNA. Our results showed a 59% correction rate of the T4709M mutation in the RYR1 gene in human myoblasts by RNA delivery of the Prime editing components. It is to be noted that the T4709M is recessive, and thus, persons having a heterozygous mutation are healthy. These results are the first demonstration that it is possible to correct mutations in the RYR1 gene.
ARTICLE | doi:10.20944/preprints202108.0368.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: pancreatic cancer; cancer subtype identification; somatic point mutations; genotype and phenotype characterization; therapeutic targets; personalized medicine
Online: 17 August 2021 (22:24:57 CEST)
It has now known that at least 10% of samples with pancreatic cancers (PC) contain a causative mutation in the known susceptibility genes, suggesting the importance of identifying cancer-associated genes that carry the causative mutations in high-risk individuals for early detection of PC. In this study, we develop a statistical pipeline using a new concept, called gene-motif, that utilizes both mutated genes and mutational processes to identify 4,211 3-nucleotide PC-associated gene-motifs within 203 significantly mutated genes in PC. Using these gene-motifs as distinguishable features for pancreatic cancer subtyping results in identifying five PC subtypes with distinguishable phenotypes and genotypes. Our comprehensive biological characterization reveals that these PC subtypes are associated with different molecular mechanisms including unique cancer related signaling pathways, in which for most of the subtypes targeted treatment options are currently available. Some of the pathways we identified in all five PC subtypes, including cell cycle and the Axon guidance pathway are frequently seen and mutated in cancer. We also identified Protein kinase C, EGFR (epidermal growth factor receptor) signaling pathway and P53 signaling pathways as potential targets for treatment of the PC subtypes. Altogether, our results uncover the importance of considering both the mutation type and mutated genes in the identification of cancer subtypes and biomarkers.
ARTICLE | doi:10.20944/preprints202307.0520.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: CCDC186 mutations; seizures; hypomyelination; low levels of cortisol; low levels of insulin; growth hormone deficiency; hypoketotic hypoglycemia
Online: 10 July 2023 (11:23:39 CEST)
Background: Protein CCDC186 is involved in the maturation of dense core vesicles in the trans-Golgi network in neurons and endocrine cells. To date, only one patient, within a large sequencing study of 1000 cases, and a single case report with variants in CCDC186 had previously been described. However, no functional studies in any of these two cases had been performed. Methods: Exome sequencing from one affected individual of each family was performed. In addition, Sanger sequencing of the parents and one of the affected siblings was also performed. CCDC186 protein was assessed in cultured fibroblasts or muscle tissue by western blot. Transcriptomic analysis was done by means of RNA sequencing. Results. We identified three patients from two gypsy families, unrelated to each other, with the same homozygous mutations in CCDC186 gene. Clinically, all patients presented with seizures, frontotemporal atrophy, hypomyelination, recurrent infections, and endocrine disturbances such as severe non ketotic hypoglycemia. Low levels of cortisol, insulin or growth hormone could only be verified in one patient. All of them had a neonatal onset and died between 7 months and 4 years of age. WES identified a homozygous variant in CCDC186 gene (c.2215C>T, p.Arg739Ter) in the index patients of both families. Protein expression studies demonstrated that the CCDC186 was practically undetectable in fibroblasts and muscle tissue. These observations correlated perfectly with the transcriptomic analysis performed in fibroblasts in one of the patients, which showed a significant reduction of CCDC186 mRNA levels. Conclusion. Our study provides functional evidence that mutations in this gene have a pathogenic effect on the protein and reinforces CCDC186 as a new disease-associated gene. In addition, mutations in CCDC186 could explain the combined endocrine and neurologic alterations detected in our patients
BRIEF REPORT | doi:10.20944/preprints202305.0123.v1
Subject: Biology And Life Sciences, Insect Science Keywords: Aedes aegypti; pyrethroid resistance; kdr mutations; detoxification enzymes; 10ème arrondissement of Cotonou; Godomey-Togoudo; Benin West Africa
Online: 3 May 2023 (09:30:25 CEST)
Epidemics of arboviruses in general, and dengue fever, in particular, are an increasing threat in areas where Aedes (Ae.) aegypti is present. The effectiveness of chemical control of Ae. aegypti is threatened by the increasing frequency of insecticide resistance. The aim of this study was to determine the susceptibility status of Ae. aegypti to public health insecticides and assess the underlying mechanisms driving insecticide resistance. Ae. aegypti eggs were collected in two study sites in the vicinity of houses for two weeks using Gravid Aedes Traps (GATs). After rearing mosquitoes to adulthood, female Ae. aegypti were exposed to the diagnostic doses of permethrin, deltamethrin and bendiocarb, using Centers for Disease Control and Prevention (CDC) bottle bioassays. Unexposed, un-engorged female Ae. aegypti were tested individually for mixed-function oxidase (MFO), glutathione-S-transferase (GST) and esterase activity. Finally, allele-specific PCR (AS-PCR) was used to detect kdr mutations (F1534C, S989P and V1016G) in the voltage-gated sodium channel gene in insecticide-exposed Ae. aegypti. Most traps were oviposition positive; 93.2% and 97% of traps contained Ae. aegypti eggs in the 10ème arrondissement of Cotonou and in Godomey-Togoudo, respectively. Insecticide bioassays assays detected resistance to permethrin and deltamethrin in both study sites and complete susceptibility to bendiocarb. By comparison to the insecticide-susceptibility Rockefeller strain, field Ae. aegypti populations had significantly higher levels of GSTs and significantly lower levels of and esterases; there was no significant difference between levels of MFOs. AS-PCR genotyping revealed the presence of the three kdr mutations (F1534C, S989P and V1016G) at high frequencies; 80.9% (228/282) of Ae. aegypti tested had at least one mutation, while the simultaneous presence of all three kdr mutations was identified in 13 resistant individuals. Study findings demonstrated phenotypic pyrethroid resistance, the overexpression of key detoxification enzymes and the presence of several kdr mutations in Ae. aegypti populations, emphasizing the urgent need to implement vector control strategies, targeting arbovirus vector species in Benin.
ARTICLE | doi:10.20944/preprints202301.0039.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: somatic point mutations; non-coding RNA; biomarker discovery; driver genes; non-coding RNAs prioritization; health data analytics
Online: 4 January 2023 (02:22:00 CET)
Previous studies demonstrate the critical importance of non-coding RNAs interfacing with chromatin-modifying machinery resulting in promoter-enhancer-based gene regulation and raise the possibility that many other enhancer-like RNAs may operate via similar mechanisms. Critically, more than 80% of the disease-linked variations identified in genome-wide studies are located in the non-coding regions of genomes, especially non-coding RNA, suggesting non-coding RNAs are relevant to disease. Thus, a critical path forward for understanding non-coding RNAs' role, especially long non-coding RNAs, is to understand the genomic regions' transcriptional regulation, especially non-coding regions. Here, we developed a user-friendly R package called SomaGene for studying and identifying enhancer-like non-coding RNAs with enriched somatic mutations in the cancer genome. SomaGene accepts different genomic variants (whole genome/exome somatic point mutations, structural variations, copy number variations) to identify those RNAs that significantly mutated in diseases (e.g., cancer). It then uses multiple publicly available genomics and epigenetics datasets including ENCODE epigenomics annotations, FANTOM5 tissue-specific expression profiles, disease-associated genome-wide association SNPs, and tissue-specific eQTL pairs to identify those RNAs with potentially enhancer function. SomaGene, as a powerful R package, can provide the opportunity to cancer scientists to study the roles of non-coding RNAs in different cancer genomes.
ARTICLE | doi:10.20944/preprints202111.0266.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Pan-Cancer; somatic point mutations; cancer subtyping; biomarker discovery; driver genes; per-sonalized medicine; health data analytics
Online: 15 November 2021 (13:51:33 CET)
The advent of high throughput sequencing has enabled researchers to systematically evaluate the genetic variations in cancer, resulting in identifying many cancer-associated genes. Although cancers in the same tissue are widely categorized in the same group, they demonstrate many differences concerning their mutational profiles. Hence there is no “silver bullet” for the treatment of a cancer type. This reveals the importance of developing a pipeline to identify cancer-associated genes accurately and re-classify patients with similar mutational profiles. Classification of cancer patients with similar mutational profiles may help discover subtypes of cancer patients who might benefit from specific treatment types. In this study, we propose a new machine learning pipeline to identify protein-coding genes mutated in a significant portion of samples to identify cancer subtypes. We applied our pipeline to 12270 samples collected from the International Cancer Genome Consortium (ICGC), covering 19 cancer types. Here we identified 17 different cancer subtypes. Comprehensive phenotypic and genotypic analysis indicates distinguishable properties, including unique cancer-related signaling pathways, in which, for most of them, targeted treatment options are currently available. This new subtyping approach offers a novel opportunity for cancer drug development based on the mutational profile of patients. We also comprehensive study the causes of mutations among samples in each subtype by mining the mutational signatures, which provides important insight into their active molecular mechanisms. Some of the pathways we identified in most subtypes, including the cell cycle and the Axon guidance pathways, are frequently observed in cancer disease. Interestingly, we also identified several mutated genes and different rates of mutation in multiple cancer subtypes. In addition, our study on “gene-motif” suggests the importance of considering both the context of the mutations and mutational processes in identifying cancer-associated genes. The source codes for our proposed clustering pipeline and analysis are publicly available at: https://github.com/bcb-sut/Pan-Cancer.
ARTICLE | doi:10.20944/preprints202104.0732.v1
A Real-World, Observational, Prospective Study to Assess the Molecular Epidemiology of Epidermal Growth Factor Receptor (EGFR) Mutations upon Progression on or after First-Line Therapy with a First or Second Generation EGFR Tyrosine Kinase Inhibitor in EGFR Mutation-Positive Locally Advanced or Metastatic Non-small Cell Lung Cancer: The ‘LUNGFUL’ Study
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Epidermal Growth Factor Receptor (EGFR); mutations, EGFR tyrosine kinase inhibitor; molecular epidemiology; Non-small-cell lung cancer
Online: 28 April 2021 (07:55:22 CEST)
Background: Real-world data on the molecular epidemiology of EGFR resistance mutations at or after progression with first- or second-generation EGFR-TKIs in patients with advanced NSCLC are lacking. Methods: This ongoing observational study was carried out by 23 hospital-based physicians in Greece. The decision to perform Cobas® EGFR Mutation Test v2 in tissue and/or plasma at disease progression was made before enrollment. For patients with negative/inconclusive T790M plasma-based results, tissue re-biopsy could be performed. Results: Ninety-six (96) eligible patients were consecutively enrolled (median age: 67.8 years) between July-2017 and September-2019. Of the patients, 98% were tested upon progression using plasma and 2% using tissue/cytology biopsy. The T790M mutation was detected in 16.0% of liquid biopsies. Tissue re-biopsy was performed in 22.8% of patients with a T790M-negative plasma result. In total, the T790M positivity rate was 21.9%, not differing between patients on first- or second-generation EGFR-TKI. Higher (≥2) ECOG performance status and longer (≥10 months) time to disease progression following EGFR-TKI treatment initiation were associated with T790M positivity. Conclusions: Results from plasma/tissue-cytology samples in a real-world setting, yielded a T790M positivity rate lower than previous reports. Fewer than one in four patients with negative plasma-based testing underwent tissue re-biopsy, indicating the challenges in routine care settings.
REVIEW | doi:10.20944/preprints202104.0376.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Diffuse large B cell lymphoma; non-Hodgkin lymphoma; apoptosis; genetics; BCL2; NF-kB; TP53; mutations; translocations; amplifications
Online: 14 April 2021 (12:32:31 CEST)
Diffuse large B cell lymphoma (DLBCL) is curable with chemoimmunotherapy in ~65% of patients. One of the hallmarks of the pathogenesis and resistance to therapy in DLBCL is inhibition of apoptosis, which allows malignant cells to survive and acquire further alterations. Inhibition of apoptosis can be the result of genetic events inhibiting the intrinsic or extrinsic apoptotic pathways, as well as their modulators, such as the inhibitor of apoptosis proteins, P53, and components of the NF-kB pathway. Mechanisms of dysregulation include upregulation of anti-apoptotic proteins and downregulation of pro-apoptotic proteins via point mutations, amplifications, deletions, translocations, and influences of other proteins. Understanding the factors contributing to resistance to apoptosis in DLBCL is crucial in order to be able to develop targeted therapies that could improve outcomes by restoring apoptosis in malignant cells. This review describes the genetic events inhibiting apoptosis in DLBCL, provides a perspective of their interactions in lymphomagenesis, and discuss their implication for the future of DLBCL therapy.
REVIEW | doi:10.20944/preprints202102.0529.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Caver Web; databases; libraries; microbial products; PredictSNPonco; molecular docking; molecular targets; mutations; treatment; virtual screening; web tools
Online: 23 February 2021 (15:59:19 CET)
The development of microbial products for cancer treatment has been in the spotlight in recent years. In order to accelerate the lengthy and expensive drug development process, in silico screening tools are systematically employed, especially during the initial discovery phase. Moreover, considering the steadily increasing number of molecules approved by authorities for commercial use, there is a demand for faster methods to repurpose such drugs. Here we present a review on virtual screening web tools, publicly available databases of molecular targets and libraries of ligands, with the aim to facilitate the discovery of potential anticancer drugs based on microbial products. We provide an entry-level step-by-step description of the workflow for virtual screening of microbial metabolites with known protein targets, as well as two practical examples using freely available web tools. The first case presents a virtual screening study of drugs developed from microbial products using Caver Web, a web tool that performs docking along a tunnel. The second case comprises a comparative analysis between a healthy isocitrate dehydrogenase 1, a mutant that results in cancer, using the recently developed web tool PredictSNPOnco. In summary, this review provides the basic and essential background information necessary for virtual screening experiments, which may accelerate the discovery of novel anticancer drugs.
ARTICLE | doi:10.20944/preprints202310.0055.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: SORL1, mutations, secretases, bAPP, Ab peptides, C-terminal fragments, neprilysin, proteasome, degradation, cellular localization, transient and stable expressions.
Online: 2 October 2023 (11:08:13 CEST)
SORL1 gene encodes LR11/SorLA, a protein that binds -amyloid precursor protein (bAPP) and drives its intracellular trafficking. SORL1 mutations occurring frequently in a subset of familial cases of Alzheimer’s disease (AD) have been documented but their pathogenic potential is not yet clear and questions remain concerning their putative influence on the physiopathological processing of bAPP. We have assessed the influence of three SORL1 mutations that were described as likely disease-causing and that were associated with either benign (SorLA924) or severe (SorLA141 and SorLA511) AD phenotypes. We examined the influence of wild-type and mutants SorLA in transiently transfected HEK293 cells expressing either wild-type or Swedish mutated bAPP on bAPP expression, secreted Ab and sAPPa levels, intracellular Ab40 and Ab42 peptides, APP-CTFs (C99 and C83) expressions, a-, b- and g-secretases expressions and activities as well as Ab and CTFs-degrading enzymes. These paradigms were studied in control conditions or after pharmacological proteasomal modulation. We also established stably transfected CHO cells expressing wild-type SorLA and established the colocalization of wild-type SorLA and bAPP. Overall, although we mostly confirmed previous data concerning the influence of wild-type SorLA on bAPP processing, we were unable to evidence significant alterations triggered by our set of SorLA mutants, whatever the cells or pharmacological conditions examined. Our study however does not rule out the possibility that other AD-linked SORL1 mutations could indeed affect bAPP processing and that pathogenic mutations examined in the present study could interfere with other cellular pathways/triggers in AD.
REVIEW | doi:10.20944/preprints202304.0736.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: advanced breast cancer; germline BRCA1/2 mutations; pathogenic/likely pathogenic variants; CDK4/6 inhibitors; Pi3Ka inhibitors; HER2-low
Online: 23 April 2023 (03:12:48 CEST)
We explored the outcomes of germline BRCA1/2 pathogenic/likely pathogenic variants (PVs/LPVs) in the endocrine-sensitive disease treated with first line standard of care cyclin-dependent kinase 4/6 (CDK4/6) inhibitors. Three studies retrospectively showed a reduction in overall survival (OS) and progression free survival (PFS) in gBRCA1/2m patients compared to both germinal BRCA1/2 wild type (gBRCA1/2wt) and to the untested population. Regarding the efficacy of PI3K inhibitors, there are no subgroup or biomarker analyses in which germinal BRCA status was explored. However, the biological interactions between the PIK3CA/AKT/mTOR pathway and BRCA1/2 at a molecular level could help us to understand the activity of these drugs when used to treat BC in BRCA1/2 PVs/LPVs carriers. The efficacy of trastuzumab deruxtecan (T-DXd), an antibody-drug conjugate (ADC) targeting HER2 for HER2-low and HER2-positive (HER2+) BC, has been increasingly described. Unfortunately, data on T-DXd in HER2+ or HER2-low metastatic BC harboring germinal BRCA1/2 PVs/LPVs is lacking. Including germinal BRCA1/2 status in the subgroup analysis of the registration trials of this ADC would be of great interest, especially in the phase III trial DESTINY-breast04. This trial enrolled patients with HER2-negative (HER2-) and both HR+ and HR- metastatic disease, which can now be categorized as HER2-low. The HER2-low subgroup includes tumors that were previously classified as triple negative, so it is highly likely that some women were germline BRCA1/2 PVs/LPVs carriers and this data was not reported. Germline BRCA1/2 status will be available for a higher number of individuals with BC in the near future and data on the prognostic and predictive role of these PVs/LPVs is needed in order to choose the best treatment options.
ARTICLE | doi:10.20944/preprints202301.0343.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Prostate cancer; Somatic point mutations; Copy number variation; Regulatory variant, Hi-C; Per-sonalized medicine; Biomedical machine learning
Online: 19 January 2023 (02:10:02 CET)
Prostate cancer (PC) is the most frequently diagnosed non-skin cancer in the world. Previous studies showed that genomic alterations represent the most common mechanism for molecular alterations that cause the development and progression of PC. Great efforts have been done to identify common protein-coding genetic variations; however, the impact of non-coding variations including regulatory genetic variants is not still well understood. To gain an understanding of the functional impact of genetic variants, particularly, regulatory variants in PC, we developed an integrative pipeline (AGV) that used whole genome/exome sequences, GWAS SNPs, chromosome conformation capture data, and ChIP-Seq signals to investigate the potential impact of genomic variants on the underlying target genes in PC. We identified 646 putative regulatory variants, of which 30 of them significantly altered the expression of at least one protein-coding gene. Our analysis of chromatin interactions data (Hi-C) revealed that the 30 putative regulatory variants may affect 131 coding and non-coding genes. Interestingly, our study showed the 131 protein-coding genes are involved in disease-related pathways including Reactome and MSigDB in which for most of them targeted treatment options are currently available. Together, our results provide a comprehensive map of genomic variants in PC and revealed their potential contribution to prostate cancer progression and development.
ARTICLE | doi:10.20944/preprints202210.0463.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Bladder cancer; Hispanics; Mexicans population; Mutations; Cancer genomics; non-muscle inva-sive bladder cancer; muscle-invasive bladder cancer
Online: 31 October 2022 (02:27:54 CET)
Bladder cancer (BC) is the most common neoplasm of the urinary tract, which originates in the epithelium that covers the inner surface of the bladder. The molecular BC profile has led to the development of different classifications of non-muscle invasive bladder cancer (NMIBC) and muscle-invasive (MIBC). However, the genomic BC landscape profile of the Mexican population, including NMIBC and MIBC, is unknown. In this study, we aimed to identify somatic single nucleotide variants (SNVs) and copy number variations (CNVs) in Mexican patients with BC and their associations with clinical and pathological characteristics. We retrospectively evaluated 37 patients treated between 2012 and 2021 at the National Cancer Institute - Mexico (INCan). DNA samples were obtained from paraffin-embedded tumor tissues and ran exome sequencing. Strelka2 and Lancet packages were used to identify SNVs and insertions or deletions. FACETS was used to determine CNVs. We found a high frequency of mutations in TP53 and KMT2D, gains in 11q15.5 and 19p13.11-q12, and losses in 7q11.23. STAG2 mutations and 1q11.23 deletions were also associated with NMIBC and low histologic grade.
REVIEW | doi:10.20944/preprints202308.0520.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: SARS-CoV-2; spike protein; mutations; viral infectivity; pathogenesis; vaccine efficacy; immune evasion; antibody neutralization; T-cell response; therapeutic targeting
Online: 7 August 2023 (10:12:28 CEST)
The SARS-CoV-2 virus, which is responsible for the COVID-19 pandemic which emerged and spread, has sparked intense research on its spike protein, which is essential for viral entrance into host cells. Viral reproduction and transmission, host immune response regulation, receptor recognition and host cell entrance mechanisms, as well as structural and functional effects have all been linked to mutations in the spike protein. Spike protein mutations can also result in immune evasion mechanisms that impair vaccine effectiveness and escape, and they are linked to illness severity and clinical consequences. Numerous studies have been conducted to determine the effects of these mutations on the spike protein structure and how it interacts with host factors. These results have important implications for the design and development of medicines and vaccines based on spike proteins as well as for the assessment of those products' efficiency against newly discovered spike protein mutations. The paper gives a general overview of how spike protein mutations are categorized and named, as well as the genomic and phylogenetic techniques that have been used to track their genesis and dissemination. Additionally, it looks at the links between spike protein mutations and clinical outcomes, illness severity, unanswered problems, and future research prospects. Additionally, explored are the effects of these mutations on vaccine effectiveness as well as the possible therapeutic targeting of spike protein mutations.
ARTICLE | doi:10.20944/preprints201708.0103.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: stem cells; somatic mutations; cancer prevention; carcinogenesis; whole genome sequencing; stem cell division theory of cancer; bad luck of cancer
Online: 30 August 2017 (12:14:52 CEST)
Recent evidence indicates that the risk of being diagnosed with cancer in a tissue is strongly correlated (0.80) with the number of stem cell divisions accumulated by the tissue. Since cell division can generate random mutations during DNA replication, this correlation has been used to propose that cancer is largely caused by the accumulation of unavoidable mutations in driver genes. However, no correlation between the number of gene mutations and cancer risk across tissues has been reported. Because many somatic mutations in cancers originate prior to tumor initiation and the number of cell divisions occurring during tumor growth is similar among tissues, here I use whole genome sequencing information from 22,086 cancer samples and incidence data from the largest cancer registry in each continent to study the relationship between the number of gene mutations and the risk of cancer across 33 tissue types. Results show a weak positive correlation (mean = 0.14) between these two parameters in each of the five cancer registries. The correlation became stronger (mean = 0.50) when gender-related cancers were excluded. Results also show that 1,003 samples from 29 cancer types have zero mutations in genes. These data suggest that cancer etiology can be better explained by the accumulation of stem cell divisions than by the accumulation of gene mutations. Possible mechanisms by which the accumulation of cell divisions in stem cells increases the risk of cancer are discussed.
REVIEW | doi:10.20944/preprints202307.0634.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: OSCC; oral cancer; genes; mutations; miRNA; expression; mir-34a; mir-155; mir-124; mir-1; mir-16; bioinformatics; in silico analysis
Online: 11 July 2023 (04:16:04 CEST)
Oral squamous cell carcinoma (OSCC) is one of the most prevalent human malignancies and a global health concern with a poor prognosis despite therapeutic advances, highlighting the need for a better understanding of its molecular background. The genomic landscape of OSCC is well-established and recent research has focused on miRNAs, which regulate gene expression and may be useful as non-invasive biomarkers. A plethora of findings regarding miRNA expression have been generated, posing challenges for their interpretation and identification of disease-specific molecules. Hence, we opted to identify the most important miRNA molecules by bridging genetics and epigenetics, focusing on the key genes implicated in OSCC development. Based on published reports, we have developed a custom panel of 15 major oncogenes and a second panel of 5 major tumor suppressor genes. Following a miRNA/target interaction analysis and a comprehensive study of the literature, we selected the miRNA molecules, which target the majority of each gene panel and are reported to be downregulated or upregulated in OSCC, respectively. As a result, miR-34a-5p, miR-155-5p, miR-124-3p, miR-1-3p and miR-16-5p appeared to be the most OSCC-specific. Their expressional patterns, their verified targets and the signaling pathways affected by their dysregulation in OSCC, are thoroughly discussed in this review.
REVIEW | doi:10.20944/preprints202011.0013.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: APOBEC; RNA virus replication; DNA virus replication; AID; HIV-1 Vif; genome hypermutation; MMTV Rem; G-to-A mutations; viral variants
Online: 2 November 2020 (10:06:10 CET)
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) proteins are a diverse and evolutionarily conserved family of cytidine deaminases that provide a variety of functions from tissue-specific gene expression and immunoglobulin diversity to control of viruses and retrotransposons. APOBEC family expansion has been documented among mammalian species, suggesting a powerful selection for their activity. Enzymes with a duplicated zinc-binding domain often have catalytically active and inactive domains, yet both have antiviral function. Although APOBEC antiviral function was discovered through hypermutation of HIV-1 genomes lacking an active Vif protein, much evidence indicates that APOBECs also inhibit virus replication through mechanisms other than mutagenesis. Multiple steps of the viral replication cycle may be affected, although nucleic acid replication is a primary target. Packaging of APOBECs into virions was first noted with HIV-1, yet is not a prerequisite for viral inhibition. APOBEC antagonism may occur in viral producer and recipient cells. Signatures of APOBEC activity include G-to-A and C-to-T mutations in a particular sequence context. The importance of APOBEC activity for viral inhibition is reflected in the identification of numerous viral factors, including Vif, which are dedicated to antagonism of these deaminases. Such viral antagonists often are only partially successful, leading to selection for viral variants.
ARTICLE | doi:10.20944/preprints202311.0738.v1
Subject: Biology And Life Sciences, Virology Keywords: Influenza A virus; A/South Africa/3626/2013 (H1N1)pdm09; H1N1pdm09 model strain; mutations in polymerase complex and hemagglutinin; pathogenicity; toxicity; immunogenicity
Online: 13 November 2023 (14:17:10 CET)
Influenza virus strain A/South Africa/3626/2013 (H1N1)pdm09 (SA-WT) is a non-mouse-adapted model strain, which has naturally high pathogenic properties for mice. It has been suggested that the high pathogenicity of this strain for mice could be due to the three strain-specific substitutions in the polymerase complex (Q687R in PB1, N102T in PB2, and E358E/K heterogeneity also in PB2). To evaluate the role of these replacements, SA-WT was passaged five times in mouse lungs, and the genome of the mouse-adapted version of the SA-WT strain (SA-M5) was sequenced. SA-M5 lost E358E/K heterogeneity and retained E358, which is the prevalent amino acid at this position among H1N1pdm09 strains. Besides, in the hemagglutinin of SA-M5, two heterogeneous substitutions (G155G/E and S190S/R) were identified. Both viruses, SA-M5 and SA-WT, were compared for their toxicity, ability to replicate, pathogenicity, and immunogenicity for mice. In mice infected with SA-M5 or SA-WT strains, toxicity, virus titer in pulmonary homogenates, and mouse survival did not differ significantly. Contrarily, an increase in the immunogenicity of SA-M5 compared to SA-WT was observed. This increase could be due to the substitutions G155G/E and S190S/R in the HA of SA-M5. The prospects for using SA-M5 in studying the immunogenicity mechanisms were also discussed.
ARTICLE | doi:10.20944/preprints202012.0697.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Repeat-Induced Point Mutations; RIP; Accessory Chromosome; Genome Compartmentalization; GC Content; Genetic Variation; Fusarium circinatum; Transposable Elements; Interstitial Telomeric Repeats; Effector Genes.
Online: 28 December 2020 (12:18:11 CET)
Repeat-Induced Point mutations (RIP) serves as a genome defence mechanism that impedes the deleterious consequences of repeated motifs such as transposable elements in fungi. Genomic regions with RIP are biased for adenosine and thymine transitions and the cumulative influence of RIP is thought to have a considerable impact on genome composition. We investigated the impact of RIP on localized genomic regions and whole-genome sequences for representatives of the pine pathogen, Fusarium circinatum. We set out to determine the intraspecific variation in acquired RIP and the role of RIP in the development of diverse F. circinatum sub-genomic compartments. The results of the study show that the AT-enriched sub-genomic compartment accounts for ca. 97% of the calculated RIP and was further prominent in both core and accessory genomic regions. However, more extensive RIP was observed in the accessory sub-compartment and more variable regions of the genome. Regions with RIP indicated increased intrinsic curvature of the DNA which may influence DNA-protein interactions and may promote constitutive heterochromatin formation. The results show that RIP is an important source of functional novelty and genome variation. RIP contributes to the evolution of the genetic landscape and differentiation of diverse sub-genomic compartments of this important fungal pathogen.
ARTICLE | doi:10.20944/preprints202109.0415.v2
Subject: Biology And Life Sciences, Virology Keywords: Delta variant; Variants of concern; Variants of interest; SARS-CoV-2; Spike protein; Nested RT-PCR; Sanger sequencing; Amino acid mutations; ACE2 RBD; N-terminal domain (NTD)
Online: 2 November 2021 (10:40:46 CET)
As SARS-CoV-2 continues to spread among human populations, genetic changes occur and accumulate in the circulating virus. Some of these genetic changes have caused amino acid mutations, including deletions, which may have potential impact on critical SARS-CoV-2 countermeasures, including vaccines, therapeutics, and diagnostics. Considerable efforts have been made to categorize the amino acid mutations of the angiotensin-converting enzyme 2 (ACE2) receptor binding domain (RBD) of the spike (S) protein along with certain mutations in other regions within the S protein as specific variants in an attempt to study the relationship between these mutations and the biological behavior of the virus. However, the currently used whole genome sequencing surveillance technologies can test only a small fraction of the positive specimens with high viral loads and often generate uncertainties in nucleic acid sequencing that needs additional verification for precision determination of mutations. This article introduces a generic protocol to routinely sequence a 437-bp nested RT-PCR cDNA amplicon of the ACE2 RBD and a 490-bp nested RT-PCR cDNA amplicon of the N-terminal domain (NTD) of the S gene for detection of the amino acid mutations needed for accurate determination of all variants of concern and variants of interest according to the definitions published by the U.S. Centers for Disease Control and Prevention. This protocol was able to amplify both nucleic acid targets into cDNA amplicons to be used as templates for Sanger sequencing on all 16 clinical specimens that were positive for SARS-CoV-2.
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Neuroendocrine Neoplasms; NOTCH; cancer driven genes; mutational mechanism; germline mutations.; small cell lung carcinoma; pancreatic NET; small bowel NET; medullary thyroid carcinoma; malignant castration-resistant prostatic cells
Online: 23 July 2019 (10:34:50 CEST)
Neuroendocrine neoplasms (NENs) comprise a heterogeneous group of rare malignancies mainly originated from hormones secreting cells, which are widespread in human tissues. The identification of mutations in ATRX/DAXX genes in sporadic NENs, as well as the high burden of mutations scattered throughout MEN-1 gene in both sporadic and inherited syndromes, provided new insights into the molecular biology of tumour development. Other molecular mechanisms, such as the NOTCH signaling pathway, have shown to play an important role in the pathogenesis of NENs. NOTCH receptors are expressed on neuroendocrine cells and generally, act as tumour suppressor proteins, but in some contexts can function as oncogenes. The biological heterogeneity of NENs suggests that to fully understand the roles and the potential therapeutic implications of gene mutations and NOTCH signaling in NENs, a comprehensive analysis of genetic alterations, NOTCH expression patterns and their potential roles across all NEN subtypes is required.
ARTICLE | doi:10.20944/preprints202203.0290.v3
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: host-virus interactions; tissue-specific model; COVID-19; SARS-CoV-2; antiviral targets; flux balance analysis; flux variability analysis; reaction knockout; host-derived enforcement; metabolic modeling; virus mutations; software engineering; Python
Online: 17 January 2023 (01:50:23 CET)
COVID-19 is one of the deadliest respiratory diseases, and its emergence caught the pharmaceutical industry off guard. While vaccines have been rapidly developed, treatment options for infected people remain scarce, and COVID-19 poses a substantial global threat. This study presents a novel workflow to predict robust druggable targets against emerging RNA viruses using metabolic networks and information of the viral structure and its genome sequence. For this purpose, we implemented pymCADRE and PREDICATE to create tissue-specific metabolic models, construct viral biomass functions and predict host-based antiviral targets from more than one genome. We observed that pymCADRE reduces the computational time of flux variability analysis for internal optimizations. We applied these tools to create a new metabolic network of primary bronchial epithelial cells infected with SARS-CoV-2 and identified enzymatic reactions with inhibitory effects. The most promising reported targets were from the purine metabolism, while targeting the pyrimidine and carbohydrate metabolisms seemed to be promising approaches to enhance viral inhibition. Finally, we computationally tested the robustness of our targets in all known variants of concern, verifying our targets’ inhibitory effects. Since laboratory tests are time-consuming and involve complex readouts to track processes, our workflow focuses on metabolic fluxes within infected cells and is applicable for rapid hypothesis-driven identification of potentially exploitable antivirals concerning various viruses and host cell types.
ARTICLE | doi:10.20944/preprints202105.0646.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Torg-Winchester Syndrome; Torg syndrome; MONA syndrome; Nodulosis-Arthropathy-Osteolysis syndrome; Al-Aqeel Sewairi Syndrome; Matrix Metalloproteinase 14; MMP2 gene mutations; Osteochondrodysplasia; genetic skeletal dysplasia; Frank-Ter Haar syndrome; Multicentric carpotarsal osteolysis syndrome; Childhood osteoporosis.
Online: 26 May 2021 (15:02:22 CEST)
Objectives: Multicentric Osteolysis, Nodulosis, and Arthropathy (MONA) syndrome is a rare genetic skeletal dysplasia. Its diagnosis can be deceptively similar to childhood-onset genetic skeletal dysplasias and juvenile idiopathic arthritis. We aimed to report the syndrome’s clinical and radiologic features with emphasis on skeletal manifestations. And establish relevant phenotype-genotype correlations. Methods: We evaluated two boys, 4-and-7-years-old with MONA syndrome. Both patients had consanguineous parents. We verified the diagnosis by correlating the outcomes of clinical, radiologic and molecular analysis. We specifically evaluated the craniofacial morphology and clinical and radiographic skeletal abnormalities. We contextualized the resultant phenotype-genotype correlations to publications on MONA and its differential diagnosis. Results: Skeletal manifestations were the presenting symptoms and mostly restricted to hands and feet in terms of fixed extension deformity of the metacarpophalangeal and flexion deformity of the interphalangeal joints with extension deformity of big toes. There were arthritic symptoms in the older patient especially of the wrists and minute pathologic fractures. The skeletal radiographs showed osteopenia/dysplastic changes of hands and feet. Both patients had variants in the matrix metalloproteinase2 gene which conformed to phenotype of previously reported literature in one patient while the other had a novel variant which conformed to MONA phenotype. Craniofacial abnormalities were present. However, minimal extra-skeletal manifestations. Conclusion: Overall, there is an emerging distinctive skeletal pattern of involvement in terms of both clinical and radiographic features. This includes age of onset and location of presenting skeletal manifestations, chronological order of joint affection, longitudinal disease progression, specifics of skeletal radiographic pathology and craniofacial features. Nevertheless, physicians are cautioned against differential diagnosis of similar genetic skeletal dysplasias and juvenile idiopathic arthritis.