Submitted:
01 June 2026
Posted:
02 June 2026
You are already at the latest version
Abstract

Keywords:
1. Introduction
2. Materials and Methods
Data Sources
Pipeline Architecture
Annotated Union Dataset Construction
Parallel Filtering Strategies
Manual Curation for Extracellular Accessibility
Composite Scoring and Prioritization
Validation Layers
Protein Expression Visualization
Transcriptomic Analysis
Immunohistochemistry and Subcellular Localization
Literature Mining and Biomarker Evidence
Protein Expression in Other Cancer Types
Clinical and Biomarker Annotation
3. Results
3.1. Pipeline Performance Across Filtering Strategies
3.2. Overlap and Robustness of Candidate Selection
3.3. Composite Scoring and Prioritization
3.4. Validation Layers
3.5. Summary of Pipeline Robustness
4. Discussion
Advantages of the Pipeline
Comparison with Existing Approaches
Limitations
Future Directions
Clinical and Translational Implications
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
| CPTAC | Clinical Proteomic Tumor Analysis Consortium |
| COAD | Colon Adenocarcinoma |
| COADREAD | Colon Adenocarcinoma and Rectal Adenocarcinoma |
| CRC | Colorectal Cancer |
| BRCA | Breast Invasive Carcinoma |
| LSCC | Lung squamous cell carcinoma |
| LUAD | Lung Adenocarcinoma |
| OV | Ovarian Serous Cystadenocarcinoma |
| PDAC | Pancreatic Ductal Adenocarcinoma |
| CDDI | Cortellis Drug Discovery Intelligence |
| HPA | Human Protein Atlas |
| GTEX | The Genotype-Tissue Expression project |
| CSPA | Cell Surface Protein Atlas |
| CCLE | Cancer Cell Line Encyclopedia |
| GO | Gene Ontology |
| TCGA | The Cancer Genome Atlas |
| PC | Prostate Cancer |
| FC | Fold Change |
References
- Di Meo, F.; et al. Mapping the cancer surface proteome in search of target antigens for immunotherapy. Mol. Ther. 2024, 32(9), 2892–2904. [Google Scholar] [CrossRef]
- Crunkhorn, S. Proteogenomics identifies anticancer targets. Nat. Rev. Drug Discov. 2024, 23(9), 660. [Google Scholar] [CrossRef]
- Vasaikar, S.; et al. Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities. Cell 2019, 177(4), 1035–1049 e19. [Google Scholar] [CrossRef]
- Zhang, B.; et al. Proteogenomic characterization of human colon and rectal cancer. Nature 2014, 513(7518), 382–7. [Google Scholar] [CrossRef]
- Wang, J.; et al. Pan-Cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics. Mol. Cell Proteom. 2023, 22(9), 100626. [Google Scholar] [CrossRef]
- Leung, K.K.; et al. Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome. Chem. Rev. 2025, 125(8), 4069–4110. [Google Scholar] [CrossRef]
- Savage, S.R.; et al. Pan-cancer proteogenomics expands the landscape of therapeutic targets. Cell 2024, 187(16), 4389–4407 e15. [Google Scholar] [CrossRef]
- Shraim, R.; et al. ImmunoTar-integrative prioritization of cell surface targets for cancer immunotherapy. Bioinformatics 2025, 41(3). [Google Scholar] [CrossRef]
- Uhlen, M.; et al. Proteomics. Tissue-based map of the human proteome. Science 2015, 347(6220), 1260419. [Google Scholar] [CrossRef]
- Thul, P.J.; et al. A subcellular map of the human proteome . Science 2017, 356(6340). [Google Scholar] [CrossRef]
- Barretina, J.; et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012, 483(7391), 603–7. [Google Scholar] [CrossRef]
- UniProt, C. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 2023, 51(D1), D523–D531. [Google Scholar]
- Aung, W.; et al. Combined treatment of pancreatic cancer xenograft with (90)Y-ITGA6B4-mediated radioimmunotherapy and PI3K/mTOR inhibitor. World J. Gastroenterol. 2017, 23(42), 7551–7562. [Google Scholar] [CrossRef] [PubMed]
- Tatsumi, T.; et al. In vivo-stable bis-iminobiotin for targeted radionuclide delivery with the mutant streptavidin. Bioorg Med. Chem. Lett. 2024, 108, 129803. [Google Scholar] [CrossRef]
- Zboralski, D.; et al. Preclinical evaluation of FAP-2286 for fibroblast activation protein targeted radionuclide imaging and therapy. Eur. J. Nucl. Med. Mol. Imaging 2022, 49(11), 3651–3667. [Google Scholar] [CrossRef]
- Bidkar, A.P.; et al. Treatment of Prostate Cancer with CD46-targeted 225Ac Alpha Particle Radioimmunotherapy. Clin. Cancer Res. 2023, 29(10), 1916–1928. [Google Scholar] [CrossRef] [PubMed]
- Feng, S.; et al. Astatine-211-Labeled Therapy Targeting Amino Acid Transporters: Overcoming Drug Resistance in Non-Small Cell Lung Cancer. Int. J. Mol. Sci. 2025, 26(21). [Google Scholar] [CrossRef] [PubMed]
- Dai, L.; Jin, X.; Liu, Z. Prognostic and clinicopathological significance of GPRC5A in various cancers: A systematic review and meta-analysis. PLoS ONE 2021, 16(3), e0249040. [Google Scholar] [CrossRef]
- He, A.; Liao, F.; Lin, X. Circ_0007351 Exerts an Oncogenic Role In Colorectal Cancer Depending on the Modulation of the miR-5195-3p/GPRC5A Cascade. Mol. Biotechnol. 2025, 67(2), 617–627. [Google Scholar] [CrossRef]
- Liu, X.S.; et al. SLC2A1 is a Diagnostic Biomarker Involved in Immune Infiltration of Colorectal Cancer and Associated With m6A Modification and ceRNA. Front Cell Dev. Biol. 2022, 10, 853596. [Google Scholar] [CrossRef]
- Ren, Z.; et al. Targeting Glucose Transporter 1 (GLUT1) in Cancer: Molecular Mechanisms and Nanomedicine Applications. Int. J. Nanomed. 2025. 20, 11859–11879. [Google Scholar] [CrossRef] [PubMed]
- Arai, H.; et al. Role of CD47 gene expression in colorectal cancer: a comprehensive molecular profiling study. J. Immunother. Cancer 2024, 12(11). [Google Scholar] [CrossRef]
- Li, Q.; et al. Expression and Clinical Significance of CD47 in Colorectal Cancer: A Review. Cancers 2025, 18(1). [Google Scholar] [CrossRef]
- Eisenach, P.A.; et al. Dipeptidase 1 (DPEP1) is a marker for the transition from low-grade to high-grade intraepithelial neoplasia and an adverse prognostic factor in colorectal cancer. Br. J. Cancer 2013, 109(3), 694–703. [Google Scholar] [CrossRef]
- Park, S.Y.; et al. Dehydropeptidase 1 promotes metastasis through regulation of E-cadherin expression in colon cancer. Oncotarget 2016, 7(8), 9501–12. [Google Scholar] [CrossRef] [PubMed]
- Sari, I.N.; et al. Interferon-induced transmembrane protein 1 (IFITM1) is required for the progression of colorectal cancer. Oncotarget 2016, 7(52), 86039–86050. [Google Scholar] [CrossRef] [PubMed]
- Jin, S.; et al. IFITM1-targeted NIR-II fluorescence imaging enables.







| Filter | Rationale | 1 | 2 | 3 | 4 | |
|---|---|---|---|---|---|---|
| Sum of scaled localization ranks (UniProt, HPA & CSPA) | Ensure localization on PM | >0,44 | >= 0,1 | > 0,4 | ||
| Mean protein rank | Overexpression of protein | >= 0,5 | ||||
| Mean stage 4 protein rank | Proteins with stage 4 protein expr | > 0 | > 0 | > 0,3 | ||
| Targeted by RIT | Protein with other RITs removed | = 0 | ||||
| UniProtKB & HPA secreted | No secreted proteins | = 0 | ||||
| GTEx mean abundance | Low normal tissue expr | < 2 | < 1,8 | |||
| HPA max abundance | Low normal tissue expr | = 0,1, 2* | ||||
| HPA mean abundance | Low normal tissue expr | < 2* | < 1,8 | |||
| Max abundance on CCLE | Expressed on tumor cells | > 0,46* | >1* | > 0,5* | > 2* | |
| Mean abundance on CCLE | Expressed on tumor cells | > 0,4* | >0,5* | > 0,4* | > 1* | |
| N detected (CRC) in CCLE | Expressed on tumor cells | > 0* | ||||
| Mean abundance CCLE (CRC) | Expressed on tumor cells | >= 1,5* | >=1,4* | >= 1,5* | ||
| Filter | Rationale | 5 | 6 | 7 | |
|---|---|---|---|---|---|
| Stage IV protein expression in COAD and COADREAD cohorts | Proteins with stage IV protein expression | At least upregulated in one cohort and up-regulated or non-differentially expressed in the other* | |||
| UniProt localization score** | Enrichment of candidate proteins with cell surface localization | >0 | >0 | ||
| Sum of scaled localization ranks (UniProt, HPA & CSPA) | Ensure localization on PM | >0,5 | >0 | ||
| Penalty for secreted proteins | Ensure localization on PM | Shedded proteins excluded | |||
| 1.6x Up-regulation observed at min in COAD cohort | Increasing selection stringency | LogFC COAD >=0.2 | |||
| 1.6x Up-regulation observed at min in one cohort | Increasing selection stringency | logFC(COAD or COADREAD)>=0.2 | |||
| Penalty for mitochondria, nucleus and peroxisome localization | Ensure localization on PM | Exclusion of intra-cellular proteins with membrane association | |||
| Mean abundance HPA | Low normal tissue expression | <=1,5 | |||
| Manual review for no extracellularly exposed proteins | Ensure relevant PM expression | Manual curation | |||
| Filter | Rationale | 8 | 9 | 10 | 11 | ||
|---|---|---|---|---|---|---|---|
| Stage IV protein expression in COAD | Proteins with stage IV protein expression | Upregulated | |||||
| Stage IV protein expression in COADREAD | Proteins with stage IV protein expression | Upregulated | |||||
| UniProt localization score** | Enrichment of candidate proteins with cell surface localization | >0 | >0 | ||||
| Manual review for no extracellularly exposed proteins | Ensure relevant PM expression | Manual curation | |||||
| Sum of scaled localization ranks (UniProt, HPA & CSPA) | Ensure localization on PM | >0 | |||||
| Penalty for secreted proteins | Ensure localization on PM | Shedded proteins excluded | |||||
| Up-regulation observed in COADREAD cohort | Increasing selection stringency | logFC >=2 | logFC >=1.4 | ||||
| Symbol | Description | Sum of scaled localization ranks | Mean stage 4 protein rank | Scaled sum of CDDI ranks | MAS* in HPA | MAS* in GTEX | MAS* in CCLE | MAS* (CRC) in CCLE | Sum weighted score |
|---|---|---|---|---|---|---|---|---|---|
| GPRC5A | G protein-coupled receptor class C group 5 member A | 1,84 | 1,00 | 0,83 | 0,71 | 0,44 | 1,70 | 2,19 | 4,47 |
| SLC2A1 | Solute carrier family 2 member 1 | 2,72 | 0,16 | 0,92 | 0,29 | 1,1 | 1,54 | 1,57 | 3,965 |
| CD47 | CD47 molecule | 2,32 | 0,19 | 0,92 | 1,22 | 1,33 | 1,59 | 1,56 | 2,46 |
| DPEP1 | Dipeptidase 1 | 0,36 | 0,30 | 0,83 | 0,42 | 0,28 | 0,59 | 1,67 | 1,92 |
| IFITM1 | Interferon induced transmembrane protein 1 | 1,5 | 0,32 | 0,83 | 0,78 | 1,87 | |||
| CD82 | CD82 molecule | 1,24 | 0,51 | 0,50 | 0,58 | 1,31 | 1,31 | 1,48 | 1,76 |
| SLC27A2 | Solute carrier family 27 member 2 | 0,25 | 0,24 | 0,00 | 0,49 | 0,45 | 1,49 | 2,41 | 1,50 |
| DSC2 | Desmocollin 2 | 1,61 | 0,23 | 0,00 | 1,31 | 0,97 | 1,65 | 2,15 | 1,46 |
| RRP12 | Ribosomal R processing 12 homolog | 0,83 | 0,41 | 0,00 | 1,30 | 1,52 | 1,52 | 1,46 | |
| IFITM3 | Interferon induced transmembrane protein 3 | 1,00 | 0,29 | 0,00 | 1,14 | 1,33 | 1,26 | 1,45 |
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