Submitted:
14 April 2026
Posted:
15 April 2026
You are already at the latest version
Abstract
Background/Objectives: Tumor suppressor genes are often inactivated by genetic and epigenetic mechanisms. However, whether genetic alterations of these genes, including CDKN2A/P16, are coupled with epigenetic changes in cancer development and progression is unknown. Methods: Freshly frozen gastric carcinoma (GC) samples, paired noncancer surgical margin (SM) samples, white blood cell (WBC) samples, and clinicopathological information were collected from 200 patients. The copy number of the CDKN2A/P16 gene in these samples was determined by a P16-Light assay and normalized to that in WBCs. The DNA methylation level of the P16 promoter in GC and SM samples was determined by a 115-bp P16-specific MethyLight assay. Results: Both the P16 copy number and DNA methylation level were significantly lower in GC samples than in SM samples (median, 1.94 vs 2.14, p<0.001 for P16 CN; 0.0004 vs. 0.0013, p=0.002 for P16 methylation) and were associated with GC metastasis. The normalized P16 copy number was significantly lower in GCs without P16 methylation than in those with P16 methylation (p=0.007). Similarly, more P16 SCNdel was detected in GCs without P16 methylation than in those with P16 methylation (38.6% vs. 24.1%, p=0.027). Conclusions: Somatic P16 copy number variations are closely coupled with P16 promoter DNA methylation in the development of GC. SCNdel and promoter DNA methylation complementarily inactivate P16 in GC development and promote GC metastasis.
Keywords:
1. Introduction
2. Methods and Materials
Patients
Preparation of Genomic DNA
Quantification of P16 Methylation Using the MethyLight Assay
Quantification of P16 Copy Number Using the P16-Light Assay
Definitions of CDKN2A/P16 SCNamp and SCNdel
Statistical Analysis
3. Results
3.1. Basic results of P16 SCNV and P16 methylation analyses in GC and paired SM samples from 200 patients
3.2. P16 SCNamp Coupled with P16M, Whereas P16 SCNdel Coupled with P16U in Gastric Tissues
3.3. P16 SCNVs and P16M in GC or SM Samples Complementally Associated with GC Metastasis
4. Discussions
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
| CN | Copy number |
| ddPCR | Droplet digital PCR |
| ESCdys | esophageal squamous cell dysplasia |
| GC | gastric carcinoma |
| OS | overall survival |
| P16M | P16 methylation positive |
| P16U | P16 methylation negative |
| SCNamp | somatic copy number amplification |
| SCNdel | somatic copy number deletion |
| SCNVs | somatic copy number variation |
| SM | surgical margin |
| TSS-CGI | CpG islands around transcription starting site |
| WBC | white blood cell |
References
- Sun, Y.; Deng, D.; You, W.-C.; Bai, H.; Zhang, L.; Zhou, J.; Shen, L.; Ma, J.-L.; Xie, Y.-Q.; Li, J.-Y. Methylation of p16 CpG Islands Associated with Malignant Transformation of Gastric Dysplasia in a Population-Based Study. Clin. Cancer Res. 2004, 10, 5087–5093. [CrossRef]
- Hall, G.L.; Shaw, R.J.; Field, E.A.; Rogers, S.N.; Sutton, D.N.; Woolgar, J.A.; Lowe, D.; Liloglou, T.; Field, J.K.; Risk, J.M. p16 Promoter Methylation Is a Potential Predictor of Malignant Transformation in Oral Epithelial Dysplasia. Cancer Epidemiology Biomarkers Prev. 2008, 17, 2174–2179. [CrossRef]
- Cao, J.; Zhou, J.; Gao, Y.; Gu, L.; Meng, H.; Liu, H.; Deng, D. Methylation of p16 CpG Island Associated with Malignant Progression of Oral Epithelial Dysplasia: A Prospective Cohort Study. Clin. Cancer Res. 2009, 15, 5178–5183. [CrossRef]
- Jin, Z.; Cheng, Y.; Gu, W.; Zheng, Y.; Sato, F.; Mori, Y.; Olaru, A.V.; Paun, B.C.; Yang, J.; Kan, T.; et al. A Multicenter, Double-Blinded Validation Study of Methylation Biomarkers for Progression Prediction in Barrett's Esophagus. Cancer Res. 2009, 69, 4112–4115. [CrossRef]
- Liu, H.; Liu, X.-W.; Dong, G.; Zhou, J.; Liu, Y.; Gao, Y.; Liu, X.-Y.; Gu, L.; Sun, Z.; Deng, D. P16 Methylation as an Early Predictor for Cancer Development From Oral Epithelial Dysplasia: A Double-blind Multicentre Prospective Study. EBioMedicine 2015, 2, 432–437. [CrossRef]
- Zhang, X.; Li, P.; Gan, Y.; Xiang, S.; Gu, L.; Zhou, J.; Zhou, X.; Wu, P.; Zhang, B.; Deng, D. Driving effect of P16 methylation on telomerase reverse transcriptase-mediated immortalization and transformation of normal human fibroblasts. Chin. Med J. 2024, 138, 332–342. [CrossRef]
- Cui, C.; Gan, Y.; Gu, L.; Wilson, J.; Liu, Z.; Zhang, B.; Deng, D. P16-specific DNA methylation by engineered zinc finger methyltransferase inactivates gene transcription and promotes cancer metastasis. Genome Biol. 2015, 16, 1–12. [CrossRef]
- Luo, D.; Zhang, B.; Lv, L.; Xiang, S.; Liu, Y.; Ji, J.; Deng, D. Methylation of CpG islands of p16 associated with progression of primary gastric carcinomas. Mod. Pathol. 2006, 86, 591–598. [CrossRef]
- Fan, Z.; Zhou, J.; Tian, Y.; Qin, Y.; Liu, Z.; Gu, L.; Dawsey, S.M.; Wei, W.; Deng, D. Somatic CDKN2A copy number variations are associated with the prognosis of esophageal squamous cell dysplasia. Chin. Med J. 2024, 137, 980–989. [CrossRef]
- Qiao, J.; Tian, Y.; Cheng, X.; Liu, Z.; Zhou, J.; Gu, L.; Zhang, B.; Zhang, L.; Ji, J.; Xing, R.; et al. CDKN2A Deletion Leading to Hematogenous Metastasis of Human Gastric Carcinoma. Front. Oncol. 2021, 11, 801219. [CrossRef]
- Deng, L.; Zhou, J.; Sun, Y.; Hu, Y.; Qiao, J.; Liu, Z.; Gu, L.; Lin, D.; Zhang, L.; Deng, D. CDKN2A somatic copy number amplification in normal tissues surrounding gastric carcinoma reduces cancer metastasis risk in droplet digital PCR analysis. Gastric Cancer 2024, 27, 986–997. [CrossRef]
- Merlo, A.; Herman, J.G.; Mao, L.; Lee, D.J.; Gabrielson, E.; Burger, P.C.; Baylin, S.B.; Sidransky, D. 5′ CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers. Nat. Med. 1995, 1, 686–692. [CrossRef]
- Mao, L.; Lee, J.S.; Fan, Y.H.; Ro, J.Y.; Batsakis, J.G.; Lippman, S.; Hittelman, W.; Hong, W.K. Frequent microsatellite alterations at chromosomes 9p21 and 3p14 in oral premalignant lesions and their value in cancer risk assessment. Nat. Med. 1996, 2, 682–685. [CrossRef]
- Serrano, M.; Hannon, G.J.; Beach, D. A new regulatory motif in cell-cycle control causing specific inhibition of cyclin D/CDK4. Nature 1993, 366, 704–707. [CrossRef]
- Weng, W.; Zhang, B.; Deng, D. P16INK4A drives RB1 degradation by UTP14A-catalyzed K810 ubiquitination. iScience 2024, 27, 110882. [CrossRef]
- Witkiewicz, A.K.; Venkata, S.A.K.; Knudsen, E.S.; Kumarasamy, V. RB loss sensitizes triple-negative breast cancer to apoptosis induced by cellular stress. Cell Death Discov. 2025, 11, 543. [CrossRef]
- Zamalloa, L.G.; Pruitt, M.M.; Hermance, N.M.; Gali, H.; Flynn, R.L.; Manning, A.L. RB loss sensitizes cells to replication-associated DNA damage after PARP inhibition by trapping. Life Sci. Alliance 2023, 6, e202302067. [CrossRef]
- Gadhikar, M.A.; Zhang, J.; Shen, L.; Rao, X.; Wang, J.; Zhao, M.; Kalu, N.N.; Johnson, F.M.; Byers, L.A.; Heymach, J.; et al. CDKN2A/p16Deletion in Head and Neck Cancer Cells Is Associated with CDK2 Activation, Replication Stress, and Vulnerability to CHK1 Inhibition. Cancer Res. 2018, 78, 781–797. [CrossRef]
- Zhou, J.; Cao, J.; Lu, Z.; Liu, H.; Deng, D. A 115-bp MethyLight assay for detection of p16 (CDKN2A) methylation as a diagnostic biomarker in human tissues. BMC Med Genet. 2011, 12, 67–67. [CrossRef]
- Tian, Y.; Zhou, J.; Qiao, J.; Liu, Z.; Gu, L.; Zhang, B.; Lu, Y.; Xing, R.; Deng, D. Detection of somatic copy number deletion of the CDKN2A gene by quantitative multiplex PCR for clinical practice. Front. Oncol. 2022, 12, 1038380. [CrossRef]
- Esteller, M.; Fraga, M.F.; Guo, M.; Garcia-Foncillas, J.; Hedenfalk, I.; Godwin, A.K.; Trojan, J.; Vaurs-Barrière, C.; Bignon, Y.J.; Ramus, S.; et al. DNA methylation patterns in hereditary human cancers mimic sporadic tumorigenesis. Hum. Mol. Genet. 2001, 10, 3001–3007. [CrossRef]
- Machado, J.C.; Oliveira, C.; Carvalho, R.; Soares, P.; Berx, G.; Caldas, C.; Seruca, R.; Carneiro, F.; Sobrinho-Simöes, M. E-cadherin gene (CDH1) promoter methylation as the second hit in sporadic diffuse gastric carcinoma. Oncogene 2001, 20, 1525–1528. [CrossRef]
- Corso, G.; Magnoni, F.; Molin, M.D.; Marino, E.; Nicosia, L.; Pesapane, F.; Noonan, D.M.; Albini, A. Second-hit CDH1 gene mechanisms in hereditary diffuse gastric and lobular breast cancer syndrome: frequency and impact on tumorigenesis. Hum. Mol. Genet. 2025, 34, 1345–1352. [CrossRef]
- Chen, S.; Sanjana, N.E.; Zheng, K.; Shalem, O.; Lee, K.; Shi, X.; Scott, D.A.; Song, J.; Pan, J.Q.; Weissleder, R.; et al. Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis. Cell 2015, 160, 1246–1260. [CrossRef]




| GC | SM | |||||||||||||
| P16 CNa | P16 CN | Case number for P16 SCNV (%) | ||||||||||||
| n | Mean±SD | p valuec | SCNdel | Diploid | SCNamp | p valued | Mean±SD | p value | SCNdel | Diploid | SCNamp | p value | ||
| Age (yr) | ≤60 | 80 | 1.95 ± 0.41 | 0.164 | 20 (25.0) | 49 (61.3) | 11 (13.7) | 0.249 | 2.08 ± 0.23 | 0.508 | 6 (7.5) | 65 (81.3) | 9 (11.2) | 0.895 |
| >60 | 120 | 1.86 ± 0.48 | 41 (34.2) | 69 (57.5) | 10 (8.3) | 2.10 ± 0.22 | 7 (5.8) | 99 (82.5) | 14 (11.7) | |||||
| Sex | Male | 140 | 1.89 ± 0.48 | 0.924 | 44 (31.4) | 81 (57.9) | 15 (10.7) | 0.880 | 2.10 ± 0.22 | 0.833 | 8 (5.7) | 115 (82.1) | 17 (12.2) | 0.736 |
| Female | 60 | 1.90 ± 0.39 | 17 (28.3) | 37 (61.7) | 6 (10.0) | 2.09 ± 0.22 | 5 (8.3) | 49 (81.7) | 6 (10.0) | |||||
| Neoadjuvant | Yes | 64 | 1.95 ± 0.45 | 0.193 | 17 (26.6) | 37 (57.8) | 10 (15.6) | 0.240 | 2.09 ± 0.27 | 0.857 | 4 (6.3) | 49 (76.6) | 11 (17.1) | 0.224 |
| chemotherapy | No | 136 | 1.86 ± 0.46 | 44 (32.4) | 81 (59.6) | 11 (8.0) | 2.09 ± 0.19 | 9 (6.6) | 115 (84.6) | 12 (8.8) | ||||
| GC location | Noncardiac | 141 | 1.92 ± 0.43 | 0.192 | 41 (29.1) | 84 (59.6) | 16 (11.3) | 0.715 | 2.09 ± 0.23 | 0.635 | 10 (7.1) | 116 (82.3) | 15 (10.6) | 0.752 |
| Cardiac | 59 | 1.83 ± 0.51 | 20 (33.9) | 34 (57.6) | 5 (8.5) | 2.10 ± 0.21 | 3 (5.1) | 48 (81.4) | 8 (13.5) | |||||
| Differentiatione | Well or mod. | 71 | 1.76 ± 0.50 | 0.004 | 32 (45.1) | 32 (45.1) | 7 (9.8) | 0.006 | 2.07 ± 0.27 | 0.456 | 7 (9.9) | 54 (76.1) | 10 (14.0) | 0.186 |
| Poor | 118 | 1.96 ± 0.43 | 27 (22.9) | 77 (65.3) | 14 (11.8) | 2.10 ± 0.18 | 6 (5.1) | 102 (86.4) | 10 (8.5) | |||||
| pTNM stage | I-II | 117 | 1.91 ± 0.45 | 0.558 | 34 (29.1) | 71 (60.7) | 12 (10.2) | 0.842 | 2.12 ± 0.23 | 0.020 | 8 (6.8) | 89 (76.1) | 20 (17.1) | 0.012 |
| III-IV | 83 | 1.87 ± 0.46 | 27 (32.5) | 47 (56.6) | 9 (10.9) | 2.05 ± 0.21 | 5 (6.0) | 75 (90.4) | 3 (3.6) | |||||
| Local invasion | T1-2 | 45 | 1.86 ± 0.46 | 0.573 | 17 (37.8) | 24 (53.3) | 4 (8.9) | 0.480 | 2.10 ± 0.26 | 0.706 | 6 (13.3) | 32 (71.1) | 7 (15.6) | 0.054 |
| T3-4 | 155 | 1.90 ± 0.46 | 44 (28.4) | 94 (60.6) | 17 (11.0) | 2.09 ± 0.21 | 7 (4.5) | 132 (85.2) | 16 (10.3) | |||||
| Lymph | N0 | 94 | 1.91 ± 0.45 | 0.589 | 26 (27.7) | 58 (61.7) | 10(10.6) | 0.708 | 2.14 ± 0.22 | 0.002 | 4 (4.3) | 72 (76.6) | 18 (19.1) | 0.004 |
| metastasis | N1-Xf | 106 | 1.88 ± 0.47 | 35 (33.0) | 60 (56.6) | 11 (10.4) | 2.05 ± 0.21 | 9 (8.5) | 92 (86.8) | 5 (4.7) | ||||
| (total) | 200 | 1.89 ± 0.46 | 61 (30.5)g | 118 (59.0) | 21 (10.5) | 2.09 ± 0.22 | 13 (6.5) | 164 (82.0) | 23 (11.5) | |||||
| Prevalence of p16 methylation | ||||||||
| GC | SM | |||||||
| n | Positive rate (%) | Methylation level (median, 25-75%) a,b | p valuec | Positive rate (%) | Methylation level (median, 25-75%) | p valuec | ||
| Age (yr) | ≤60 | 80 | 52 (65.0) | 0.20 (0.08-0.71) | 0.580 | 69 (86.3) | 0.18 (0.07-0.37) | 0.524 |
| >60 | 120 | 60 (50.0) | 0.20 (0.07-2.19) | 93 (77.5) | 0.19 (0.07-0.39) | |||
| Sex | Male | 140 | 78 (55.7) | 0.14 (0.07-1.48) | 0.437 | 111 (79.3) | 0.17 (0.07-0.33) | 0.164 |
| Female | 60 | 34 (56.7) | 0.34 (0.08-0.98) | 51 (85.0) | 0.23 (0.07-0.62) | |||
| Neoadjuvant | Yes | 64 | 33 (51.6) | 0.12 (0.06-0.52) | 0.293 | 48 (75.0) | 0.14 (0.05-0.27) | 0.011 |
| chemotherapy | No | 136 | 79 (58.1) | 0.32 (0.08-1.47) | 114 (83.8) | 0.21 (0.09-0.60) | ||
| GC location | Noncardiac | 141 | 85 (60.3) | 0.20 (0.08-0.99) | 0.724 | 119 (84.4) | 0.19 (0.07-0.42) | 0.383 |
| Cardiac | 59 | 27 (45.8) | 0.12 (0.07-3.79) | 43 (72.9) | 0.14 (0.06-0.31) | |||
| Differentiation | Well or mod. | 71 | 30 (42.3) | 0.19 (0.08-1.65) | 0.873 | 56 (78.9) | 0.13 (0.06-0.29) | 0.018 |
| Poor | 118 | 75 (63.6) | 0.20 (0.07-1.32) | 99 (83.9) | 0.21 (0.11-0.40) | |||
| pTNM stage | I-II | 117 | 64 (54.7) | 0.13 (0.06-0.51) | 0.037 | 90 (76.9) | 0.21 (0.07-0.37) | 0.950 |
| III-IV | 83 | 48 (57.8) | 0.36 (0.08-2.57) | 72 (86.7) | 0.17 (0.07-0.52) | |||
| Local invasion | T1-2 | 45 | 25 (55.6) | 0.13 (0.06-1.14) | 0.663 | 39 (86.7) | 0.21 (0.07-0.37) | 0.842 |
| T3-4 | 155 | 87 (56.1) | 0.20 (0.08-1.08) | 123 (79.4) | 0.18 (0.07-0.39) | |||
| Lymph | N0 | 94 | 51 (54.3) | 0.13 (0.07-0.52) | 0.097 | 70 (74.5) | 0.23 (0.07-0.37) | 0.627 |
| metastasis | N1-X | 106 | 61 (57.5) | 0.25 (0.07-2.56) | 92 (86.8) | 0.16 (0.07-0.52) | ||
| (total) | 200 | 112 (56.0) d | 0.20 (0.07-1.06) | 162 (81.0) | 0.18 (0.07-0.37) | |||
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2026 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.