Integrative proteogenomic characterization of early esophageal cancer
Open accessPublished version of a preprint
Abstract
Esophageal squamous cell carcinoma (ESCC) is malignant while the carcinogenesis is still unclear. Here, we perform a comprehensive multi-omics analysis of 786 trace-tumor-samples from 154 ESCC patients, covering 9 histopathological stages and 3 phases. Proteogenomics elucidates cancer-driving waves in ESCC progression, and reveals the molecular characterization of alcohol drinking habit associated signatures. We discover chromosome 3q gain functions in the transmit from nontumor to intraepithelial neoplasia phases, and find TP53 mutation enhances DNA replication in intraepithelial neoplasia phase. The mutations of AKAP9 and MCAF1 upregulate glycolysis and Wnt signaling, respectively, in advanced-stage ESCC phase. Six major tracks related to different clinical features during ESCC progression are identified, which is validated by an independent cohort with another 256 samples. Hyperphosphorylated phosphoglycerate kinase 1 (PGK1, S203) is considered as a drug target in ESCC progression. This study provides insight into the understanding of ESCC molecular mechanism and the development of therapeutic targets.
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Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works
Global quantification of mammalian gene expression control
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works
Self-citationxCell: digitally portraying the tissue cellular heterogeneity landscape
Aran, D., Hu, Z., & Butte, A. J. (2017) · Genome Biology · doi:10.1186/s13059-017-1349-1 · Cited by 4,397 · see citing works
Oncogenic Signaling Pathways in The Cancer Genome Atlas
Sanchez-Vega, F., Mina, M., Armenia, J., Chatila, W. K., Luna, A., La, K. C., Dimitriadoy, S., Liu, D. L., Kantheti, H. S., Saghafinia, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.035 · Cited by 3,201 · see citing works
Self-citationPembrolizumab in Microsatellite-Instability-High Advanced Colorectal Cancer
André, T., Shiu, K.-K., Kim, T. W., Jensen, B. V., Jensen, L. H., Punt, C., Smith, D., Garcia-Carbonero, R., Benavides, M., Gibbs, P., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2017699 · Cited by 3,099 · see citing works
Hoadley, K. A., Yau, C., Hinoue, T., Wolf, D. M., Lazar, A. J., Drill, E., Shen, R., Taylor, A. M., Cherniack, A. D., Thorsson, V., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.022 · Cited by 2,546 · see citing works
Self-citationComprehensive Characterization of Cancer Driver Genes and Mutations
Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.060 · Cited by 2,256 · see citing works
Self-citationProteogenomic and metabolomic characterization of human glioblastoma
Wang, L.-B., Karpova, A., Gritsenko, M. A., Kyle, J. E., Cao, S., Li, Y., Rykunov, D., Colaprico, A., Rothstein, J. H., Hong, R., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.01.006 · Cited by 661 · see citing works
Self-citationCommon markers of proliferation
Whitfield, M. L., George, L. K., Grant, G. D., & Perou, C. M. (2006) · Nature Reviews Cancer · doi:10.1038/nrc1802 · Cited by 650 · see citing works
Comprehensive Characterization of Cancer Driver Genes and Mutations
Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell · doi:10.1016/j.cell.2018.07.034 · Cited by 552 · see citing works
Self-citationIntegrated Omics of Metastatic Colorectal Cancer
Li, C., Sun, Y.-D., Yu, G.-Y., Cui, J.-R., Lou, Z., Zhang, H., Huang, Y., Bai, C.-G., Deng, L.-L., Liu, P., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.08.002 · Cited by 297 · see citing works
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- Authors
- Li, L., Jiang, D., Zhang, Q., Liu, H., Xu, F., Guo, C., Qin, Z., Wang, H., Feng, J., Liu, Y., Chen, W., Zhang, X., Bai, L., Tian, S., Tan, S., Xu, C., Song, Q., Liu, Y., Zhong, Y., Chen, T., Zhou, P., Zhao, J.-Y., Hou, Y., & Ding, C.
- Affiliations
- Fudan University (CN)
- Southwest Medical University (CN)
- Shanghai Jiao Tong University (CN)
- Corresponding author
- Chen, Tianyin
- Zhou, Pinghong
- ORCID
- Venue
- Nature Communications
- Published
- 2023-03-25
- Volume
- 14
- Issue
- 1
- Pages
- 1666-1666
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10039899
- OpenAlex
- W4360949193
- Cited by
- 67
- References
- 11
- Citations by year
- 2026: 13 · 2025: 28 · 2024: 19 · 2023: 7
- FWCI
- 17.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Natural Science Foundation of Shanghai (81702372, 18ZR1406800, 2017SHZDZX01)
- National Natural Science Foundation of China (31972933, 973 Program, 2018YFA0507501, 2012CB910300, 2016YFA0502500, 18ZR1406800, 2017YFA0505100, 81702372, 2014CBA02000, 2014DFB30010, 22XD1420100, 2017SHZDZX01, 31700682, 31270822, 31770886)
- Ministry of Science and Technology of the People's Republic of China (2014DFB30010, 2016YFA0502500, 2014CBA02000, 2012CB910300, 973 Program)
- Shanghai Education Development Foundation (19SG02)
- Shanghai Municipal Education Commission (19SG02)
- National High-tech Research and Development Program
- National Key Research and Development Program of China (2016YFA0502500, 2014CBA02000, 2012CB910300)
- Program of Shanghai Academic Research Leader (22XD1420100)
- Topics
- Health Sciences › Medicine › Surgery › Esophageal Cancer Research and Treatment
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Gastric Cancer Management and Outcomes
- Keywords
- esophageal squamous cell carcinoma, early esophageal cancer, tumor progression, intraepithelial neoplasia, proteogenomics, multi-omics, alcohol consumption, chromosome 3q gain, TP53 mutation, DNA replication, AKAP9, glycolysis, Wnt signaling, therapeutic target
- MeSH terms
- Proteogenomics, Esophageal Squamous Cell Carcinoma, Carcinoma, Squamous Cell, Esophageal Neoplasms, Humans, Mutation
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