Literature DB >> 31031003

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities.

Suhas Vasaikar1, Chen Huang1, Xiaojing Wang1, Vladislav A Petyuk2, Sara R Savage3, Bo Wen1, Yongchao Dou1, Yun Zhang4, Zhiao Shi1, Osama A Arshad2, Marina A Gritsenko2, Lisa J Zimmerman5, Jason E McDermott2, Therese R Clauss2, Ronald J Moore2, Rui Zhao2, Matthew E Monroe2, Yi-Ting Wang2, Matthew C Chambers5, Robbert J C Slebos5, Ken S Lau6, Qianxing Mo7, Li Ding8, Matthew Ellis9, Mathangi Thiagarajan10, Christopher R Kinsinger11, Henry Rodriguez11, Richard D Smith2, Karin D Rodland12, Daniel C Liebler13, Tao Liu14, Bing Zhang15.   

Abstract

We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.
Copyright © 2019 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  RB1; SOX9; biomarkers; colon cancer; drug targets; glycolysis; immune evasion; proteogenomics; proteomics; tumor antigen

Mesh：

Substances：

Year:  2019        PMID： 31031003      PMCID： PMC6768830          DOI： 10.1016/j.cell.2019.03.030

Source DB:  PubMed          Journal:  Cell        ISSN： 0092-8674            Impact factor:   41.582


  77 in total

1.  DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets.

Authors:  Vladislav A Petyuk; Anoop M Mayampurath; Matthew E Monroe; Ashoka D Polpitiya; Samuel O Purvine; Gordon A Anderson; David G Camp; Richard D Smith
Journal:  Mol Cell Proteomics       Date:  2009-12-17       Impact factor: 5.911

Review 2.  Primary, Adaptive, and Acquired Resistance to Cancer Immunotherapy.

Authors:  Padmanee Sharma; Siwen Hu-Lieskovan; Jennifer A Wargo; Antoni Ribas
Journal:  Cell       Date:  2017-02-09       Impact factor: 41.582

3.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

4.  Identification of human leukocyte antigen-A24-restricted epitope peptides derived from gene products upregulated in lung and esophageal cancers as novel targets for immunotherapy.

Authors:  Takako Suda; Takuya Tsunoda; Yataro Daigo; Yusuke Nakamura; Hideaki Tahara
Journal:  Cancer Sci       Date:  2007-11       Impact factor: 6.716

5.  Global patterns and trends in colorectal cancer incidence and mortality.

Authors:  Melina Arnold; Mónica S Sierra; Mathieu Laversanne; Isabelle Soerjomataram; Ahmedin Jemal; Freddie Bray
Journal:  Gut       Date:  2016-01-27       Impact factor: 23.059

6.  customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search.

Authors:  Xiaojing Wang; Bing Zhang
Journal:  Bioinformatics       Date:  2013-09-20       Impact factor: 6.937

7.  HTSeq--a Python framework to work with high-throughput sequencing data.

Authors:  Simon Anders; Paul Theodor Pyl; Wolfgang Huber
Journal:  Bioinformatics       Date:  2014-09-25       Impact factor: 6.937

8.  Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction.

Authors:  Jing Wang; Zihao Ma; Steven A Carr; Philipp Mertins; Hui Zhang; Zhen Zhang; Daniel W Chan; Matthew J C Ellis; R Reid Townsend; Richard D Smith; Jason E McDermott; Xian Chen; Amanda G Paulovich; Emily S Boja; Mehdi Mesri; Christopher R Kinsinger; Henry Rodriguez; Karin D Rodland; Daniel C Liebler; Bing Zhang
Journal:  Mol Cell Proteomics       Date:  2016-11-11       Impact factor: 5.911

9.  Oncogenicity of the developmental transcription factor Sox9.

Authors:  Ander Matheu; Manuel Collado; Clare Wise; Lorea Manterola; Lina Cekaite; Angela J Tye; Marta Canamero; Luis Bujanda; Andreas Schedl; Kathryn S E Cheah; Rolf I Skotheim; Ragnhild A Lothe; Adolfo López de Munain; James Briscoe; Manuel Serrano; Robin Lovell-Badge
Journal:  Cancer Res       Date:  2012-01-13       Impact factor: 12.701

10.  The consensus molecular subtypes of colorectal cancer.

Authors:  Justin Guinney; Rodrigo Dienstmann; Xin Wang; Aurélien de Reyniès; Andreas Schlicker; Charlotte Soneson; Laetitia Marisa; Paul Roepman; Gift Nyamundanda; Paolo Angelino; Brian M Bot; Jeffrey S Morris; Iris M Simon; Sarah Gerster; Evelyn Fessler; Felipe De Sousa E Melo; Edoardo Missiaglia; Hena Ramay; David Barras; Krisztian Homicsko; Dipen Maru; Ganiraju C Manyam; Bradley Broom; Valerie Boige; Beatriz Perez-Villamil; Ted Laderas; Ramon Salazar; Joe W Gray; Douglas Hanahan; Josep Tabernero; Rene Bernards; Stephen H Friend; Pierre Laurent-Puig; Jan Paul Medema; Anguraj Sadanandam; Lodewyk Wessels; Mauro Delorenzi; Scott Kopetz; Louis Vermeulen; Sabine Tejpar
Journal:  Nat Med       Date:  2015-10-12       Impact factor: 53.440
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  164 in total

1.  An Integrative Analysis of Tumor Proteomic and Phosphoproteomic Profiles to Examine the Relationships Between Kinase Activity and Phosphorylation.

Authors:  Osama A Arshad; Vincent Danna; Vladislav A Petyuk; Paul D Piehowski; Tao Liu; Karin D Rodland; Jason E McDermott
Journal:  Mol Cell Proteomics       Date:  2019-06-21       Impact factor: 5.911

2.  An Integrated Workflow for Global, Glyco-, and Phospho-proteomic Analysis of Tumor Tissues.

Authors:  Yangying Zhou; Tung-Shing Mamie Lih; Ganglong Yang; Shao-Yung Chen; Lijun Chen; Daniel W Chan; Hui Zhang; Qing Kay Li
Journal:  Anal Chem       Date:  2020-01-03       Impact factor: 6.986

3.  α-Linolenic and γ-linolenic acids exercise differential antitumor effects on HT-29 human colorectal cancer cells.

Authors:  María José González-Fernández; Ignacio Ortea; José Luis Guil-Guerrero
Journal:  Toxicol Res (Camb)       Date:  2020-07-27       Impact factor: 3.524

4.  Proteogenomic Characterization of Endometrial Carcinoma.

Authors:  Yongchao Dou; Emily A Kawaler; Daniel Cui Zhou; Marina A Gritsenko; Chen Huang; Lili Blumenberg; Alla Karpova; Vladislav A Petyuk; Sara R Savage; Shankha Satpathy; Wenke Liu; Yige Wu; Chia-Feng Tsai; Bo Wen; Zhi Li; Song Cao; Jamie Moon; Zhiao Shi; MacIntosh Cornwell; Matthew A Wyczalkowski; Rosalie K Chu; Suhas Vasaikar; Hua Zhou; Qingsong Gao; Ronald J Moore; Kai Li; Sunantha Sethuraman; Matthew E Monroe; Rui Zhao; David Heiman; Karsten Krug; Karl Clauser; Ramani Kothadia; Yosef Maruvka; Alexander R Pico; Amanda E Oliphant; Emily L Hoskins; Samuel L Pugh; Sean J I Beecroft; David W Adams; Jonathan C Jarman; Andy Kong; Hui-Yin Chang; Boris Reva; Yuxing Liao; Dmitry Rykunov; Antonio Colaprico; Xi Steven Chen; Andrzej Czekański; Marcin Jędryka; Rafał Matkowski; Maciej Wiznerowicz; Tara Hiltke; Emily Boja; Christopher R Kinsinger; Mehdi Mesri; Ana I Robles; Henry Rodriguez; David Mutch; Katherine Fuh; Matthew J Ellis; Deborah DeLair; Mathangi Thiagarajan; D R Mani; Gad Getz; Michael Noble; Alexey I Nesvizhskii; Pei Wang; Matthew L Anderson; Douglas A Levine; Richard D Smith; Samuel H Payne; Kelly V Ruggles; Karin D Rodland; Li Ding; Bing Zhang; Tao Liu; David Fenyö
Journal:  Cell       Date:  2020-02-13       Impact factor: 41.582

Review 5.  Serrated Colorectal Cancer: The Road Less Travelled?

Authors:  Yuki Nakanishi; Maria T Diaz-Meco; Jorge Moscat
Journal:  Trends Cancer       Date:  2019-10-28

6.  Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project.

Authors:  Gilbert S Omenn; Lydie Lane; Christopher M Overall; Ileana M Cristea; Fernando J Corrales; Cecilia Lindskog; Young-Ki Paik; Jennifer E Van Eyk; Siqi Liu; Stephen R Pennington; Michael P Snyder; Mark S Baker; Nuno Bandeira; Ruedi Aebersold; Robert L Moritz; Eric W Deutsch
Journal:  J Proteome Res       Date:  2020-10-19       Impact factor: 4.466

7.  Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.

Authors:  Karsten Krug; Eric J Jaehnig; Shankha Satpathy; Lili Blumenberg; Alla Karpova; Meenakshi Anurag; George Miles; Philipp Mertins; Yifat Geffen; Lauren C Tang; David I Heiman; Song Cao; Yosef E Maruvka; Jonathan T Lei; Chen Huang; Ramani B Kothadia; Antonio Colaprico; Chet Birger; Jarey Wang; Yongchao Dou; Bo Wen; Zhiao Shi; Yuxing Liao; Maciej Wiznerowicz; Matthew A Wyczalkowski; Xi Steven Chen; Jacob J Kennedy; Amanda G Paulovich; Mathangi Thiagarajan; Christopher R Kinsinger; Tara Hiltke; Emily S Boja; Mehdi Mesri; Ana I Robles; Henry Rodriguez; Thomas F Westbrook; Li Ding; Gad Getz; Karl R Clauser; David Fenyö; Kelly V Ruggles; Bing Zhang; D R Mani; Steven A Carr; Matthew J Ellis; Michael A Gillette
Journal:  Cell       Date:  2020-11-18       Impact factor: 41.582

8.  Targeted Inhibition of the E3 Ligase SCFSkp2/Cks1 Has Antitumor Activity in RB1-Deficient Human and Mouse Small-Cell Lung Cancer.

Authors:  Hongling Zhao; Niloy J Iqbal; Vineeth Sukrithan; Cari Nicholas; Yingjiao Xue; Cindy Yu; Joseph Locker; Juntao Zou; Edward L Schwartz; Liang Zhu
Journal:  Cancer Res       Date:  2020-04-07       Impact factor: 12.701

9.  Quantitative Proteomics of the Cancer Cell Line Encyclopedia.

Authors:  David P Nusinow; John Szpyt; Mahmoud Ghandi; Christopher M Rose; E Robert McDonald; Marian Kalocsay; Judit Jané-Valbuena; Ellen Gelfand; Devin K Schweppe; Mark Jedrychowski; Javad Golji; Dale A Porter; Tomas Rejtar; Y Karen Wang; Gregory V Kryukov; Frank Stegmeier; Brian K Erickson; Levi A Garraway; William R Sellers; Steven P Gygi
Journal:  Cell       Date:  2020-01-23       Impact factor: 41.582

Review 10.  Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features.

Authors:  Mirazul Islam; Bob Chen; Jeffrey M Spraggins; Ryan T Kelly; Ken S Lau
Journal:  Gastroenterology       Date:  2020-05-14       Impact factor: 22.682
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