Literature DB >> 33798439

The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment.

Henry Rodriguez1, Jean Claude Zenklusen2, Louis M Staudt2, James H Doroshow3, Douglas R Lowy4.   

Abstract

When it comes to precision oncology, proteogenomics may provide better prospects to the clinical characterization of tumors, help make a more accurate diagnosis of cancer, and improve treatment for patients with cancer. This perspective describes the significant contributions of The Cancer Genome Atlas and the Clinical Proteomic Tumor Analysis Consortium to precision oncology and makes the case that proteogenomics needs to be fully integrated into clinical trials and patient care in order for precision oncology to deliver the right cancer treatment to the right patient at the right dose and at the right time. Published by Elsevier Inc.

Entities:  

Keywords:  cancer diagnosis; cancer treatment; clinical trial; collaboration; data sharing; genomics; molecular medicine; open access; precision medicine; precision oncology; proteogenomics; proteomics; targeted therapy

Mesh:

Year:  2021        PMID: 33798439      PMCID: PMC8459793          DOI: 10.1016/j.cell.2021.02.055

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


  73 in total

1.  Initial sequencing and analysis of the human genome.

Authors:  E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

Review 2.  Collaboration to Accelerate Proteogenomics Cancer Care: The Department of Veterans Affairs, Department of Defense, and the National Cancer Institute's Applied Proteogenomics OrganizationaL Learning and Outcomes (APOLLO) Network.

Authors:  L D Fiore; H Rodriguez; C D Shriver
Journal:  Clin Pharmacol Ther       Date:  2017-05       Impact factor: 6.875

3.  Declines in Vaccine-Type Human Papillomavirus Prevalence in Females Across Racial/Ethnic Groups: Data From a National Survey.

Authors:  Nancy M McClung; Rayleen M Lewis; Julia W Gargano; Troy Querec; Elizabeth R Unger; Lauri E Markowitz
Journal:  J Adolesc Health       Date:  2019-09-09       Impact factor: 5.012

Review 4.  Clinical potential of mass spectrometry-based proteogenomics.

Authors:  Bing Zhang; Jeffrey R Whiteaker; Andrew N Hoofnagle; Geoffrey S Baird; Karin D Rodland; Amanda G Paulovich
Journal:  Nat Rev Clin Oncol       Date:  2019-04       Impact factor: 66.675

Review 5.  Genomics and the History of Precision Oncology.

Authors:  Deborah B Doroshow; James H Doroshow
Journal:  Surg Oncol Clin N Am       Date:  2019-10-29       Impact factor: 3.495

6.  Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.

Authors:  Steven A Carr; Susan E Abbatiello; Bradley L Ackermann; Christoph Borchers; Bruno Domon; Eric W Deutsch; Russell P Grant; Andrew N Hoofnagle; Ruth Hüttenhain; John M Koomen; Daniel C Liebler; Tao Liu; Brendan MacLean; D R Mani; Elizabeth Mansfield; Hendrik Neubert; Amanda G Paulovich; Lukas Reiter; Olga Vitek; Ruedi Aebersold; Leigh Anderson; Robert Bethem; Josip Blonder; Emily Boja; Julianne Botelho; Michael Boyne; Ralph A Bradshaw; Alma L Burlingame; Daniel Chan; Hasmik Keshishian; Eric Kuhn; Christopher Kinsinger; Jerry S H Lee; Sang-Won Lee; Robert Moritz; Juan Oses-Prieto; Nader Rifai; James Ritchie; Henry Rodriguez; Pothur R Srinivas; R Reid Townsend; Jennifer Van Eyk; Gordon Whiteley; Arun Wiita; Susan Weintraub
Journal:  Mol Cell Proteomics       Date:  2014-01-17       Impact factor: 5.911

7.  Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins.

Authors:  Jacob J Kennedy; Susan E Abbatiello; Kyunggon Kim; Ping Yan; Jeffrey R Whiteaker; Chenwei Lin; Jun Seok Kim; Yuzheng Zhang; Xianlong Wang; Richard G Ivey; Lei Zhao; Hophil Min; Youngju Lee; Myeong-Hee Yu; Eun Gyeong Yang; Cheolju Lee; Pei Wang; Henry Rodriguez; Youngsoo Kim; Steven A Carr; Amanda G Paulovich
Journal:  Nat Methods       Date:  2013-12-08       Impact factor: 28.547

8.  Selected reaction monitoring for quantitative proteomics: a tutorial.

Authors:  Vinzenz Lange; Paola Picotti; Bruno Domon; Ruedi Aebersold
Journal:  Mol Syst Biol       Date:  2008-10-14       Impact factor: 11.429

9.  Integrated genomic characterization of endometrial carcinoma.

Authors:  Cyriac Kandoth; Nikolaus Schultz; Andrew D Cherniack; Rehan Akbani; Yuexin Liu; Hui Shen; A Gordon Robertson; Itai Pashtan; Ronglai Shen; Christopher C Benz; Christina Yau; Peter W Laird; Li Ding; Wei Zhang; Gordon B Mills; Raju Kucherlapati; Elaine R Mardis; Douglas A Levine
Journal:  Nature       Date:  2013-05-02       Impact factor: 49.962

10.  Proteogenomics connects somatic mutations to signalling in breast cancer.

Authors:  Philipp Mertins; D R Mani; Kelly V Ruggles; Michael A Gillette; Karl R Clauser; Pei Wang; Xianlong Wang; Jana W Qiao; Song Cao; Francesca Petralia; Emily Kawaler; Filip Mundt; Karsten Krug; Zhidong Tu; Jonathan T Lei; Michael L Gatza; Matthew Wilkerson; Charles M Perou; Venkata Yellapantula; Kuan-lin Huang; Chenwei Lin; Michael D McLellan; Ping Yan; Sherri R Davies; R Reid Townsend; Steven J Skates; Jing Wang; Bing Zhang; Christopher R Kinsinger; Mehdi Mesri; Henry Rodriguez; Li Ding; Amanda G Paulovich; David Fenyö; Matthew J Ellis; Steven A Carr
Journal:  Nature       Date:  2016-05-25       Impact factor: 49.962

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  16 in total

Review 1.  Cancer proteogenomics: current impact and future prospects.

Authors:  D R Mani; Karsten Krug; Bing Zhang; Shankha Satpathy; Karl R Clauser; Li Ding; Matthew Ellis; Michael A Gillette; Steven A Carr
Journal:  Nat Rev Cancer       Date:  2022-03-02       Impact factor: 60.716

Review 2.  Nano-omics: nanotechnology-based multidimensional harvesting of the blood-circulating cancerome.

Authors:  Lois Gardner; Kostas Kostarelos; Parag Mallick; Caroline Dive; Marilena Hadjidemetriou
Journal:  Nat Rev Clin Oncol       Date:  2022-06-23       Impact factor: 65.011

3.  Proteogenomic analysis of cancer aneuploidy and normal tissues reveals divergent modes of gene regulation across cellular pathways.

Authors:  Pan Cheng; Xin Zhao; Lizabeth Katsnelson; Elaine M Camacho-Hernandez; Angela Mermerian; Joseph C Mays; Scott M Lippman; Reyna Edith Rosales-Alvarez; Raquel Moya; Jasmine Shwetar; Dominic Grun; David Fenyo; Teresa Davoli
Journal:  Elife       Date:  2022-09-21       Impact factor: 8.713

4.  A Self-Assembling Probe for Imaging the States of Golgi Apparatus in Live Single Cells.

Authors:  Weiyi Tan; Qiuxin Zhang; Pengyu Hong; Bing Xu
Journal:  Bioconjug Chem       Date:  2022-03-21       Impact factor: 6.069

5.  Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens.

Authors:  Jeffrey R Whiteaker; Rachel A Lundeen; Lei Zhao; Regine M Schoenherr; Aura Burian; Dongqing Huang; Ulianna Voytovich; Tao Wang; Jacob J Kennedy; Richard G Ivey; Chenwei Lin; Oscar D Murillo; Travis D Lorentzen; Mathangi Thiagarajan; Simona Colantonio; Tessa W Caceres; Rhonda R Roberts; Joseph G Knotts; Joshua J Reading; Jan A Kaczmarczyk; Christopher W Richardson; Sandra S Garcia-Buntley; William Bocik; Stephen M Hewitt; Karen E Murray; Nhan Do; Mary Brophy; Stephen W Wilz; Hongbo Yu; Samuel Ajjarapu; Emily Boja; Tara Hiltke; Henry Rodriguez; Amanda G Paulovich
Journal:  Front Immunol       Date:  2021-11-11       Impact factor: 8.786

6.  Utility of a Recombinant HSV-1 Vaccine Vector for Personalized Cancer Vaccines.

Authors:  Ifeanyi Kingsley Uche; Brent A Stanfield; Jared S Rudd; Konstantin G Kousoulas; Paul J F Rider
Journal:  Front Mol Biosci       Date:  2022-01-26

7.  Integrated weighted gene co-expression network analysis reveals biomarkers associated with prognosis of high-grade serous ovarian cancer.

Authors:  Bo Wang; Shan Chao; Bo Guo
Journal:  J Clin Lab Anal       Date:  2022-01-08       Impact factor: 2.352

8.  Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals.

Authors:  Leyla A Erozenci; Sander R Piersma; Thang V Pham; Irene V Bijnsdorp; Connie R Jimenez
Journal:  Sci Rep       Date:  2021-08-02       Impact factor: 4.379

Review 9.  Shifting Gears in Precision Oncology-Challenges and Opportunities of Integrative Data Analysis.

Authors:  Ka-Won Noh; Reinhard Buettner; Sebastian Klein
Journal:  Biomolecules       Date:  2021-09-04

10.  A highly multiplexed quantitative phosphosite assay for biology and preclinical studies.

Authors:  Hasmik Keshishian; E Robert McDonald; Filip Mundt; Randy Melanson; Karsten Krug; Dale A Porter; Luke Wallace; Dominique Forestier; Bokang Rabasha; Sara E Marlow; Judit Jane-Valbuena; Ellen Todres; Harrison Specht; Margaret Lea Robinson; Pierre M Jean Beltran; Ozgun Babur; Meagan E Olive; Javad Golji; Eric Kuhn; Michael Burgess; Melanie A MacMullan; Tomas Rejtar; Karen Wang; D R Mani; Shankha Satpathy; Michael A Gillette; William R Sellers; Steven A Carr
Journal:  Mol Syst Biol       Date:  2021-09       Impact factor: 11.429

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