PEOPLE

Peter Choi, PhD

Assistant Professor of Pathology and Laboratory Medicine
Perelman School of Medicine at the University of Pennsylvania

Contact Information3501 Civic Center Blvd
Colket Translational Research Building, Room 4064
Philadelphia, PA, 19104
Office: 267-425-5490
Fax: 267-425-0025

Email: choip@chop.edu

Research Expertise

Research Interests
Our laboratory is interested in the genetics of cancer and in particular, how genetic alterations affecting processes such as RNA splicing drive cancer and expose potential therapeutic vulnerabilities.

Keywords
Cancer biology; Lung cancer; Genome editing; RNA splicing; Next-generation sequencing; Synthetic lethality

Research Details
Alternative splicing is an essential mode of gene regulation that greatly diversifies the coding potential of the transcriptome. However, this process is often dysregulated in human cancer. Recent large-scale genomic surveys of multiple cancer types have identified somatic alterations in splicing factors and other RNA-binding proteins, demonstrating that global changes in RNA processing can play a significant role in tumorigenesis. Despite our ability to comprehensively detect the landscape of alternatively spliced transcripts through next-generation sequencing, it has remained difficult to predict much of the functional impact of aberrant splicing.
Our group aims to decipher how patterns of alternative splicing control cellular processes, and when perturbed, can lead to pathogenic states such as cancer. We are particularly interested in characterizing RNA-binding proteins known to be mutated in cancer and their functional role in alternative splicing and other steps in RNA processing. We are also interested in understanding how the expression of specific isoforms may regulate fundamental pathways involved in cell division and cell death. To tackle these questions, we make extensive use of genome editing to engineer faithful models of cancer-associated mutations and more rapidly characterize the function of alternatively spliced isoforms. We are also applying genome-wide CRISPR/Cas9 screens to identify genotype-specific dependencies in a systematic and unbiased fashion.

Rotation Projects
Potential rotation projects include (but are not limited to):
-Characterization of cancer-specific alternative splicing
-Role of RNA-binding proteins in tumor suppression

Please contact Peter Choi (choip@email.chop.edu) for further details.

Lab Personnel
Kevin Yang - MD/PhD Graduate Student (GCB Program)
Amanda Lee - PhD Graduate Student (CAMB CB Program)
Amanda Weiss - PhD Graduate Student (CAMB G&E Program)
Josue Medor - PhD Graduate Student (CAMB CB Program)
Anna Tangiyan - Research Technician

Education

B.S. (Biology), Cornell University, 2002
Ph.D. (Immunology), Stanford University, 2012

Specialty Certification

Postgraduate Training

Postdoctoral Scholar, Cancer Program, Broad Institute, 2012-2018
Post-doctoral Scholar, Department of Medicine, Stanford University, 2012-2012
Research Fellow, Department of Medical Oncology, Dana Farber Cancer Institute, 2012-2016

Awards and Honors

Memberships and Professional Organizations

RNA Society, 2022 - Present

Web Links


Selected Publications

A genome-scale CRISPR screen reveals PRMT1 as a critical regulator of androgen receptor signaling in prostate cancer

Tang S, Sethunath V, Metaferia NY, Nogueira MF, Gallant DS, Garner ER, Lairson LA, Penney CM, Li J, Gelbard MK, Alaiwi SA, Seo JH, Hwang JH, Strathdee CA, Baca SC, AbuHammad S, Zhang X, Doench JG, Hahn WC, Takeda DY, Freedman ML, Choi PS*, Viswanathan SR*., Cell Rep 38(): 110417, 2022, PMID:35196489

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RNA-binding proteins of COSMIC importance in cancer

Choi PS, Thomas-Tikhonenko A., J Clin Invest 131(): e151627, 2021, PMID:34523614

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An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer.

Li Ji*, Choi Peter S*, Chaffer Christine L, Labella Katherine, Hwang Justin H, Giacomelli Andrew O, Kim Jong Wook, Ilic Nina, Doench John G, Ly Seav Huong, Dai Chao, Hagel Kimberly, Hong Andrew L, Gjoerup Ole, Goel Shom, Ge Jennifer Y, Root David E, Zhao Jean J, Brooks Angela N, Weinberg Robert A, Hahn William C, eLife 7(): , 2018, PMID:30059005

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Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers.

Zhang Xiaoyang*, Choi Peter S*, Francis Joshua M, Imielinski Marcin, Watanabe Hideo, Cherniack Andrew D, Meyerson Matthew, Nature Genetics 48(2): 176-82, 2016, PMID:26656844

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Targeted genomic rearrangements using CRISPR/Cas technology.

Choi Peter S, Meyerson Matthew, Nature Communications 5(): 3728, 2014, PMID:24759083

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A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events.

Brooks Angela N, Choi Peter S, de Waal Luc, Sharifnia Tanaz, Imielinski Marcin, Saksena Gordon, Pedamallu Chandra Sekhar, Sivachenko Andrey, Rosenberg Mara, Chmielecki Juliann, Lawrence Michael S, DeLuca David S, Getz Gad, Meyerson Matthew, PloS One 9(1): e87361, 2014, PMID:24498085

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Addiction to multiple oncogenes can be exploited to prevent the emergence of therapeutic resistance.

Choi Peter S, Li Yulin, Felsher Dean W, Proceedings of the National Academy of Sciences of the United States of America 111(32): E3316-24, 2014, PMID:25071175

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MYC through miR-17-92 suppresses specific target genes to maintain survival, autonomous proliferation, and a neoplastic state.

Li Yulin, Choi Peter S, Casey Stephanie C, Dill David L, Felsher Dean W, Cancer Cell 26(2): 262-72, 2014, PMID:25117713

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Lymphomas that recur after MYC suppression continue to exhibit oncogene addiction.

Choi Peter S*, van Riggelen Jan*, Gentles Andrew J, Bachireddy Pavan, Rakhra Kavya, Adam Stacey J, Plevritis Sylvia K, Felsher Dean W, Proceedings of the National Academy of Sciences of the United States of America 108(42): 17432-7, 2011, PMID:21969595

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