Peter Choi, PhD
Assistant Professor of Pathology and Laboratory MedicinePerelman 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
RNA-binding proteins of COSMIC importance in cancer
Choi PS, Thomas-Tikhonenko A., J Clin Invest 131(): e151627, 2021, PMID:34523614
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
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
Targeted genomic rearrangements using CRISPR/Cas technology.
Choi Peter S, Meyerson Matthew, Nature Communications 5(): 3728, 2014, PMID:24759083
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
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
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
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
