Chonghui Cheng, M.D., Ph.D.

Professor

Email

chonghui.cheng@bcm.edu

Positions

Professor: Lester and Sue Smith Breast Center
Baylor College of Medicine
Houston, TX, US

Professor: Molecular and Human Genetics
Baylor College of Medicine

Professor: Department of Molecular and Cellular Biology
Baylor College of Medicine
Houston, Texas

Member: Dan L Duncan Comprehensive Cancer Center
Baylor College of Medicine
Houston, Texas, United States

Education

MD from Peking University Health Science Center: Beijing, China

PhD from Sloan-Kettering Institute/Cornell University Weill Graduate School of Medical Sciences: New York, New York, United States

Postdoctoral Fellowship at Massachusetts Institute of Technology: Cambridge, Massachusetts, United States

Honors & Awards

CPRIT Scholar in Cancer Research: Cancer Prevention Research Institute of Texas (CPRIT) (06/2016 - 05/2021)

American Cancer Society Research Scholar: American Cancer Society (01/2009 - 01/2014)

Lynn Sage Scholar: Lynn Sage Foundation (01/2011 - 01/2013)

Career Development Award: American Association for Cancer Research (01/2008 - 01/2010)

Stuart Scott Memorial Cancer Research Scholar: V Foundation (07/2026 - 07/2030)

Career Development Award: The Schweppe Foundation (01/2008 - 01/2010)

Postdoctoral Fellowship: Damon Runyon Cancer Research Foundation (01/2001 - 12/2003)

Frank Lappin Horsfall, Jr. Fellowship: Sloan-Kettering Institute (07/1998 - 06/1999)

Professional Interests

RNA Binding Proteins
RNA Splicing
Breast Cancer Metastasis
Clinical Applications
Multi-Omics

Professional Statement

The Cheng Lab seeks to transform discoveries in RNA biology into innovative strategies to understand, prevent, and treat metastatic breast cancer. Working at the interface of RNA biology, cancer biology, and immunology, we investigate the molecular mechanisms by which RNA processing and surveillance govern breast cancer metastasis, tumor-immune interactions, and therapeutic outcomes.
Our research established alternative RNA splicing as a fundamental regulator of epithelial-mesenchymal transition (EMT), a developmental program that is frequently reactivated during tumor metastasis and recurrence. We have also uncovered a previously unrecognized role for RNA-binding proteins in maintaining transcriptome integrity. We found that these proteins suppress aberrant RNA processing, including cryptic splicing events that can generate immunostimulatory double-stranded RNAs and potentially tumor-specific neoantigens. We are investigating how disruption of these RNA quality-control mechanisms reshapes immune signaling and the tumor microenvironment, revealing new opportunities for cancer immunotherapy.
To address these questions, we integrate molecular biology, functional genomics, computational biology, genetic models, and patient-derived samples to define RNA regulatory networks that drive cancer progression. We work closely with physician-scientists to translate our discoveries into biomarkers and RNA-based therapeutic strategies for metastatic breast cancer while developing new genomic and molecular approaches to study RNA regulation in tumors and patient samples. Ultimately, we aim to harness discoveries in RNA biology to develop innovative therapeutic strategies that improve outcomes for patients with metastatic breast cancer.

Websites

Lab Website

Selected Publications

Hu X, Harvey SE, Zheng R, Lyu J, Grzeskowiak CL, Powell E, Piwnica-Worms H, Scott KL, Cheng C. " The RNA-binding protein AKAP8 suppresses tumor metastasis by antagonizing EMT-associated alternative splicing " Nat Commun.. 2020 ; 11: 486
Pubmed PMID: 31980632.
Huang H*, Zhang J*, Harvey SE*, Hu X, Cheng C. " RNA G-quadruplex secondary structure promotes alternative splicing via the RNA binding protein hnRNPF " Genes Dev.. 2017 ; 31 : 2296-2309.
Pubmed PMID: 29269483.
Xu Y, Gao XG, Lee JH, Huang H, Tan H, Ahn J, Reinke L, Peter ME, Feng Y, Gius D, Siziopikou KP, Peng J, Xiao X, Cheng C. " Cell type-restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing " Genes Dev. 2014 ; 28 : 1191-1203.
Pubmed PMID: 24840202.
Brown RL, Reinke LM, Damerow MS, Perez D, Chodosh LA, Yang J, Cheng C. " CD44 splice isoform switching in human and mouse epithelium is essential for epithelial-mesenchymal transition and breast cancer progression " J Clin Invest. 2011 ; 121 : 1064-1074.
Pubmed PMID: 21393860.
Zheng R, Dunlap M, Bobkov GOM, Gonzalez-Figueroa C, Patel KJ, Lyu J, Harvey SE, Chan TW, Quinones-Valdez G, Choudhury M, Le Roux CA, Bartels MD, Vuong A, Flynn RA, Chang HY, Van Nostrand EL, Xiao X*, Cheng C*. " hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing " Mol Cell. 2024 ; 84 : 2087-2103.
Pubmed PMID: 38815579.
Bobkov GOM*, Patel KJ*, Lege BM, Zheng R, Shaulsky G, Ellis MJ, Cheng C. " ECM mediates circulating tumor cell clustering in triple-negative breast cancer metastasis " Nat Commun.. 2026 ;
Pubmed PMID: 41651843.

Funding

Regulation and consequences of cryptic splicing #R35 GM131876: (04/01/2024 - 03/31/2029); NIH/NIGMS

Mechanisms of tumor cell clustering in breast cancer metastasis #R01CA276432: (07/28/2023 - 06/30/2028); Grant funding from NIH/NCI

Targeting Cryptic Splicing-Derived Neoantigens in hnRNPM-Dysregulated Triple-Negative Breast Cancer #BC241088: (09/01/2025 - 08/31/2028); Grant funding from DoD

Translational Award #T2025-013: (07/15/2025 - 07/14/2029); V Foundation

Enhancing tumor immunogenicity of TNBC through cryptic splicing-derived neopeptide #Individual Investigator Research Awards: (08/31/2026 - 08/30/2029); CPRIT