Chun-Liang Chen, Ph.D.
Associate Professor - Research
I am currently utilizing single-cell omics approaches to study heterogeneity in normal stem/progenitor, cancer-initiating cells (CIC), circulating tumor cells (CTC) and organoids to identify biomarkers for prostate or breast cancer detection, diagnosis and therapy. Currently, I serve as the Deputy Director of CPRIT-supported BioAnalytics and Single-Cell Core (BASiC) at UTHSCSA. I have been collaborating in several NIH- and V foundation-funded grants in breast cancer research. In collaboration with Drs. Tim Huang, we have developed a clinical platform to collect blood samples and primary tumors from triple negative breast cancer patients for single-cell omics and oncogenic metabolism research. I have developed ex vivo expansion and 3-dimentional (3D) organoid culture for CTC and tumor cell study. Development of cancer starts with rare single initiating and stem cells. Single stem/progenitor, CICs, and CTCs are isolated using cell markers, size-based ScreenCell filters, micromanipulators, DEPArray and C1 system. Isolated single cells are subject to high throughput omics analysis including single-cell RNA-seq, ChIP-seq and ATAC-seq using Illumina HiSeq and CyTOF for profiling of oncogenic transcriptomes as well as proteomic and global epigenetic analysis. This single cell approach will reveal driver tumorigenic mutations, transcriptional fluctuations, proteomic and epigenetic modifications during the development of castration resistance and metastasis. It also facilitates and broadens translational studies on clinical samples, leading to new and effective therapeutic strategies for patient treatment.
- 1998 - PhD - Entomology - University of Illinois at Champaign-Urbana
- 2004 - Postdoctoral Fellow - Gene Therapy - The Research Institute at Nationwide Children’s Hospital
- 2000 - Postdoctoral Fellow - Molecular Genetics - The Ohio State University
- 8/2018 - Associate Professor/Research - UTHSCSA
- 11/2011 - Assistant Professor/Research - UTHSCSA
- 6/2014 - Deputy Director of Bioanalytics and Single-Cell Core (BASiC) - UTHSCSA
- 2/2020 - The recruitment Chair of Personalized Molecular Medicine Program - UTHSCSA
Research & Grants
1. Single-cell omics to study the molecular and cellular mechanisms underlying cancer stem and initiation cells and circulating tumor cells
2. Biomarkers for early detection of advanced and metastatic prostate and breast cancers
3. EMT-related biomarkers and drugs targeting circulating tumor cells and metastasis
1U54CA217297-02 Huang (PI) 04/01/2017-03/31/2022
Systems Analysis of Epigenomic Architecture in Cancer Progression
Despite anti-hormone therapies in patients, the cognate receptors ERα and AR can remain functional to support oncogenic signaling for advanced progression of breast and prostate cancers. Intensive studies have uncovered cellular and biochemical changes underlying the development of hormone resistance. However, epigenetic mechanisms for establishing and maintaining a hormone-resistant phenotype remain to be explored. This process has multifaceted components, involving trans- and cis-acting elements, nucleosome reorganization, and chromatin interactions. To understand this complex mechanism, the U54 Center for Cancer Systems Biology has assembled a team of 21 experimental and computational investigators, and oncologists who plan to study a three-tiered epigenetic framework for gene regulation.
RP150600 -04 Huang (PI) 06/01/2015-05/30/2020
Bioanalysis and Single Cell Core (BASiC)
The goals are to advance research, diagnosis, and treatment options for cancers affecting the Texas population generally, and South Texas specifically, at the level of single cancer cells.
Role: Co-Investigator and Deputy Director
T2017-010 Xu (PI) 11/01/2017-10/30/2020
The V-Foundation Translational Award
A novel therapeutic approach for endocrine resistant breast cancer by inhibiting a targeted epigenetic program. The goal of this project is to determine the epigenomic regulation by activated EZH1 and the targeting therapy in endocrine resistant breast cancer.
PC170821 Huang (PI) 09/01/2018 -08/31/2021
Early Detection of Castration-Resistant Prostate Cancer by Assessing Interactions Between Circulating Tumor Cells and Accompanying Immune Cells
The goal is to develop a procedure to early identify patients with a risk score based on nanomechanical/ immuno profiling of blood-isolated cells. For its future clinical use, collection and analysis of cells’ nanomechanical parameters, vetted for essentiality in this study, will be condensed into a bedside device.
Completed Research Support
5 R01 ES017594-03 Huang (PI) 09/01/2009-06/30/2014
Epigenomics of Bisphenol A Exposure and Disease Risk
The major goal of this project is to determine epigenetic changes of normal epithelial cells in response to low-dose bisphenol A exposure. The study may conclusively determine whether low-dose bisphenol A may act as an estrogenic plasticizer with a harmful effect to human health.
5 R01 CA069065-14 Huang (PI) 08/1/2007-05/31/2012
CpG Island Methylator Phenotypes in Breast Cancer
In this project, we determined whether concurrent hypermethylation occurs during breast cancer development.
5 U54 CA113001-09 Huang (PI) 05/01/2010 - 02/28/2015
NIH / NCI
Interrogating Epigenetic Changes in Cancer Genomes
The overall goal of this project is to use mathematical/statistical tools to define complex epigenetic changes in cancer.
1. The recruitment Chair of Personalized Molecular Medicine Program, The Graduate School of Biomedical Medicine, UTHSA. 01/2020-present.
2. Director of MMED 6016
3. Co-director of MMED 6018
1. Graduate Faculty of Personalized Molecular Medicine Program, The Graduate School of Biomedical Medicine, UTHSA. 08/2019-present.
1. Deputy Director of Cancer Prevention Research Institute of Texas’s (CPRIT’s) Bioanalytics and Single-Cell Core (BASiC), UTHSCSA, San Antonio, TX. 05/2015-present.