Chun-Liang Chen, Ph.D.

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.

• Professional Background

  Education

  • 1998 - PhD - Entomology - University of Illinois at Champaign-Urbana

  Training

  • 2004 - Postdoctoral Fellow - Gene Therapy - The Research Institute at Nationwide Children’s Hospital
  • 2000 - Postdoctoral Fellow - Molecular Genetics - The Ohio State University

  Appointments

  • 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

  Grants

  1U54CA217297-02                 Huang (PI)                              04/01/2017-03/31/2022

  NIH/NCI

  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.

  Role: Co-Investigator

   

  RP150600 -04                                    Huang (PI)                              06/01/2015-05/30/2020

  CPRIT

  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.

  Role: Co-Investigator

   

  PC170821                                                       Huang (PI)                                          09/01/2018 -08/31/2021        

  DOD/CDMRP                                                                        

  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.

  Role: Co-Investigator

   

  Completed Research Support

  5 R01 ES017594-03   Huang (PI)                                          09/01/2009-06/30/2014

  NIH/NIEHS                                                                

  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.

  Role:  Co-Investigator

   

  5 R01 CA069065-14   Huang (PI)                                          08/1/2007-05/31/2012            

  NIH/NCI                                                                     

  CpG Island Methylator Phenotypes in Breast Cancer

  In this project, we determined whether concurrent hypermethylation occurs during breast cancer development. 

  Role: Co-Investigator

   

  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.

  Role:  Co-Investigator

   

• Service

  Department

  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

   

  School

  1. Graduate Faculty of Personalized Molecular Medicine Program, The Graduate School of Biomedical Medicine, UTHSA. 08/2019-present.

  Institutional

  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.

• Publications

  • Publication List