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Chen

Contact

210-567-0362

chenc4@uthscsa.edu

Institutes & Centers

Chun-Liang Chen, Ph.D.

Professor

My research is to bridge basic biomedical science and personalized patient care. I am currently utilizing single-cell omics approaches to study heterogeneity in circulating tumor-related cells (e.g., circulating tumor cells (CTCs), hybrid tumor cells and immune cells), for prostate or breast cancer progression, detection, diagnosis, and therapy. Since 2015, I have served as the Deputy Director of CPRIT-funded BioAnalytics and Single-Cell Core (BASiC), a cutting-edge single-cell analysis facility. Development of cancer starts with rare single initiating and stem cells. Lately, we have found circulating hybrid tumor cells in the blood of advanced prostate cancer patients, that evade immune surveillance for metastasis. Integrative single-cell approaches reveal driver mutations, transcriptional signatures and proteomic and epigenetic modifications in tumor recurrence or metastasis. Recently, I joined the School of Nursing and serve as the Director of Biobehavior Laboratory, to direct omics research for underlying mechanisms of stress-, trauma-, aging-, metabolism-, addiction- and cancer-related diseases. Data showed that patients are highly heterogeneous in the response to medical treatments and interventions. The advanced single-cell omics will shed new light on the development of biomarkers for diseases and intervention response, so achieve the goals of personalized patient care.

  • Professional Background

    Education

    • 2010 - MA - Christian Study - Trinity Evangelical Divinity School, IL
    • 1998 - PhD - Entomology - University of Illinois at Champaign-Urbana
    • 1996 - MS - Entomology - University of Illinois at Urbana-Champaign, IL
    • 1987 - MS - Entomology - National Chung-Hsing University, Taiwan
    • 1985 - BS - Entomology - National Chung-Hsing University, Taiwan

    Training

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

    Highlights

    Licensure and Certifications

    1997, Certificate of Beckman Institute Symposium on Bioinformatics, Structure, and Function, University of Illinois at Urbana-Champaign

    HONORS AND AWARDS

    • 2019, AACR Minority & MSI Fac. Scholar in Cancer Research Awards
    • 2014, MGaP region 4 NCI Early Career Cancer Health Disparity Researcher Scholarship
    • 1996, University of Illinois Sigma Xi Travel Award
    • 1994, University of Illinois Graduate Travel Support Grant

    Appointments

    • 2023-Present - Professor tenured - UT Health San Antonio, School of Nursing
    • 2023-Present - Director of Biobehavior Laboratory - UT Health San Antonio, School of Nursing
    • 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

  • Instruction & Training

    • 2021-2023, INTD 6009 Advanced Molecular Biology , UT Health San Antonio
    • 2018-2022 , MMED 6016 Advanced Molecular Biology and Synthetic Biology , UT Health San Antonio
    • 2019-2023 , MMED 6018 Personalized PMM Journal Club , UT Health San Antonio
    • 2015-2022 , MMED 5015 Modern Methods in Molecular and Cellular Biology, UT Health San Antonio

  • 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

    Currently Funded:

    2023 – 2025    Funder: ONRS            Dollars: $200,00 Title: Single cell analysis for discovery of biomarkers for cancer and patient care Role: PI

    Pending Submissions:

    2024 – 2027    Funder: CPRIT (Investigator Award)  Dollars: $1,050,000 Title: The role of phagocytosis-initiated hybrid tumor cells in castration resistance Role: PI

    2024 – 2027    Funder: DoD (Idea Development Award) Dollars: $1,395,000 Title: Metastasis and castration resistance of macrophage-initiated hybrid tumor cells Role: PI

    2024 – 2027    Funder: CPRIT (Investigator Award) Dollars: $ 999,909 Title: Metastasis and castration resistance of macrophage-initiated hybrid tumor cells Role: Co-I (PI, April Risinger)

     

    Completed Research/Projects:

    2021 –2023     Funder: NCI (R21) Grant# CA264353-01     Dollars: $276,161.00 Title: scDECO: A novel statistical framework to systematically identify differential co-expression gene combinations using single-cell RNA sequencing data Role:  Co-I (PI: Yen-Yi Ho)

    2018 –2021     Funder: DOD (CDMRP) Grant# PC170821  Dollars: $915,000 Title: Early Detection of Castration-Resistant Prostate Cancer by Assessing Interactions Between Circulating Tumor Cells and Accompanying Immune Cells Role:  Co-I (PI: Tim HM Huang)

    2017 –2023     Funder: NCI (U54) Grant# CA217297-01     Dollars: $9,200,000 Title: Systems Analysis of Epigenomic Architecture in Endocrine-Resistant Cancers Role:  Co-I (PI: Tim HM Huang)

    2017 –2023     Funder: The V-Foundation Grant# T2017-010          Dollars: $600,000 Title: A novel therapeutic approach for endocrine resistant breast cancer by inhibiting a targeted epigenetic program Role:  Co-I (PI: Kexin Xu)

    2016 –2018     Funder: Molecular Medicine (Start UP)         Dollars: $200,000 Title: Predictive Biomarkers for Advanced Prostate Cancer Using Single Cell Analysis Role:  PI

    2015 –2020     Funder: CPRIT Grant# RP150600     Dollars: $3,200,000 Title: The Single-Cell Biopsy and Characterization Core (SBCC) at The University of Texas Health Science at San Antonio Role: Co-I (PI: Tim HM Huang)

     

  • Service

    Department

    STUDENT MENTEES/TRAINEES

    2023, Shiva Kazempour Dehkordi, IBMS PhD candidacy examinations

    2020-2023, Hsiang-Ling Chiu, Visiting Scientist

    2020-2021, Ning He, Nursing School SUNRISE Undergraduate Research Awardee summer research, 6 months

    2020-2021, Anthony Lopez, PMM master student. Served in his thesis committee.

    2019 –2020, Nathaniel Alvarez, PMM Master Program Research Practicum, 12 months

    2017-2023, Chih-Wei Chou, Postdoctoral Fellow and then research scientist, 6 years

    2015-2023, Chia-Nung Hung, Visiting Scholar and postdoctoral fellow, Tunghai University, 8 years

    2017-2019, Brandon Lieberman, U54 summer student and research assistant, Department of Biology, Trinity University, San Antonio, TX.

    2015-2023, Xi Tan, Research Associate, UTHSCSA

    2014-2023, Meizhen Chen, Postdoctoral Fellow, Molecular Medicine, UTHSCSA

     

    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

    Service to the Institution:

    2023-present   School of Nursing, UTHSA, Director of Biobehavior Laboratory

    2023-present   Graduate School of Biomedical, Graduate Faculty Sciences, UTHSCSA                  

    2022-2023      Graduate School of Biomedical, The Recruitment Committee Member Sciences, UTHSCSA         

    2020-2023       Personalized Molecular Medicine, The Recruitment Chair Program,  UTHSCSA

    2019-2023       Personalized Molecular Medicine, Graduate Faculty Program, UTHSCSA

    2015-2023       Bioanalytics and Single Cell Core,  Deputy Director UTHSCSA

    Service to the Profession

    Service to the Profession:

    2023     Reviewer, CDMRP’s DoD Translational Team Science Award

    2021     Reviewer, CDMRP’s DoD Translational Team Science Award

    2021     Reviewer, European Natl Science Foundation

    2020     Reviewer, CDMRP’s DoD Idea Development Award

    2020-present    Member, Cancers (Journal)

    2022-2023        Member, The Recruitment Committee, Graduate School of Biomedical Sciences, UTHSA

    2020-2023        Chair, The recruitment Committee of Personalized Molecular Medicine Program, The Graduate School of Biomedical Sciences, UTHSA

    2019-2023        Graduate Faculty, Personalized Molecular Medicine Program, The Graduate School of Biomedical Sciences, UTHSA

    2019                 Reviewer, CDMRP’s DoD Concept Award

    2019                 Reviewer, Europe Research Council Grant

    2015-2023       Deputy Director, Cancer Prevention Research Institute of Texas’s (CPRIT’s) Bioanalytics and Single-Cell Core (BASiC), UTHSCSA

    National

    Professional Affiliations (memberships)

    2013-present     Mays Cancer Center, UTHSCSA

    2004-present     American Association for Cancer Research

    2017-2019         The EMT International Association

    2002-2016         American Society of Gene & Cell Therapy

    1997-2018         Society for Neuroscience

  • Publications

      Peer-reviewed Articles (*indicates data-based)

      1. Chou CW*, Hung CN*, Chiu CHL*, Tan X, Chen M, Saeed M, Liss MA, Wang CM, Lai Z, Alvarez N, Osmulski P, Gaczynska ME, Lin LL, Ortega V, Kirma NB, Xu K, Liu Z, Taverna JA, Velagaleti GVN, Chen CL**, Zhang Z**, and Huang THM**. (2023) Phagocytosis-initiated hybrid tumor cells acquire a c-Myc-mediated quasi-polarization state for immunoevasion and distant dissemination. * co-first authors, ** co-senior authors. Nature Commun, 14 (1), 6569.
      2. Hung CN, Chen M, DeArmond D, Kusi M, Chou CW, Lin LL, Tan X, Wang CM, Chen CL, Mitsuya K, Osmulski P, Gaczynska M, Garcia M, Kirma N, Vadlamudi R, Gibbons D, Bearss D, Warner S, Brenner A, Mahadevan D, Mesa R, Michalek J, Huang THM, and Taverna J. (2023) Targeting concordant AXL-STAT3 signaling disturbs symbiotic microenvironment for lung cancer progression. In press. 42(9): 11306
      3. Mukherjee N, Ji N, Tan X, Chen CL, Rodriguez-Padron M, Lin CL, Alonzo D, Huang THM, and Svatek R. (2022) KLRF1, a novel marker of CD56bright NK cells, predicts improved survival for patients with locally advanced bladder cancer. Cancer Med doi: 10.1002/cam4.5579.
      4. Burleson M, Deng JJ, Qin T, Duong TM, Yan Y, Gu X, Das D, Easley A, Liss MA, Yew PR, Bedolla R, Kumar AP, Huang TH, Chen Y, Chen CL, Huang THM, Sun L, Boyer TG. (2022) GLI3 is stabilized by SPOP mutations and functionally crosstalks with androgen receptor to drive prostate cancer progression. Mol Cancer Res 20(1):6276
      5. Mukherjee N, Ji N, Tan X, Lin CL, Rios E, Chen CL, Huang T, Svatek RS. (2021) Bladder tumor ILC1s undergo Th17-like differentiation in human bladder cancer. Cancer Med 10(20):7101-7110.
      6. Osmulski PA, Cunsolo A, Chen M, Qian Y, Lin, CL, Hung CN, Mahalingam D, Kirma NB, Chen CL, Taverna JA, Liss MA, Thompson IM, Huang TH, Gaczynska ME. (2021) Contacts with macrophages promote an aggressive nanomechanical phenotype of circulating tumor cells in prostate cancer. Cancer Res 81:4110-23.
      7. Lieberman B, Meena K, Hung CN, Chou CW, He N, Ho YY, Taverna JA, Huang THM, Chen CL*. (2021) Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq: J Transl Genet Genom 2021;5:1-21 *Corresponding author
      8. Chou CW, Tan X, Hung CN, Lieberman B, Chen M, Kusi M, Mitsuya K, Lin CL,Morita M, Liu Z, Chen CL* and Huang TH*. (2020) Menin and menin-associated proteins coregulate cancer energy metabolism. Cancers 12:2715. *Co-corresponding authors
      9. Taverna J, Hung CN, DeArmond D, Chen M, Lin CL, Osmulski P, Gaczynska M, Wang CM, Lucio N, Chou CW, Chen CL, Nazarullah A, Lampkin S, Qiu L, Bearss D, Warner S, Whatcott C, Mouritsen L, Wade M, Weitman S, Mesa R, Kirma N, Chao WT, and Huang THM. (2020) Single-cell proteomic profiling of treatment-naïve lung tumors for rational clinical trial design of anti-AXL therapies. Cancer Res 80(7):1551-1563.
      10. Lin Cl, Tan X, Chen M, Kusi M, Hung CN, Cho CW, Hsu YT, Wang CM, Kirma N, Chen CL, Lin CH, Lathrop KI, Elledge R, Kaklamani VG, Mitsuya K and Huang TH. (2020) ERa-related chromothripsis enhances concordant gene transcription on chromosome 17q11.1-q24.1 in luminal breast cancer. BMC Med Genomics 13:69.
      11. Liu YL, Horning AM, Lieberman B, Lin CK, Hung CN, Chou CW, Wang CM, Liss MA, Kim M, Vasisht R, Perillo ER, Blocher K, Horng H, Dunn AK, Huang THM, Yeh HC and Chen CL. (2019) Spatial EGFR dynamics and metastatic phenotypes modulated by upregulated EphB2 and Src pathways in advanced prostate cancer. Cancers 11: 1910.
      12. Thapa D, Huang SB, Muñoz AR, Yang X, Bedolla RG, Hung CN, Chen CL, Huang THM, Liss MA, Reddick RL, Miyamoto H, Kumar AP and Ghosh R. (2019) Attenuation of NADPH:Quinone Oxidoreductase 1 aggravates prostate cancer and tumor cell plasticity by TGFβ signaling. Commun Biol 3, 12.
      13. Lotan Y, Boorjian SA, Zhang J, Bivalacqua TJ, Porten SP, Wheeler T, Lerner SP, Hutchinson R, Francis F, Davicioni E, Svatek RS, Chen CL, Black PC, Gibb EA. (2019) Molecular subtyping of clinically localized urothelial carcinoma reveals lower rates of pathological upstaging at radical cystectomy among luminal tumors. Eur Urol 76(2):200-206.
      14. Polusani SR, Huang YW, Huang G., Chen CW, Wang CM, Lin LL, Osmulski P, Lucio ND, Liu L, Hsu YT, Zhou Y, Lin CL, Aguilera-Barrantes I, Valente PT, Kost ER, Chen CL, Shim EY, Lee SE, Ruan J, Gaczynska ME,  Yan P, Goodfellow PJ, Mutch DG, Jin VX, Nicholson BJ,  Huang THM, and Kirma NB. (2018) Adipokines deregulate cellular communication via epigenetic repression of gap junction loci in obese endometrial cancer. Cancer Res 79(1):196-208.

      15. Horning AM., Wang, Y., Lin, CK., Louie, AD., Jadhav, RR., Hung, CN., Wang, CM., Lin, CL., Kirma, NB., Liss, MA., Kumar, AP., Sun, L., Liu, Z., Chao, WT., Wang, Q., Jin, VX., Chen CL*, Huang TH*. 2017. Single-cell RNA-seq reveals a subpopulation of prostate cancer cells with enhanced cell cycle-related transcription and attenuated androgen response. Cancer Res 78(4): 853-864. *Co-correspondent

      Invited Podium Presentations (i. e. keynotes presentations)

      • 2022    “Phagocytosis-initiated hybrid tumor cells acquire a c-Myc-mediated quasi-polarization state for immunoevasion and distant dissemination”. Departmental Retreat of Molecular Medicine, UTHSA. 
      • 2022    “Multimodal analyses reveal aberrant signaling pathways of advanced prostate Cancer”. Invited distinguished speaker talk. Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, Georgia.
      • 2022     "Targeting concordant AXL-STAT3 signaling disturbs symbiotic microenvironment for lung cancer progression. Departmental Retreat.
      • 2021     “Menin and menin-associated proteins coregulate cancer energy metabolism”. NCI Cancer Systems Biology Consortium Annual Meeting.  
      • 2021     “Aberrant signaling pathways of advanced prostate cancer”. Seminar of the Department of Molecular Medicine, UTHSA.
      • 2021     “Modeling biophysical dynamics of receptor tyrosine kinases in castration resistant prostate cancer”. NCI Cancer Systems Biology Consortium U54 conference.
      • 2018     “Androgen independence and castration resistance in prostate cancer revealed by single-cell RNA-seq”. Invited talk. The Agriculture Research Institute, Wufong, Taiwan.
      • 2018     “Androgen independence and castration resistance in prostate cancer revealed by single-cell RNA-seq”. Invited talk by The Young Investigator Award committee. The Prostate Cancer Foundation.
      • 2017     “Single Cell Analysis”. Invited talk. U54 Summer Outreach and Education Workshop.

      Peer Reviewed Poster Presentations

      • 2019    “Bioanalytics and single-cell core: a UT core facility”. Mays Cancer Center annual research symposium, UTHSA.
      • 2019    “Upregulated EPHB2 and SRC pathways modulate spatial EGFR dynamics and advanced invasive phenotypes and predict poor prognosis in prostate cancer. AACR Annual Meeting, Atlanta, GA.
      • 2019    “Amplification-associated upregulation of genes involved in oxidative phosphorylation for disseminated prostate cancer cells”. AACR Annual Meeting, Atlanta, GA.
      • 2018    “The metabolism-regulating role of MEN1 in breast cancer”. Mays Cancer Center Conference, San Antonio, TX.
      • 2018    “Single-cell RNA-seq reveals a potential dasatinib-resistant subpopulation via upregulating WNT and non-canonical WNT pathways in colorectal cancer cells”. Mays Cancer Center Conference, San Antonio, TX.
      • 2018    “Amplification-associated upregulation of genes involved in oxidative phosphorylation for disseminated prostate tumor cells”. 2018 CSBC & PS-ON annual meeting, Bethesda, MD
      • 2018    “Amplification-associated upregulation of genes involved in oxidative phosphorylation for disseminated prostate tumor cells”. 2018 CSBC & PS-ON JI meeting, Bethesda, MD