Department of Molecular Medicine

Chun-Liang Chen, PhD Chun-Liang  ChenPh.D.

Associate Professor/Research

Profile and Contact Information | Research



Research Program

I am currently utilizing single-cell omic approaches to study tumor heterogeneity and cancerous stem/progenitor, cancer-initiating cells (CIC) and circulating tumor cells (CTC) to discover biomarkers for cancer detection and therapeutic targets. In collaboration with clinical physicians, I have developed a clinical platform to collect blood samples from prostate cancer and breast cancer patients for ex vivo expansion of stem-like CTCs and single-cell omics research at UT Health San Antonio. The 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 microfilters, micromanipulators, DEPArray and C1 system. Isolated single cells are subject to high throughput omics analysis including single-cell RNA-seq (SMART-seq2) and whole genome sequencing using Illumina HiSeq, Nanopore technology, DNA methylation detection and molecular profiling using qRT-PCR with BioMark HD system. This single cell approach will reveal driver tumorigenic mutations, transcriptional profiles and epigenetic modifications during the early tumorigenesis and advanced metastasis. The research of CTCs will open an important window to understanding the metastatic mechanism of cancer, and will facilitate high-throughput drug susceptibility screenings for precision personalized medicine.


Selected Publications

  1. 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. European Urology. In Press.

  2. 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. 2019. Adipokines deregulate cellular communication via epigenetic repression of gap junction loci in obese endometrial cancer. Cancer Res. 79(1):196-208.

  3. 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. (Co-correspondent) 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.

  4. Ruan J, Jahid MJ, Gu F, Lei C, Huang YW, Hsu YT, Mutch DG, Chen CL, Kirma NB, Huang TH. 2016. A novel algorithm for network-based prediction of cancer recurrence. Genomics. doi:10.1016/j.ygeno.2016.07.005.

  5. Mahalingam D, Osmulski P, Wang CM, Horning AM, Louie AE, Lin CL, Gaczynska ME and Chen CL (Corresponding author). (2016) Chapter 16: Single-cell molecular profiles and biophysical assessment of circulating tumor cells. Circulating Tumor Cells: Isolation and Analysis. John Wiley & Sons, Inc. pp. 329 - 350.

  6. Sunkel B, Wu D, Chen Z, Wang CM, Liu X, Ye Z, Horning A, Liu J, Mahalingam D, Lopez-Nicora H, Lin CL, Goodfellow, PJ, Clinton S, Jin V, Chen CL, Huang TH, Wang Q: (2016) Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence. Nucleic Acids Res. In Press.

  7. Horning AM, Awe JA, Wang CM, Liu J, Lai, Wang VY, Jadhav RR, Louie AD, Lin CL, Kroczak T, Chen Y, Jin VX, Abboud-Werner SL, Leach RJ, Hernandez J, Thompson IM, Saranchuk J, Drachenberg D, Chen CL, Mai S, Huang THM: (2015) DNA methylation screening of primary prostate tumors identifies SRD5A2 and CYP11A1 as candidate markers for assessing risk of biochemical recurrence. Prostate. 75(15):1790-801.

  8. Osmulski P, Mahalingam P, Gaczynska ME, Liu J, Huang S, Horning MA, Wang CM, Thompson IM, Huang THM and Chen CL(senior correspondence author): (2014) Nanomechanical biomarkers of single circulating tumor cells for detection of castration resistant prostate cancer. Prostate, 74 (13), 1297-1307. Highlighted in Nature Urology Reviews. 11, 486. 2014.

  9. Choi DS, Blanco E, Kim YS, Rodriguez AA, Zhao H, Huang THM, Chen CL, Jin G, Landis MD, Burey LA, Wei Q, Granados SM, Dave B, Wong HH, Ferrari M, Wong STC, Chang JC: (2014) Chloroquine eliminates cancer stem cells through deregulation of Jak2 and DNMT1. Stem Cells. 32(9):2309-23.

  10. Chen CL, Yang J, James IOA, Zhang H, Besner GE. 2014. Heparin-binding EGF-like Growth Factor Restores Wnt/beta-catenin Signaling in Intestinal Stem Cells Exposed to Ischemia/Reperfusion Injury. Surgery. 155(6):1069-80.

  11. Hsu YT, Gu F, Huang YW, Liu J, Ruan J, Huang RL, Wang CM, Chen CL, Jadhav R. Lai HC, Mutch DG, Goodfellow PJ, Thompson IM, Kirma NB, Huang THM: (2013) Promoter hypomethylation of EpCAM-regulated bone morphogenetic protein gene family in recurrent endometrial cancer. Clinical Cancer Research, 19(22):6272-85.

  12. Mishra S, Deng JJ, Gowda PS, Rao MK, Lin CL, Chen CL, Huang T, Sun LZ: (2013) Androgen receptor and microRNA-21 axis down-regulates transforming growth factor beta receptor II (TGFBR2) expression in Prostate Cancer. Oncogene. 2013 Sep 16.

  13. Huang RL, Gu F, Kirma NB, Ruan J, Chen CL, Wang HC, Liao YP, Chang CC, Yu MH, Pilrose JM, Thompson IM, Huang HC, Huang TH, Lai HC, Nephew KP: (2013) Comprehensive methylome analysis of ovarian tumors reveals hedgehog signaling pathway regulators as prognostic DNA methylation biomarkers. Epigenetics. 2013 Jun;8(6):624-34.

  14. Chen CL, Mahalingam D, Osmulski P, Jadhav RR, Wang CM, Leach RJ, Chang TC, Weitman SD, Kumar AP, Sun L, Gaczynska ME, Thompson IM, and Huang TH: (2013) Single-cell analysis of circulating tumor cells identifies cumulative expression patterns of EMT-related genes in metastatic prostate cancer. Prostate 73(8): 813-26.

  15. Yang J, Radulescu A, Chen CL, Zhang HY, James IO, and Besner GE: (2013) Heparin-binding epidermal growth factor-like growth factor improves intestinal barrier function and reduces mortality in a murine model of peritonitis. Surgery. 153(1): 52-62.

  16. Yang J, Watkins D, Chen CL, Zhang HY, Zhou Y, Velten M, and Besner GE: (2012) A technique for systemic mesenchymal stem cell transplantation in newborn rat pups. J Invest Surg. 25(6): 405-14.

  17. Yang J, Watkins D, Chen CL, Bhushan B, Zhou Y, and Besner GE: (2012) Heparin-binding epidermal growth factor-like growth factor and mesenchymal stem cells act synergistically to prevent experimental necrotizing enterocolitis. J Am Coll Surg. 215(4): 534-45.

  18. Watkins DJ, Zhou Y, Chen CL, Darbyshire A, and Besner GE: (2012) Heparin-binding epidermal growth factor-like growth factor protects mesenchymal stem cells. J Surg Res. 177(2): 359-64.

  19. Zhang HY, James I, Chen CL, and Besner GE: (2012) Heparin-binding epidermal growth factor-like growth factor (HB-EGF) preserves gut barrier function by blocking neutrophil-endothelial cell adhesion after hemorrhagic shock and resuscitation in mice. Surgery. 151(4): 594-605.

  20. Chen CL, Yu X, James IO, Zhang HY, Yang J, Radulescu A, Zhou Y, and Besner GE: (2012) Heparin-binding EGF-like growth factor protects intestinal stem cells from injury in a rat model of necrotizing enterocolitis. Lab Invest. 92(3): 331-44.

  21. Yu X, Radulescu A, Chen CL, James IO, and Besner GE: (2012) Heparin-binding EGF-like growth factor protects pericytes from injury. J Surg Res. 172(1): 165-76.

  22. Radulescu A, Zhang HY, Chen CL, Chen Y, Zhou Y, Yu X, Otabor I, Olson JK, and Besner GE: (2011) Heparin-binding EGF-like growth factor promotes intestinal anastomotic healing. J Surg Res. 171(2): 540-50.

  23. Zhang HY, Radulescu A, Chen CL, Olson JK, Darbyshire AK, and Besner GE: (2011) Mice overexpressing the gene for heparin-binding epidermal growth factor-like growth factor (HB-EGF) have increased resistance to hemorrhagic shock and resuscitation. Surgery. 149(2): 276-83.

  24. James IA, Chen CL, Huang G, Zhang HY, Velten M, and Besner GE: (2010) HB-EGF protects the lungs after intestinal ischemia / reperfusion injury. J Surg Res. 163(1) 86-95.

  25. Chen CL, Mehta VB, Zhang HY, Wu D, Otabor I, Radulescu A, El-Assal ON, Feng J, Chen Y, and Besner GE: (2010) Intestinal phenotype in mice overexpressing a heparin-binding EGF-like growth factor transgene in enterocytes. Growth Factors. 28(2): 82-97.

  26. Cen L, Hutzen B, Ball S, DeAngelis S, Chen CL, Fuchs JR, Li C, Li PK, and Lin J: (2009) New structural analogues of curcumin exhibit potent growth suppressive activity in human colorectal carcinoma cells. BMC Cancer. 9:99.

  27. Chen CL, Cen L, Kohout J, Hutzen B, Chan C, Hsieh FC, Loy A, Huang V, Cheng G, and Lin J: (2008) Signal transducer and activator of transcription 3 activation is associated with bladder cancer cell growth and survival. Mol Cancer. 7:78.

  28. Chen CL, Loy A, Cen L, Chan C, Hsieh FC, Cheng G, Wu B, Qualman SJ, Kunisada K, Yamauchi-Takihara K, and Lin J: (2007) Signal transducer and activator of transcription 3 is involved in cell growth and survival of human rhabdomyosarcoma and osteosarcoma cells. BMC Cancer. 7: 111.

  29. Chen CL, Hsieh FC, Lieblein JC, Brown J, Chan C, Wallace JA, Cheng G, Hall BM, and Lin J: (2007) Stat3 activation in human endometrial and cervical cancers. Br J Cancer. 96(4): 591-9.

  30. Chen CL, Hsieh FC, and Lin J: (2006) Systemic evaluation of total Stat3 and Stat3 tyrosine phosphorylation in normal human tissues. Exp Mol Pathol. 80(3): 295-305.

  31. Chen CL, Jensen RL, Schnepp BC, Connell MJ, Shell R, Sferra TJ, Bartlett JS, Clark KR, and Johnson PR: (2005) Molecular characterization of adeno-associated viruses infecting children. J Virol. 79(23): 14781-92.

  32. Schnepp BC, Jensen RL, Chen CL, Johnson PR, and Clark KR: (2005) Characterization of adeno-associated virus genomes isolated from human tissues. J Virol. 79(23): 14793-803.

  33. Wang CM, Chen CL, Robertson HM, and Fahrbach SE: (2003) A new member of the GM130 golgin subfamily is expressed in the optic lobe anlagen of the metamorphosing brain of Manduca sexta. J Insect Sci. 3: 35.
  34. Chen C: (2001) Two methods to improve permeability of wing discs for neuronal and glial immunostaining. Plant Prot Bull. 43: 199-204.

  35. Chen CL, Lampe DJ, Robertson HM, and Nardi JB: (1997) Neuroglian is expressed on cells destined to form the prothoracic glands of Manduca embryos as they segregate from surrounding cells and rearrange during morphogenesis. Dev Biol. 181(1): 1-13.