Chun-Liang Chen, Ph.D.

Peer-reviewed Articles (*indicates data-based)

1. Mukherjee N, Ji N, Hassouneh Z, Furman J, Fisher O, Gelfond J, Noel O, Tan X, Chen CL, Woldu SL, Lotan Y, and Svatek RS. (2025). Unveiling the paradoxical tumor-suppressive role of CCL2/CCR2 in bladder cancer: a novel immunotherapeutic strategy. Under review of Nature Immunology.
2. Fu L, Song L, Zhou X, Chen L, Zheng L, Hu D, Zhu S, Hu Y, Gong D, Chen CL, Ye X, Yu S. (2024). Serum metabolomics analysis of malnutrition in patients with gastric cancer: A cross sectional study. BMC Cancer. 24(1): 1195.
3. Shen M, Marqués FG, Muruganantham A, Liu S, Bermudez A, Rice MA, Thompson K, Chen CL, Hung CN, Zhang Z, Huang TH, Liss MA, Pienta KJ, Pitteri S, Stoyanova T. (2024) Identification of a 5-gene signature panel for the prediction of prostate cancer progression. British J Cancer 131:1748-1761.
4. Taverna J*, Chia-Nung Hung CN, Williams M, Williams R, Chen M, Kamali S, Sambandam V, Chiu CHL, Osmulski P, Gaczynska M, DeArmond D, Gaspard C, Mancini M, Lee SE, Jiang JX, Kusi M, Song L, Jin L, Schiavini P, Chen CL*. (2024) Ex vivo drug testing of patient-derived lung organoids to predict treatment responses for personalized medicine. *: corresponding authors. Lung Cancer 190:107533.
5. 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.
6. 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): 113067.
7. 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.
8. 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
9. 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.
10. 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.
11. 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
12. 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
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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

20. 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.

21. Huang C, Osmulski P, Bouamar H, Mahalingam D, Lin CL, Liss MA, Kuma AP, Chen CL, Thompson IM, Sun LZ, Gaczynska ME, Huang THM. (2016). TGF-β Signal Rewiring Sustains Epithelial-Mesenchymal Transition of Circulating Tumor Cells in Prostate Cancer Xenograft Hosts. Oncotarget 7(47):77124-77137.

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

23. Sunkel B, Wu D, Chen, Zhon G; Wang CM; Liu X, Ye Z, Horning MA, Liu J; Mahalingam D, Lopez-Nicora H, Lin CL, Goodfellow, PJ, Clinton S, Jin V; Chen CL; Huang T, Wang Q. (2016) Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence. Nucleic Acids Res 44(9):4105-22.

24. 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.

25. 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):1297-307. Highlighted in Nature Urology Reviews. 11, 486. 2014.

26. 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.

27. Invited Author for a book chapter in “Circulating tumor cells: isolation and analysis” edited by Dr. Z. Hugh Fan, 2014

28. 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. 

29. Chen CL, Mahalingam D, Osmulski P, Jadhav RR, Wang CM, Leach RJ, Chang TC, Weitman SD, Kumar AP, Sun L, Gaczynska ME, Thompson IM, Huang TH. (2013) Single-cell analysis of circulating tumor cells identifies cumulative expression patterns of EMT-related genes in metastatic prostate cancer. Prostate73(8): 813-26. 

30. 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. Clin Cancer Res 19(22):6272-85. 

31. J Lutmer, D Watkins, CL Chen, M Velten, G Besner. (2013) Heparin-binding epidermal growth factor–like growth factor attenuates acute lung injury and multiorgan dysfunction after scald burn. J Surg Res 185(1), 329-337

32. 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 transforminggrowth factor beta receptor II (TGFBR2) expression in Prostate Cancer.  Oncogene 33(31): 4097-106.  

33. 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 8(6): 624-34. 

34. Yang J, Radulescu A, Chen CL, Zhang HY, James IO, 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. 

35. Ruan J, Jahid MJ, Gu F, Lei C, Huang YW, Hsu YT, Mutch DG, Chen CL, Kirma NB, Huang THM. (2012) Network-based classification of recurrent endometrial cancers using high-throughput DNA methylation data. AMC-BCB conference. Orlando, Florida. 

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

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

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

39. Zhang HY, James I, Chen CL, 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: 594-605. 

40. Yu, XY, Radulescu, A. Chen CL, James IO, Besner GE. (2012) Heparin-Binding EGF-Like Growth Factor Protects Pericytes from Injury. J Surg Res 172:165-76.

41. Radulescu, A., Zhang H-Y, Chen C-L, Chen Y, Zhou Y, Olson J, Besner G. (2011) Expression Levels of HB-EGF Affect Intestinal Anastomotic Wound Healing. J Surg Res 171: 540-50.

42. Zhang HY, Radulescu A, Chen CL, Olson JK, Darbyshire AK, 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.

43. James IA, Chen CL, Huang G, Zhang HY, Velten M, Besner GE. (2010) HB-EGF Protects the Lungs from Intestinal Ischemia/Reperfusion Injury. J Surg Res 163(1):86-95.

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

45. Cen L, Hutzen B, Ball S, DeAngelis S, Chen CL, 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.

46. Chen CL, Ling C, Kohout J, Hutzen B, Chan C, Hsieh FC, Loy A, Huang V, Cheng G, and Lin J. (2008) Stat3 activation is associated with bladder cancer cell growth and survival. Mole Cancer 7(1):78.

47. Chen CL, Loy A., Cen L., Hsieh FH, Wu B, Cheng G, Kunisada K, Yamauchi-Takihara K, Hall B, Qualman S 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.

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

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

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

51. Schnnep BC, Jensen RM, Chen CL, Clark KR and Johnson PR. (2005) Characterization of adeno-associated virus genomes isolated from human tissues. J Virol 79(23):14793-80.

52. Wang CM, Chen CL, Robertson HM and Fahrbach S.  (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 3:36.

53. Chen CL. (2002) Two methods to improve permeability of wing discs for neuronal and glial immunostaining. Plant Prot Bull 43: 199-204.

54. 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 rearrangement during morphogenesis.  Dev Biol 181: 1-13.

55. Chen CL. (1998) PhD thesis. Distribution of P elements in Muscomorpha. 

56. Chen CL. (1996) Master thesis. Generation of antibodies to cell adhesion molecules involved in pathfinding and molecular cloning of neuroglian in Manduca sexta.

Invited Podium Presentations (i. e. keynotes presentations)

• 2025 “1+1>2, advanced malignancies of tumor-immune hybrid cells”. Department of Bioscience, China Medical University, Taichung, Taiwan. 

• 2024  “Aberrant gene expression and regulation in advanced prostate cancer”. Department of Medical and Molecular Genetics, Indiana University at Bloomington.

• 2024 “Ready for the uncharted: personalized omics-based patient care”. Department of Nursing, Taichung Veteran General Hospital, Taichung, Taiwan.

• 2023 “Ready for the uncharted: personalized omics-based patient care”. School of Nursing Fall Research Day, UTHSA.

• 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

• 2025 “Chromosome 9p deletions are associated with higher rates of R1 resection across GI cancers” The Society of Surgical Oncology Annual Meeting, Tampa, FL.

• 2025 “Biobehavior Laboratory: A Core to Facilitate Omics-Driven Precision and Personalized Health Care” ONRS Research Day Showcase, UTHSA.

• 2025 “Biobehavior Laboratory: A Core to Facilitate Omics-Driven Precision and Personalized Health Care” SON Research Fiesta, UTHSA.

• 2025 “Biobehavior Laboratory: A Core to Facilitate Omics-Driven Precision and Personalized Health Care” Regeneration Medicine and Stem Cell Conference, UTSA, San Antonio. 

• 2025 “Biobehavior Laboratory: A Core to Facilitate Omics-Driven Precision and Personalized Health Care” Trauma Research for C4 (TRC4) Annual Meeting, Austin, Texas. 

• 2024 “Multiomics reveal regulation of aberrant signaling pathways of castration resistant and metastatic prostate cancer”. School of Nursing Research Fiesta, UTHSA. 

• 2024 “Multiomics reveal regulation of aberrant signaling pathways of castration resistant and metastatic prostate cancer”. American Cancer Research Association Annual Meeting, San Diego, CA. 

• 2024 “Phagocytosis-initiated hybrid tumor cells acquire a c-Myc-mediated quasi-polarization state for immunoevasion and distant dissemination”. Mays Cancer Center Research Symposium, UTHSA

• 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