Chun-Liang Chen, Ph.D.

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