Lab Publications

Faber EB, Krause H, Amin K, Phillip P, Walker P, Hosein P, Sheilds AF, Lenz H, Prakash A, Goel S, Oberley M, Luchini C, Hwang J, Florou V, Garrido-laguna I, Lou E. Genomic profiling of rare undifferentiated sacromatoid subtypes of pancreatic carcinoma for potential response to immunotherapy. Archives  of Pathology and Lab Medicine. (accepted 2024, in press). 

Miller CD, Lozada JR, Zorko NA, Elliott A, Makovec A, Radovich M, Heath E, Agarwal N, Mckay RR, Garje R, Bastos BR, Hoon DSB, Orme JJ, Sartor O, VanderWalde A, Nabhan C, Sledge G, Shenderov E, Dehm SM, Lou E, Miller J, Hwang JH, Antonarakis ES. Pan-Cancer Interrogation of B7-H3 (CD276) as an Actionable Therapeutic Target across Human Malignancies. (accepted 2024, in press).  

Faber E, Baca Y, Xiu J, Walker P, Manji G, Gholami S, Saeed A, Prakash A, Botta G, Sohal D, Lenz H, Shields A, Nabhan C, El-Deiry W, Seeber A, Chiu V, Hwang J, Lou E. (2024) Exploring the differences in the tumor microenvironment and immuno-oncologic targets in pancreatic ductal adenocarcinomas (PDAC) according to KRAS mutational status. ESMO Gastrointestinal Oncology. 06; 4:100042.

Zorko NA, Makovec A, Elliott A, Kellen S, Lozada JR, Arafa AT, Felices M, Shackelford M, Barata P, Zakharia Y, Narayan V, Stein MN, Zarrabi KK, Patniak A, Bilen MA, Radovich M, Sledge G, El-Deiry WS, Heath EI, Hoon DSB, Nabhan C, Miller JS, Hwang JH, Antonarakis ES. (2024) Natural Killer Cell Infiltration in Prostate Cancers Predict Improved Patient Outcomes. Prostate Cancer Prostatic Dis. doi: 10.1038/s41391-024-00797-0. [Epub ahead of print] PubMed PMID: 38418892.

Sychev ZE, Day A, Bergom HE, Larson G, Ali A, Ludwig M, Boytim E, Coleman I, Corey E, Plymate SR, Nelson PS, Hwang JH, Drake JM. (2024) Unraveling the Global Proteome and Phosphoproteome of Prostate Cancer Patient-Derived Xenografts. Mol Cancer Res. doi: 10.1158/1541-7786.MCR-23-0976. PubMed PMID: 38345532.

Bergom HE, Sena LA, Day A, Miller B, Miller CD, Lozada JR, Zorko N, Wang J, Shenderov E, Lobo FP, Caramella-Pereira F, Marchionni L, Drake CG, Lotan T, De Marzo AM, Hwang J, Antonarakis ES.  (2024) Divergent immune microenvironments in two tumor nodules from a patient with mismatch repair-deficient prostate cancer. NPJ Genom Med. 22;9(1):7. doi: 10.1038/s41525-024-00392-1. PubMed PMID: 38253539; PubMed Central PMCID: PMC10803790.

Orme JJ, Taza F, De Sarkar N, Tewari AK, Arsalan Naqvi S, Riaz IB, Childs DS, Omar N, Adra N, Ashkar R, Cheng HH, Schweizer MT, Sokolova AO, Agarwal N, Barata P, Sartor O, Bastos D, Smaletz O, Berchuck JE, McClure H, Taplin ME, Aggarwal R, Sternberg CN, Vlachostergios PJ, Alva AS, Mehra N, Nelson PS, Hwang J, Dehm SM, Shi Q, Fleischmann Z, Sokol ES, Elliott A, Huang H, Bryce A, Marshall CH, Antonarakis ES. (2023) Co-occurring BRCA2/SPOP Mutations Predict Exceptional Poly (ADP-ribose) Polymerase Inhibitor Sensitivity in Metastatic Castration-Resistant Prostate Cancer. Eur Urol Oncol. doi: 10.1016/j.euo.2023.11.014. PMID: 38072760.

Phoenix JT, Budreika A, Kostlan RJ, Hwang JH, Fanning SW, Kregel S. (2023) Editorial: Hormone resistance in cancer. Front Endocrinol (Lausanne).14:1272932. doi:10.3389/fendo.2023.1272932. eCollection 2023. PubMed PMID: 37693345; PubMed Central PMCID: PMC10484586.

Cichocki, F., Zhang, B., Wu, C. Y., Chiu, E., Day, A., O'Connor, R. S., Yackoubov, D., Simantov, R., McKenna, D. H., Cao, Q., Defor, T. E., Janakiram, M., Wangen, R., Cayci, Z., Snyder, N., Kumar, A., Grzywacz, B., Hwang, J., Geffen, Y., Miller, J. S., Maakaron, J., Bachanova, V. (2023). Nicotinamide enhances natural killer cell function and yields remissions in patients with non-Hodgkin lymphoma. Science translational medicine, 15(705), eade3341. PMID: 37467318 doi: 10.1126/scitranslmed.ade3341

White, R. E., Bannister, M., Day, A., Bergom, H. E., Tan, V. M., Hwang, J., Dang Nguyen, H., Drake, J. M. (2023). Saracatinib synergizes with enzalutamide to downregulate AR activity in CRPC. Frontiers in Oncology, 13. doi: 10.3389/fonc.2023.1210487

Chehrazi-Raffle, A., Tukachinsky, H., Toye, E., Sivakumar, S., Schrock, A. B., Bergom, H. E., Ebrahimi, H., Pal, S., Dorff, T., Agarwal, N., Mahal, B. A., Oxnard, G. R., Hwang, J., Antonarakis, E. S. (2023). Unique spectrum of activating BRAF alterations in prostate cancer. Clinical Cancer Research. doi: 10.1158/1078-0432.ccr-23-1393

Bae, S. Y., Bergom, H. E., Day, A., Greene, J. T., Freedman, T. S., Hwang, J., Drake, J. M. (2023). ZBTB7A as a novel vulnerability in neuroendocrine prostate cancer. Frontiers in Endocrinology. doi: https://doi.org/10.3389/fendo.2023.1093332

Crymes, A., Evans, M.G., Elliott, A., Lozada, J.R., Carneiro, E., Carneiro, B.A, Lou, E., Soares, H.P., Antonarakis, E.S., Ryan C.J., Nabhan, C., Marks, J., Beltran, H., Hwang, J.H., (2023) 1188P Landscape of Delta-like-ligand 3 (DLL3) expression across neuroendocrine neoplasms (NENs). Annals of Oncology, 34, S703-S704. doi: 10.1016/j.annonc.2023.09.721

Hwang, J., Shi, X., Elliott, A., Arnoff, T. E., McGrath, J., Xiu, J., Walker, P., Bergom, H. E., Day, A., Ahmed, S., Tape, S., Makovec, A., Ali, A., Shaker, R. M., Toye, E., Passow, R., Lozada, J. R., Wang, J., Lou, E., Mouw, K. W., Carneiro, B. A., Heath, E. I., McKay, R. R., Korn, W. M., Nabhan, C., Ryan, C. J., Antonarakis, E. S. (2023). Metastatic Prostate Cancers with BRCA2 versus ATM Mutations Exhibit Divergent Molecular Features and Clinical Outcomes. Clinical cancer research : an official journal of the American Association for Cancer Research, 29(14), 2702-2713. PMID: 37126020 doi: 10.1158/1078-0432.CCR-22- 3394

Bergom, H. E., Shabaneh, A., Day, A., Ali, A., Boytim, E., Tape, S., Lozada, J. R., Shi, X., Kerkvliet, C. P., McSweeney, S., Pitzen, S. P., Ludwig, M., Antonarakis, E. S., Drake, J. M., Dehm, S. M., Ryan, C. J., Wang, J., Hwang, J. (Corresponding Author) (2023). ALAN is a computational approach that interprets genomic findings in the context of tumor ecosystems. Communications biology, 6(1), 417. PMID: 37059746 PMCID: PMC10104859 doi: 10.1038/s42003-023-04795-1

Shi, X., Day, A., Bergom, H. E., Tape, S., Baca, S. C., Sychev, Z. E., Larson, G., Bozicevich, A., Drake, J. M., Zorko, N., Wang, J., Ryan, C. J., Antonarakis, E. S., Hwang, J. (2022). Integrative molecular analyses define correlates of high B7-H3 expression in metastatic castrate-resistant prostate cancer. NPJ precision oncology, 6(1), 80. PMID: 36323882 PMCID: PMC9630314 doi: 10.1038/s41698-022-00323-2

So, J., Mabe, N. W., Englinger, B., Chow, K.-H., Moyer, S. M., Yerrum, S., Trissal, M. C., Gracca Marques, J., Kwon, J. J., Shim, B. H., Pal, S., Panditharatna, E., Quinn, T. W., Schaefer, D. A., Jeong, D., Mayhew, D. L., Hwang, J., Beroukhim, R., Ligon, K. L., Stegmaier, K., Filbin, M. G., Hahn, W. C. (2022). VRK1 as a synthetic lethal target in VRK2- methylated cancers of the nervous system. JCI Insight. doi: 10.1172/jci.insight.158755

McSweeney, S., Bergom, H. E., Prizment, A., Halabi, S., Sharifi, N., Ryan, C., Hwang, J. (2022). Regulatory genes in the androgen production, uptake and conversion (APUC) pathway in advanced prostate cancer. Endocrine Oncology, 2(1), R51-R64. doi: 10.1530/EO-22-0058

Hwang, J. H., Arafeh, R., Seo, J. H., Baca, S. C., Ludwig, M., Arnoff, T. E., Sawyer, L., Richter, C., Tape, S., Bergom, H. E., McSweeney, S., Rennhack, J. P., Klingenberg, S. A., Cheung, A. T.M., Kwon, J., So, J., Kregel, S., Van Allen, E. M., Drake, J. M., Freedman, M. L., Hahn, W. C. (2022). CREB5 reprograms FOXA1 nuclear interactions to promote resistance to androgen receptor-targeting therapies. eLife, 11. doi: 10.7554/eLife.73223

Tang, S., Sethunath, V., Metaferia, N. Y., Nogueira, M. F., Gallant, D. S., Garner, E. R., Lairson, L. A., Penney, C. M., Li, J., Gelbard, M. K., Alaiwi, S. A., Seo, J. H., Hwang, J. H., Strathdee, C. A., Baca, S. C., AbuHammad, S., Zhang, X., Doench, J. G., Hahn, W. C., Takeda, D. Y., Freedman, M. L., Choi, P. S., Viswanathan, S. R. (2022). A genome-scale CRISPR screen reveals PRMT1 as a critical regulator of androgen receptor signaling in prostate cancer. Cell Reports, 38(8). doi: 10.1016/j.celrep.2022.110417

Kim, M., Ly, S. H., Xie, Y., Duronio, G. N., Ford-Roshon, D., Hwang, J. H., Sulahian, R., Rennhack, J. P., So, J., Gjoerup, O., Talamas, J. A., Grandclaudon, M., Long, H. W., Doench, J. G., Sethi, N. S., Giannakis, M., Hahn, W. C. (2022). YAP1 and PRDM14 converge to promote cell survival and tumorigenesis. Developmental Cell, 57(2), 212-227.e8. doi: 10.1016/j.devcel.2021.12.006

Bekele, R. T., Samant, A. S., Nassar, A. H., So, J., Garcia, E. P., Curran, C. R., Hwang, J. H., Mayhew, D. L., Nag, A., Thorner, A. R., Borcsok, J., Sztupinszki, Z., Pan, C.-X., Bellmunt, J., Kwiatkowski, D. J., Sonpavde, G. P., Van Allen, E. M., Mouw, K. W. (2021). RAF1 amplification drives a subset of bladder tumors and confers sensitivity to MAPK-directed therapeutics. Journal of Clinical Investigation. doi: 10.1172/JCI147849

Dai, C., Rennhack, J. P., Arnoff, T. E., Thaker, M., Younger, S. T., Doench, J. G., Huang, A. Y., Yang, A., Aguirre, A. J., Wang, B., Mun, E., O'Connell, J. T., Huang, Y., Labella, K., Talamas, J. A., Li, J., Ilic, N., Hwang, J., Hong, A. L., Giacomelli, A. O., Gjoerup, O., Root, D. E., Hahn, W. C. (2021). SMAD4 represses FOSL1 expression and pancreatic cancer metastatic colonization. Cell Reports, 36(4). doi: 10.1016/j.celrep.2021.109443

Prizment, A. E., McSweeney, S., Pankratz, N., Joshu, C. E., Hwang, J. H., Platz, E. A., Ryan, C. J. (2021). Prostate Cancer Mortality Associated with Aggregate Polymorphisms in Androgen-Regulating Genes: The Atherosclerosis Risk in the Communities (ARIC) Study. Cancers, 13(8). PMID: 33921650 PMCID: PMC8072683 doi: 10.3390/cancers13081958

Baca, S. C., Takeda, D. Y., Seo, J.-H., Hwang, J., Ku, S. Y., Arafeh, R., Arnoff, T., Agarwal, S., Bell, C., O’Connor, E., Qiu, X., Abou Alaiwi, S., Corona, R. I., Fonseca, M. A. S., Giambartolomei, C., Cejas, P., Lim, K., He, M., Sheahan, A., Nassar, A., Berchuck, J. E., Brown, L., Nguyen, H. M., Coleman, I. M., Kaipainen, A., De Sarkar, N., Nelson, P. S., Morrissey, C., Korthauer, K., Pomerantz, M. M., Ellis, L., Pasaniuc, B., Lawrenson, K., Kelly, K., Zoubeidi, A., Hahn, W. C., Beltran, H., Long, H. W., Brown, M., Corey, E., Freedman, M. L. (2021). Reprogramming of the FOXA1 Cistrome in Treatment-emergent Neuroendocrine Prostate Cancer. Nature Communications. doi: 10.1038/s41467-021-22139-7

Elmarakeby, H. A., Hwang, J., Arafeh, R., Crowdis, J., Gang, S., Liu, D., AlDubayan, S. H., Salari, K., Kregel, S., Richter, C., Arnoff, T. E., Park, J., Hahn, W. C., M. Van Allen, E. (2021). Biologically informed deep neural network for prostate cancer discovery. Nature. doi: 10.1038/s41586-021-03922-4

Richter, C., Mayhew, D., Rennhack, J. P., So, J., Stover, E. H., Hwang, J. H., SzczesnaCordary, D. (2020). Genomic Amplification and Functional Dependency of the Gamma Actin Gene ACTG1 in Uterine Cancer. International Journal of Molecular Sciences, 21(22). doi: 10.3390/ijms21228690

Tang, S., Metaferia, N., Nogueira, M., Gelbard, M., Alaiwi, S. A., Seo, J. H., Hwang, J., Strathdee, C., Baca, S., Li, J., Abuhammad, S., Zhang, X., Doench, J., Hahn, W., Takeda, D., Freedman, M., Choi, P., Viswanathan, S. (2020). Genome-scale genetic screening identifies PRMT1 as a critical vulnerability in castration-resistant prostate cancer. European Journal of Cancer, 138, S7. doi: 10.1016/S0959-8049(20)31085-6

VanDeusen, H. R., Ramroop, J. R., Morel, K. L., Bae, S. Y., Sheahan, A. V., Sychev, Z., Lau, N. A., Cheng, L. C., Tan, V. M., Li, Z., Peterson, A., Lee, J. K., Park, J. W., Yang, R., Hwang, J. H., Coleman, I., Witte, O. N., Morrissey, C., Corey, E., Nelson, P. S., Ellis, L., Drake, J. M. (2020). Targeting RET Kinase in Neuroendocrine Prostate Cancer. Molecular Cancer Research, 18(8). doi: 10.1158/1541-7786.MCR-19-1245

Rafiei, S., Fitzpatrick, K., Liu, D., Cai, M., Elmarakeby, H. A., Park, J., Ricker, C., Kochupurakkal, B. S., Choudhury, A. D., Hahn, W. C., Balk, S. P., Hwang, J. H., Van Allen, E. M., Mouw, K. W. (2020). ATM Loss Confers Greater Sensitivity to ATR Inhibition Than PARP Inhibition in Prostate Cancer. Cancer Research, 80(11), 2094-2100. doi: 10.1158/0008-5472.CAN-19-3126

Hwang, J. H., Seo, J., Beshiri, M. L., Wankowicz, S., Liu, D., Cheung, A., Li, J., Qiu, X., Hong, A. L., Botta, G., Golumb, L., Richter, C., So, J., Sandoval, G. J., Giacomelli, A. O., Ly, S. H., Han, C., Dai, C., Pakula, H., Sheahan, A., Piccioni, F., Gjoerup, O., Loda, M., Sowalsky, A. G., Ellis, L., Long, H., Root, D. E., Kelly, K., Van Allen, E. M., Freedman, M. L., Choudhury, A. D., Hahn, W. C. (2019). CREB5 Promotes Resistance to AndrogenReceptor Antagonists and Androgen Deprivation in Prostate Cancer. Cell Reports, 29(8), 2355-2370. PMID: 31747605 doi: 10.1016/j.celrep.2019.10.068

Howard, T. P., Arnoff, T. E., Song, M. R., Giacomelli, A. O., Wang, X., Hong, A. L., Dharia, N. V., Wang, S., Vazquez, F., Pham, M., Morgan, A. M., Wachter, F., Bird, G. H., Kugener, G., Oberlick, E. M., Rees, M. G., Tiv, H. L., Hwang, J. H., Walsh, K. H., Cook, A., KrillBurger, J. M., Tsherniak, A., Gokhale, P. C., Park, P. J., Stegmaier, K., Walensky, L. D., Hahn, W. C., Roberts, C. W. (2019). MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer Research, 79(9), 2404-2414. PMID: 30755442 doi: 10.1158/0008-5472.CAN-18-3066

Li, J., Choi, P. S., Chaffer, C. L., Labella, K., Hwang, J. H., Giacomelli, A. O., Kim, J. W., Ilic, N., Doench, J. G., Ly, S. H., Dai, C., Hagel, K., Hong, A. L., Gjoerup, O., Goel, S., Ge, J. Y., Root, D. E., Zhao, J. J., Brooks, A. N., Weinberg, R. A., Hahn, W. C. (2018). An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. eLife, 7, e37184. PMID: 30059005 doi: 10.7554/eLife.37184

 Han, G. C., Hwang, J., Wankowicz, S. A., Zhang, Z., Liu, D., Cibulskis, C., Gaviola, G. C., Ghazikhanian, V., McKay, R. R., Bubley, G. J., Carter, S. L., Balk, S. P., Hahn, W. C., Taplin, M., Van Allen, E. M. (2017). Genomic Resistance Patterns to Second-Generation Androgen Blockade in Paired Tumor Biopsies of Metastatic Castration-Resistant Prostate Cancer. JCO Precision Oncology. doi: 10.1200/PO.17.00140

Rouleau, C., Pores Fernando, A. T., Hwang, J. H., Faure, N., Jiang, T., White, E. A., Roberts, T. M., Schaffhausen, B. S. (2016). Transformation by Polyomavirus Middle T Antigen Involves a Unique Bimodal Interaction with the Hippo Effector YAP. Journal of Virology, 90(16). PMID: 27194756 doi: 10.1128/JVI.00417-16

White, E. A., Kramer, R. E., Hwang, J. H., Pores Fernando, A. T., Naeter, N., Hahn, W. C., Roberts, T. M., Schaffhausen, B. S., Livingston, D. M., Howley, P. M. (2015). Papillomavirus E7 Oncoproteins Share Functions with Polyomavirus Small T Antigens. Journal of Virology. PMID: 25540383 doi: 10.1128/JVI.03282-14

Hwang, J. H., Pores Fernando, A. T., Faure, N., Andrabi, S., Adelmant, G., Hahn, W. C., Marto, J. A., Schaffhausen, B. S., Roberts, T. M. (2014). Polyomavirus Small t Antigen Interacts with Yes-Associated Protein To Regulate Cell Survival and Differentiation. Journal of Virology, 88(20), 12055-12064. PMID: 25122798 doi: 10.1128/JVI.01399-14

Hwang, J. H., Jiang, T., Kulkarni, S., Faure, N., Schaffhausen, B. S. (2013). Protein phosphatase 2A isoforms utilizing Aβ scaffolds regulate differentiation through control of Akt protein. Journal of Biological Chemistry, 288(44), 32064-32073. PMID: 24052256 doi: 10.1074/jbc.M113.497644

Andrabi, S., Hwang, J. H., Choe, J. K., Roberts, T. M., Schaffhausen, B. S. (2011). Comparisons between murine polyomavirus and Simian virus 40 show significant differences in small T antigen function. Journal of Virology, 85(20), 10649-10658. PMID: 21835797 doi: 10.1128/jvi.05034-11

Shi, Q., Harris, L. N., Lu, X., Li, X., Hwang, J., Gentleman, R., Iglehart, J. D., Miron, A. (2006). Declining plasma fibrinogen alpha fragment identifies HER2-positive breast cancer patients and reverts to normal levels after surgery. Journal of Proteome Research, 5(11), 2947-2955. PMID: 17081046 doi: 10.1021/pr060099u