Joshua Gruber

All Publications

• Endotrophin is a circulating fibroinflammatory biomarker associated with treatment response in human metastatic ER+ breast cancer. Clinical cancer research : an official journal of the American Association for Cancer Research Santos, B., Bu, D., Virostek, M., Johnson, E., Lewis, C., Vumma, L., Sahoo, S., Peng, Y., Zhang, N., An, Z., McArthur, H., Scherer, P. E., Gruber, J. J. 2026

  Abstract

  Soluble factors emanating from fibroinflammatory processes are emerging as cancer biomarkers and therapeutic targets. Endotrophin (ETP), a collagen VI proteolytic fragment, is elevated in human breast cancer patients and drives tumor progression in rodent breast cancer models, an effect which neutralizing antibodies can abrogate. This implies that tracking or targeting elevated ETP levels could inform breast cancer therapeutic strategies. However, we lack precise knowledge about the impact of ETP in specific breast cancer subtypes and whether circulating levels provide predictive or prognostic information.To address these gaps, we assessed circulating ETP levels among breast cancer patients (n=191 samples from 98 patients) undergoing various treatment modalities, as well as patients with ovarian neoplasia (n=29) and healthy controls (n=19).We observed higher circulating ETP levels in estrogen receptor-positive (ER+/HER2-) tumors compared with triple-negative breast cancer (TNBC) in both early-stage and metastatic settings (median [IQR]: 35.98 [25.31-55.05] vs. 19.67 [9.23-42.07] ng/mL, respectively). However, circulating ETP levels were associated with treatment response only in the metastatic setting. ETP was readily detected in tumor specimens (n=54) and adjacent benign sections (n=28) from various breast tumor types, suggesting that both autocrine and paracrine ETP production may be important drivers of tumor growth.In summary, these findings identify circulating ETP as a potential biomarker in ER+ metastatic breast cancer and support further investigation of its relationship with disease activity and the development of endotrophin-targeting agents.

  View details for DOI 10.1158/1078-0432.CCR-25-3775

  View details for PubMedID 42832372

• Results of phase 1 first-in-human clinical trial of HMBD-002, an IgG4 monoclonal antibody targeting VISTA, in advanced solid tumors Rodon, J., Gruber, J. J., Telli, M. L., Hendifar, A., Kim, J. W., Bhardwaj, S., Sharma, P., Thakkar, D., Boyd-Kirkup, J., Kennedy, E. AMER ASSOC CANCER RESEARCH. 2026

  View details for DOI 10.1158/1538-7445.AM2026-CT126

  View details for Web of Science ID 001744449600021

• Etirinotecan Pegol (NKTR-102) in Patients With Active Brain Metastases From Lung or Breast Cancer. Cancer reports (Hoboken, N.J.) Nagpal, S., Nguyen, K. S., Bertrand, S., Cunanan, K. M., Padda, S. K., Pagtama, J. Y., Tisch, A. H., Coffey, G., Thomas, R. P., Sledge, G. W., Gruber, J., Telli, M. L., Pegram, M., Recht, L. D., Wakelee, H. A., Soltys, S. G., Massarweh, S. A., Neal, J. W. 2025; 8 (9): e70330

  Abstract

  Brain metastases are common in patients with lung and breast cancer and are associated with poor outcomes. While there is some intracranial activity with systemic therapies, most chemotherapies are minimally effective. Etirinotecan pegol (EP) is a PEGylated chemotherapy with favorable pharmacokinetics over irinotecan.We conducted a phase 2 trial of EP in patients with previously treated metastatic non-small cell lung cancer (NSCLC, n = 12), small cell lung cancer (SCLC, N = 3) and breast cancer (MBC, n = 12), having progressive brain metastases after brain-directed radiotherapy (or refusal). The primary endpoint was a 25% or greater disease control rate, defined as CR, PR+SD, in the central nervous system (CNS) at 12 weeks; secondary endpoints included toxicity and systemic disease control.The CNS control rate at 12 weeks in NSCLC and MBC was 17% (two patients in each cohort) and 0% in SCLC. The median overall progression-free survival for NSCLC was 2.7 months (95% CI: 1.3, 6.7) and MBC was 1.4 months (95% CI: 1.3, 6.9). The most common adverse events were diarrhea (48%), nausea (48%) and fatigue (26%). Six patient deaths occurred in this study. Dehydration/diarrhea (1) and neutropenic sepsis (3) from study treatment were at least possibly related to these deaths.This study demonstrates that EP did not meet the threshold of clinical efficacy in patients with refractory CNS metastases from lung or breast cancer.

  View details for DOI 10.1002/cnr2.70330

  View details for PubMedID 40877204

• A Four Amino Acid Intracellular Motif of VISTA Blocks Growth Receptor Signaling in Cancer Cells to Induce Tumor Suppression. Cancer research Zhao, Y., Andoh, T., Charles, F., Reddy, P., Paul, K., Goar, H., Durdana, I., Golder, C. J., Hardy, A. N., Juntilla, M. M., Yang, S. R., Lin, C. Y., Sagiv-Barfi, I., Geller, B. S., Moore, S., Thakkar, D., Boyd-Kirkup, J. D., Peng, Y., Ford, J. M., Telli, M. L., Zhang, S., Kurian, A. W., West, R. B., Yue, T., Lipchik, A. M., Snyder, M. P., Gruber, J. J. 2025

  Abstract

  VISTA is a key immune checkpoint receptor under investigation as a target for cancer immunotherapy. However, a better understanding of the signaling mechanisms of VISTA is needed to optimize the therapeutic potential. Here, we identified a conserved four amino acid (NPGF) intracellular motif in VISTA that suppresses cell proliferation by constraining cell-intrinsic growth receptor signaling. A class of triple-negative breast cancers (TNBC) with high VISTA expression and low proliferative index was identified and characterized. The NPGF motif bound to the adapter protein NUMB and recruited Rab11 endosomal recycling machinery. The NPGF motif sequestered NUMB at endosomes, which interfered with EGFR trafficking and signaling to suppress tumor growth. These tumor suppressive effects did not require canonical VISTA ligands or a functioning immune system. Mutation of the VISTA NPGF domain reverted VISTA-induced growth suppression in multiple breast cancer mouse models. The NPGF motif was also required for response of VISTA+ TNBCs to VISTA-blocking antibodies. These results define a mechanism by which VISTA recruits adapter proteins to control malignant epithelial cell growth and signaling. They also define distinct intracellular residues that are critical for response to therapeutic antibodies that could be exploited to improve immunotherapy.

  View details for DOI 10.1158/0008-5472.CAN-24-4774

  View details for PubMedID 40658599

• Short-chain fatty acid metabolites propionate and butyrate are unique epigenetic regulatory elements linking diet, metabolism and gene expression. Nature metabolism Nshanian, M., Gruber, J. J., Geller, B. S., Chleilat, F., Lancaster, S. M., White, S. M., Alexandrova, L., Camarillo, J. M., Kelleher, N. L., Zhao, Y., Snyder, M. P. 2025

  Abstract

  The short-chain fatty acids (SCFAs) propionate and butyrate have beneficial health effects, are produced in large amounts by microbial metabolism and have been identified as unique acyl lysine histone marks. To better understand the function of these modifications, we used chromatin immunoprecipitation followed by sequencing to map the genome-wide location of four short-chain acyl histone marks, H3K18pr, H3K18bu, H4K12pr and H4K12bu, in treated and untreated colorectal cancer (CRC) and normal cells as well as in mouse intestines in vivo. We correlate these marks with open chromatin regions and gene expression to access the function of the target regions. Our data demonstrate that propionate and butyrate bind and act as promoters of genes involved in growth, differentiation and ion transport. We propose a mechanism involving direct modification of specific genomic regions by SCFAs resulting in increased chromatin accessibility and, in the case of butyrate, opposing effects on the proliferation of normal versus CRC cells.

  View details for DOI 10.1038/s42255-024-01191-9

  View details for PubMedID 39789354

  View details for PubMedCentralID 4393657

• VISTA-induced tumor suppression by a four amino acid intracellular motif. bioRxiv : the preprint server for biology Zhao, Y., Andoh, T., Charles, F., Reddy, P., Paul, K., Goar, H., Durdana, I., Golder, C., Hardy, A., Juntilla, M. M., Yang, S. R., Lin, C. Y., Sagiv-Barfi, I., Geller, B. S., Moore, S., Thakkar, D., Boyd-Kirkup, J. D., Peng, Y., Ford, J. M., Telli, M. L., Zhang, S., Kurian, A. W., West, R. B., Yue, T., Lipchik, A. M., Snyder, M. P., Gruber, J. J. 2025

  Abstract

  VISTA is a key immune checkpoint receptor under investigation for cancer immunotherapy; however, its signaling mechanisms remain unclear. Here we identify a conserved four amino acid (NPGF) intracellular motif in VISTA that suppresses cell proliferation by constraining cell-intrinsic growth receptor signaling. The NPGF motif binds to the adapter protein NUMB and recruits Rab11 endosomal recycling machinery. We identify and characterize a class of triple-negative breast cancers with high VISTA expression and low proliferative index. In tumor cells with high VISTA levels, the NPGF motif sequesters NUMB at endosomes, which interferes with epidermal growth factor receptor (EGFR) trafficking and signaling to suppress tumor growth. These effects do not require canonical VISTA ligands, nor a functioning immune system. As a consequence of VISTA expression, EGFR receptor remains abnormally phosphorylated and cannot propagate ligand-induced signaling. Mutation of the VISTA NPGF domain reverts VISTA-induced growth suppression in multiple breast cancer mouse models. These results define a mechanism by which VISTA represses NUMB to control malignant epithelial cell growth and signaling. They also define distinct intracellular residues that are critical for VISTA-induced cell-intrinsic signaling that could be exploited to improve immunotherapy.

  View details for DOI 10.1101/2025.01.05.631401

  View details for PubMedID 39803490

  View details for PubMedCentralID PMC11722267

• AI is a viable alternative to high throughput screening: a 318-target study SCIENTIFIC REPORTS Wallach, I., Bernard, D., Nguyen, K., Ho, G., Morrison, A., Stecula, A., Rosnik, A., O'Sullivan, A., Davtyan, A., Samudio, B., Thomas, B., Worley, B., Butler, B., Laggner, C., Thayer, D., Moharreri, E., Friedland, G., Truong, H., van den Bedem, H., Ng, H., Stafford, K., Sarangapani, K., Giesler, K., Ngo, L., Mysinger, M., Ahmed, M., Anthis, N. J., Henriksen, N., Gniewek, P., Eckert, S., de Oliveira, S., Suterwala, S., PrasadPrasad, S., Shek, S., Contreras, S., Hare, S., Palazzo, T., O'Brien, T. E., Van Grack, T., Williams, T., Chern, T., Kenyon, V., Lee, A. H., Cann, A. B., Bergman, B., Anderson, B. M., Cox, B. D., Warrington, J. M., Sorenson, J. M., Goldenberg, J. M., Young, M. A., DeHaan, N., Pemberton, R. P., Schroedl, S., Abramyan, T. M., Gupta, T., Mysore, V., Presser, A. G., Ferrando, A. A., Andricopulo, A. D., Ghosh, A., Ayachi, A., Mushtaq, A., Shaqra, A. M., Toh, A., Smrcka, A. V., Ciccia, A., de Oliveira, A., Sverzhinsky, A., de Sousa, A., Agoulnik, A. I., Kushnir, A., Freiberg, A. N., Statsyuk, A. V., Gingras, A. R., Degterev, A., Tomilov, A., Vrielink, A., Garaeva, A. A., Bryant-Friedrich, A., Caflisch, A., Patel, A. K., Rangarajan, A., Matheeussen, A., Battistoni, A., Caporali, A., Chini, A., Ilari, A., Mattevi, A., Foote, A., Trabocchi, A., Stahl, A., Herr, A. B., Berti, A., Freywald, A., Reidenbach, A. G., Lam, A., Cuddihy, A. R., White, A., Taglialatela, A., Ojha, A. K., Cathcart, A. M., Motyl, A. A. L., Borowska, A., D'Antuono, A., Hirsch, A. K. H., Porcelli, A., Minakova, A., Montanaro, A., Mueller, A., Fiorillo, A., Virtanen, A., O'Donoghue, A. J., Flores, A., Garmendia, A. E., Pineda-Lucena, A., Panganiban, A. T., Samantha, A., Chatterjee, A. K., Haas, A. L., Paparella, A. S., John, A., Prince, A., ElSheikh, A., Apfel, A., Colomba, A., O'Dea, A., Diallo, B., Ribeiro, B., Bailey-Elkin, B. A., Edelman, B. L., Liou, B., Perry, B., Chua, B., Kovats, B., Englinger, B., Balakrishnan, B., Gong, B., Agianian, B., Pressly, B., Salas, B., Duggan, B. M., Geisbrecht, B. V., Dymock, B. W., Morten, B. C., Hammock, B. D., Mota, B., Dickinson, B. C., Fraser, C., Lempicki, C., Novina, C. D., Torner, C., Ballatore, C., Bon, C., Chapman, C. J., Partch, C. L., Chaton, C. T., Huang, C., Yang, C., Kahler, C. M., Karan, C., Keller, C., Dieck, C. L., Chen Huimei, Liu, C., Peltier, C., Mantri, C., Kemet, C., Mueller, C. E., Weber, C., Zeina, C. M., Muli, C. S., Morisseau, C., Alkan, C., Reglero, C., Loy, C. A., Wilson, C. M., Myhr, C., Arrigoni, C., Paulino, C., Santiago, C., Luo, D., Tumes, D. J., Keedy, D. A., Lawrence, D. A., Chen, D., Manor, D., Trader, D. J., Hildeman, D. A., Drewry, D. H., Dowling, D. J., Hosfield, D. J., Smith, D. M., Moreira, D., Siderovski, D. P., Shum, D., Krist, D. T., Riches, D. W. H., Ferraris, D., Anderson, D. H., Coombe, D. R., Welsbie, D. S., Hu, D., Ortiz, D., Alramadhani, D., Zhang, D., Chaudhuri, D., Slotboom, D. J., Ronning, D. R., Lee, D., Dirksen, D., Shoue, D. A., Zochodne, D., Krishnamurthy, D., Duncan, D., Glubb, D. M., Gelardi, E., Hsiao, E. C., Lynn, E. G., Silva, E., Aguilera, E., Lenci, E., Abraham, E., Lama, E., Mameli, E., Leung, E., Christensen, E. M., Mason, E. R., Petretto, E., Trakhtenberg, E. F., Rubin, E. J., Strauss, E., Thompson, E. W., Cione, E., Lisabeth, E., Fan, E., Kroon, E., Jo, E., Garcia-Cuesta, E. M., Glukhov, E., Gavathiotis, E., Yu, F., Xiang, F., Leng, F., Wang, F., Ingoglia, F., van den Akker, F., Borriello, F., Vizeacoumar, F. J., Luh, F., Buckner, F. S., Vizeacoumar, F. S., Ben Bdira, F., Svensson, F., Rodriguez, G., Bognar, G., Lembo, G., Zhang, G., Dempsey, G., Eitzen, G., Mayer, G., Greene, G. L., Garcia, G. A., Lukacs, G. L., Prikler, G., Parico, G. G., Colotti, G., De Keulenaer, G., Cortopassi, G., Roti, G., Girolimetti, G., Fiermonte, G., Gasparre, G., Leuzzi, G., Dahal, G., Michlewski, G., Conn, G. L., Stuchbury, G., Bowman, G. R., Popowicz, G., Veit, G., de Souza, G., Akk, G., Caljon, G., Alvarez, G., Rucinski, G., Lee, G., Cildir, G., Li, H., Breton, H. E., Jafar-Nejad, H., Zhou, H., Moore, H. P., Tilford, H., Yuan, H., Shim, H., Wulff, H., Hoppe, H., Chaytow, H., Tam, H., Van Remmen, H., Xu, H., Debonsi, H., Lieberman, H. B., Jung, H., Fan, H., Feng, H., Zhou, H., Kim, H., Greig, I. R., Caliandro, I., Corvo, I., Arozarena, I., Mungrue, I. N., Verhamme, I. M., Qureshi, I., Lotsaris, I., Cakir, I., Perry, J. P., Kwiatkowski, J., Boorman, J., Ferreira, J., Fries, J., Kratz, J., Miner, J., Siqueira-Neto, J. L., Granneman, J. G., Ng, J., Shorter, J., Voss, J., Gebauer, J. M., Chuah, J., Mousa, J. J., Maynes, J. T., Evans, J. D., Dickhout, J., MacKeigan, J. P., Jossart, J. N., Zhou, J., Lin, J., Xu, J., Wang, J., Zhu, J., Liao, J., Xu, J., Zhao, J., Lin, J., Lee, J., Reis, J., Stetefeld, J., Bruning, J. B., Bruning, J., Coles, J. G., Tanner, J. J., Pascal, J. M., So, J., Pederick, J. L., Costoya, J. A., Rayman, J. B., Maciag, J. J., Nasburg, J., Gruber, J. J., Finkelstein, J. M., Watkins, J., Rodriguez-Frade, J., Arias, J., Lasarte, J., Oyarzabal, J., Milosavljevic, J., Cools, J., Lescar, J., Bogomolovas, J., Wang, J., Kee, J., Kee, J., Liao, J., Sistla, J. C., Abrahao, J., Sishtla, K., Francisco, K. R., Hansen, K. B., Molyneaux, K. A., Cunningham, K. A., Martin, K. R., Gadar, K., Ojo, K. K., Wong, K. S., Wentworth, K. L., Lai, K., Lobb, K. A., Hopkins, K. M., Parang, K., Machaca, K., Pham, K., Ghilarducci, K., Sugamori, K. S., McManus, K., Musta, K., Faller, K. M. E., Nagamori, K., Mostert, K. J., Korotkov, K. V., Liu, K., Smith, K. S., Sarosiek, K., Rohde, K. H., Kim, K., Lee, K., Pusztai, L., Lehtio, L., Haupt, L. M., Cowen, L. E., Byrne, L. J., Su, L., Wert-Lamas, L., Puchades-Carrasco, L., Chen, L., Malkas, L. H., Zhuo, L., Hedstrom, L., Hedstrom, L., Walensky, L. D., Antonelli, L., Iommarini, L., Whitesell, L., Randall, L. M., Fathallah, M., Nagai, M., Kilkenny, M., Ben-Johny, M., Lussier, M. P., Windisch, M. P., Lolicato, M., Lolli, M., Vleminckx, M., Caroleo, M., Macias, M. J., Valli, M., Barghash, M. M., Mellado, M., Tye, M. A., Wilson, M. A., Hannink, M., Ashton, M. R., dela Cerna, M. C., Giorgis, M., Safo, M. K., St Maurice, M., McDowell, M., Pasquali, M., Mehedi, M., Serafim, M., Soellner, M. B., Alteen, M. G., Champion, M. M., Skorodinsky, M., O'Mara, M. L., Bedi, M., Rizzi, M., Levin, M., Mowat, M., Jackson, M. R., Paige, M., Al-Yozbaki, M., Giardini, M. A., Maksimainen, M. M., De Luise, M., Hussain, M., Christodoulides, M., Stec, N., Zelinskaya, N., Van Pelt, N., Merrill, N. M., Singh, N., Kootstra, N. A., Singh, N., Gandhi, N. S., Chan, N., Trinh, N., Schneider, N. O., Matovic, N., Horstmann, N., Longo, N., Bharambe, N., Rouzbeh, N., Mahmoodi, N., Gumede, N., Anastasio, N. C., Ben Khalaf, N., Rabal, O., Kandror, O., Escaffre, O., Silvennoinen, O., Bishop, O., Iglesias, P., Sobrado, P., Chuong, P., O'Connell, P., Martin-Malpartida, P., Mellor, P., Fish, P. V., Moreira, P., Zhou, P., Liu, P., Liu, P., Wu, P., Agogo-Mawuli, P., Jones, P. L., Ngoi, P., Toogood, P., Ip, P., von Hundelshausen, P., Lee, P. H., Rowswell-Turner, R. B., Balana-Fouce, R., Rocha, R., Guido, R. V. C., Ferreira, R., Agrawal, R. K., Harijan, R. K., Ramachandran, R., Verma, R., Singh, R. K., Tiwari, R., Mazitschek, R., Koppisetti, R. K., Dame, R. T., Douville, R. N., Austin, R. C., Taylor, R. E., Moore, R. G., Ebright, R. H., Angell, R. M., Yan, R., Kejriwal, R., Batey, R. A., Blelloch, R., Vandenberg, R. J., Hickey, R. J., Kelm, R. J., Lake, R. J., Bradley, R. K., Blumenthal, R. M., Solano, R., Gierse, R., Viola, R. E., McCarthy, R. R., Reguera, R., Uribe, R., do Monte-Neto, R., Gorgoglione, R., Cullinane, R. T., Katyal, S., Hossain, S., Phadke, S., Shelburne, S. A., Geden, S. E., Johannsen, S., Wazir, S., Legare, S., Landfear, S. M., Radhakrishnan, S. K., Ammendola, S., Dzhumaev, S., Seo, S., Li, S., Zhou, S., Chu, S., Chauhan, S., Maruta, S., Ashkar, S. R., Shyng, S., Conticello, S. G., Buroni, S., Garavaglia, S., White, S. J., Zhu, S., Tsimbalyuk, S., Chadni, S., Byun, S., Park, S., Xu, S. Q., Banerjee, S., Zahler, S., Espinoza, S., Gustincich, S., Sainas, S., Celano, S. L., Capuzzi, S. J., Waggoner, S. N., Poirier, S., Olson, S. H., Marx, S. O., Van Doren, S. R., Sarilla, S., Brady-Kalnay, S. M., Dallman, S., Azeem, S., Teramoto, T., Mehlman, T., Swart, T., Abaffy, T., Akopian, T., Haikarainen, T., Moreda, T., Ikegami, T., Teixeira, T., Jayasinghe, T. D., Gillingwater, T. H., Kampourakis, T., Richardson, T. I., Herdendorf, T. J., Kotze, T. J., O'Meara, T. R., Corson, T. W., Hermle, T., Ogunwa, T., Lan, T., Su, T., Banjo, T., O'Mara, T. A., Chou, T., Chou, T., Baumann, U., Desai, U. R., Pai, V. P., Thai, V., Tandon, V., Banerji, V., Robinson, V. L., Gunasekharan, V., Namasivayam, V., Segers, V. F. M., Maranda, V., Dolce, V., Maltarollo, V., Scoffone, V., Woods, V. A., Ronchi, V., Le, V., Clayton, W., Lowther, W., Houry, W. A., Li, W., Tang, W., Zhang, W., Van Voorhis, W. C., Donaldson, W. A., Hahn, W. C., Kerr, W. G., Gerwick, W. H., Bradshaw, W. J., Foong, W., Blanchet, X., Wu, X., Lu, X., Qi, X., Xu, X., Yu, X., Qin, X., Wang, X., Yuan, X., Zhang, X., Zhang, Y., Hu, Y., Aldhamen, Y., Chen, Y., Li, Y., Sun, Y., Zhu, Y., Gupta, Y. K., Perez-Pertejo, Y., Li, Y., Tang, Y., He, Y., Tse-Dinh, Y., Sidorova, Y. A., Yen, Y., Li, Y., Frangos, Z. J., Chung, Z., Su, Z., Wang, Z., Zhang, Z., Liu, Z., Inde, Z., Artia, Z., Heifets, A., Atomwise AIMS Program 2024; 14 (1): 7526

  Abstract

  High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.

  View details for DOI 10.1038/s41598-024-54655-z

  View details for Web of Science ID 001253148000001

  View details for PubMedID 38565852

  View details for PubMedCentralID PMC10987645

• Serine starvation silences estrogen receptor signaling through histone hypoacetylation. Proceedings of the National Academy of Sciences of the United States of America Li, A. M., He, B., Karagiannis, D., Li, Y., Jiang, H., Srinivasan, P., Ramirez, Y., Zhou, M. N., Curtis, C., Gruber, J. J., Lu, C., Rankin, E. B., Ye, J. 2023; 120 (38): e2302489120

  Abstract

  Loss of estrogen receptor (ER) pathway activity promotes breast cancer progression, yet how this occurs remains poorly understood. Here, we show that serine starvation, a metabolic stress often found in breast cancer, represses estrogen receptor alpha (ERα) signaling by reprogramming glucose metabolism and epigenetics. Using isotope tracing and time-resolved metabolomic analyses, we demonstrate that serine is required to maintain glucose flux through glycolysis and the TCA cycle to support acetyl-CoA generation for histone acetylation. Consequently, limiting serine depletes histone H3 lysine 27 acetylation (H3K27ac), particularly at the promoter region of ER pathway genes including the gene encoding ERα, ESR1. Mechanistically, serine starvation impairs acetyl-CoA-dependent gene expression by inhibiting the entry of glycolytic carbon into the TCA cycle and down-regulating the mitochondrial citrate exporter SLC25A1, a critical enzyme in the production of nucleocytosolic acetyl-CoA from glucose. Consistent with this model, total H3K27ac and ERα expression are suppressed by SLC25A1 inhibition and restored by acetate, an alternate source of acetyl-CoA, in serine-free conditions. We thus uncover an unexpected role for serine in sustaining ER signaling through the regulation of acetyl-CoA metabolism.

  View details for DOI 10.1073/pnas.2302489120

  View details for PubMedID 37695911

• A phase 1 first-in-human clinical trial of HMBD-002, an IgG4 monoclonal antibody targeting VISTA, in advanced solid tumors Ahnert, J., Gruber, J., Telli, M. L., Mita, M. M., Mita, A. C., Kim, J. W., Villalona-Calero, M., Patel, M., Yadav, S. S., Sharma, P., Haber, T., Lauren, J., Seet, S., Dharmadhikari, B., Thakkar, D., Kwek, K., DiMascio, L., Rowinsky, E., Ingram, P., Boyd-Kirkup, J. LIPPINCOTT WILLIAMS & WILKINS. 2023

  View details for Web of Science ID 001053772005575

• Acetyl-Click Screening Platform Identifies Small-Molecule Inhibitors of Histone Acetyltransferase 1 (HAT1). Journal of medicinal chemistry Gaddameedi, J. D., Chou, T., Geller, B. S., Rangarajan, A., Swaminathan, T. A., Dixon, D., Long, K., Golder, C. J., Vuong, V. A., Banuelos, S., Greenhouse, R., Snyder, M. P., Lipchik, A. M., Gruber, J. J. 2023

  Abstract

  HAT1 is a central regulator of chromatin synthesis that acetylates nascent histone H4. To ascertain whether targeting HAT1 is a viable anticancer treatment strategy, we sought to identify small-molecule inhibitors of HAT1 by developing a high-throughput HAT1 acetyl-click assay. Screening of small-molecule libraries led to the discovery of multiple riboflavin analogs that inhibited HAT1 enzymatic activity. Compounds were refined by synthesis and testing of over 70 analogs, which yielded structure-activity relationships. The isoalloxazine core was required for enzymatic inhibition, whereas modifications of the ribityl side chain improved enzymatic potency and cellular growth suppression. One compound (JG-2016 [24a]) showed relative specificity toward HAT1 compared to other acetyltransferases, suppressed the growth of human cancer cell lines, impaired enzymatic activity in cellulo, and interfered with tumor growth. This is the first report of a small-molecule inhibitor of the HAT1 enzyme complex and represents a step toward targeting this pathway for cancer therapy.

  View details for DOI 10.1021/acs.jmedchem.3c00039

  View details for PubMedID 37027002

• Mitochondrial uncoupling induces epigenome remodeling and promotes differentiation in neuroblastoma. Cancer research Jiang, H., Greathouse, R. L., Tiche, S. J., Zhao, M., He, B., Li, Y., Li, A. M., Forgo, B., Yip, M., Li, A., Shih, M., Banuelos, S., Zhou, M., Gruber, J. J., Rankin, E. B., Hu, Z., Shimada, H., Chiu, B., Ye, J. 2022

  Abstract

  The Warburg effect is the major metabolic hallmark of cancer. According to Warburg himself, the consequence of the Warburg effect is cell dedifferentiation. Therefore, reversing the Warburg effect might be an approach to restore cell differentiation in cancer. In this study, we used a mitochondrial uncoupler, niclosamide ethanolamine (NEN), to activate mitochondrial respiration, which induced neural differentiation in neuroblastoma cells. NEN treatment increased the nicotinamide adenine dinucleotide (NAD)+/NADH and pyruvate/lactate ratios and also the alpha-ketoglutarate (alpha-KG)/2- hydroxyglutarate (2-HG) ratio. Consequently, NEN treatment induced promoter CpG island demethylation and epigenetic landscape remodeling, activating the neural differentiation program. In addition, NEN treatment upregulated p53 but downregulated N-Myc and beta-catenin signaling in neuroblastoma cells. Importantly, even under hypoxia, NEN treatment remained effective in inhibiting 2-HG generation, promoting DNA demethylation, and suppressing hypoxia-inducible factor signaling. Dietary NEN intervention reduced tumor growth rate, 2-HG levels, and expression of N-Myc and beta-catenin in tumors in an orthotopic neuroblastoma mouse model. Integrative analysis indicated that NEN treatment upregulated favorable prognosis genes and downregulated unfavorable prognosis genes, which were defined using multiple neuroblastoma patient datasets. Altogether, these results suggest that mitochondrial uncoupling is an effective metabolic and epigenetic therapy for reversing the Warburg effect and inducing differentiation in neuroblastoma.

  View details for DOI 10.1158/0008-5472.CAN-22-1029

  View details for PubMedID 36318118

• A phase II study of talazoparib monotherapy in patients with wild-type BRCA1 and BRCA2 with a mutation in other homologous recombination genes. Nature cancer Gruber, J. J., Afghahi, A., Timms, K., DeWees, A., Gross, W., Aushev, V. N., Wu, H., Balcioglu, M., Sethi, H., Scott, D., Foran, J., McMillan, A., Ford, J. M., Telli, M. L. 2022

  Abstract

  Talazoparib, a PARP inhibitor, is active in germline BRCA1 and BRCA2 (gBRCA1/2)-mutant advanced breast cancer, but its activity beyond gBRCA1/2 is poorly understood. We conducted Talazoparib Beyond BRCA ( NCT02401347 ), an open-label phase II trial, to evaluate talazoparib in patients with pretreated advanced HER2-negative breast cancer (n=13) or other solid tumors (n=7) with mutations in homologous recombination (HR) pathway genes other than BRCA1 and BRCA2. In patients with breast cancer, four patients had a Response Evaluation Criteria in Solid Tumors (RECIST) partial response (overall response rate,31%), and three additional patients had stable disease of ≥6 months (clinical benefit rate, 54%). All patients with germline mutations in PALB2 (gPALB2; encoding partner and localizer of BRCA2) had treatment-associated tumor regression. Tumor or plasma circulating tumor DNA (ctDNA) HR deficiency (HRD) scores were correlated with treatment outcomes and were increased in all gPALB2 tumors. In addition, a gPALB2-associated mutational signature was associated with tumor response. Thus, talazoparib has been demonstrated to have efficacy in patients with advanced breast cancer who have gPALB2 mutations, showing activity in the context of HR pathway gene mutations beyond gBRCA1/2.

  View details for DOI 10.1038/s43018-022-00439-1

  View details for PubMedID 36253484

• Deciphering the Warburg effect: Redox is the key to tumor differentiation Jiang Haowen, Greathouse, R. L., He, B., Li, Y., Li, A. M., Forgo, B., Banuelos, S., Gruber, J., Shimada, H., Chiu, B., Ye, J. AMER ASSOC CANCER RESEARCH. 2022

  View details for Web of Science ID 000892509506053

• Serine starvation silences estrogen receptor signaling through histone hypoacetylation Li, A. M., Li, Y., He, B., Jiang, H., Lu, C., Gruber, J. J., Rankin, E. B., Ye, J. AMER ASSOC CANCER RESEARCH. 2022

  View details for Web of Science ID 000892509508045

• Rationally targeted anti-VISTA antibody that blockades the C-C' loop region can reverse VISTA immune suppression and remodel the immune microenvironment to potently inhibit tumor growth in an Fc independent manner. Journal for immunotherapy of cancer Thakkar, D., Paliwal, S., Dharmadhikari, B., Guan, S., Liu, L., Kar, S., Tulsian, N. K., Gruber, J. J., DiMascio, L., Paszkiewicz, K. H., Ingram, P. J., D Boyd-Kirkup, J. 2022; 10 (2)

  Abstract

  BACKGROUND: Despite significant progress in cancer immunotherapy in recent years, resistance to existing immune checkpoint therapies (ICT) is common. V-domain Ig suppressor of T cell activation (VISTA), a predominantly myeloid immune checkpoint regulator, represents a promising therapeutic target due to its role in suppressing proinflammatory antitumor responses in myeloid-enriched tumor microenvironments. However, uncertainty around the cognate VISTA ligand has made the development of effective anti-VISTA antibodies challenging. The expression of VISTA on normal immune cell subtypes argues for a neutralizing non-depleting antibody, however, previous reported anti-VISTA antibodies use IgG1 Fc isotypes that deplete VISTA+ cells by antibody dependent cellular cytotoxicity/complement dependent cytotoxicity and these antibodies have shown fast serum clearance and immune toxicities.METHOD: Here we used a rational antibody discovery approach to develop the first Fc-independent anti-VISTA antibody, HMBD-002, that binds a computationally predicted functional epitope within the C-C-loop, distinct from other known anti-VISTA antibodies. This epitope is species-conserved allowing robust in vitro and in vivo testing of HMBD-002 in human and murine models of immune activation and cancer including humanized mouse models.RESULTS: We demonstrate here that blockade by HMBD-002 inhibits VISTA binding to potential partners, including V-Set and Immunoglobulin domain containing 3, to reduce myeloid-derived suppression of T cell activity and prevent neutrophil migration. Analysis of immune cell milieu suggests that HMBD-002 treatment stimulates a proinflammatory phenotype characterized by a Th1/Th17 response, recapitulating a phenotype previously noted in VISTA knockout models. This mechanism of action is further supported by immune-competent syngenic and humanized mouse models of colorectal, breast and lung cancer where neutralizing VISTA, without depleting VISTA expressing cells, significantly inhibited tumor growth while decreasing infiltration of suppressive myeloid cells and increasing T cell activity. Finally, we did not observe either the fast serum clearance or immune toxicities that have been reported for IgG1 antibodies.CONCLUSION: In conclusion, we have shown that VISTA-induced immune suppression can be reversed by blockade of the functional C-C' loop region of VISTA with a first-in-class rationally targeted and non-depleting IgG4 isotype anti-VISTA antibody, HMBD-002. This antibody represents a highly promising novel therapy in the VISTA-suppressed ICT non-responder population.

  View details for DOI 10.1136/jitc-2021-003382

  View details for PubMedID 35131861

• Chromatin accessibility associates with protein-RNA correlation in human cancer. Nature communications Sanghi, A., Gruber, J. J., Metwally, A., Jiang, L., Reynolds, W., Sunwoo, J., Orloff, L., Chang, H. Y., Kasowski, M., Snyder, M. P. 2021; 12 (1): 5732

  Abstract

  Although alterations in chromatin structure are known to exist in tumors, how these alterations relate to molecular phenotypes in cancer remains to be demonstrated. Multi-omics profiling of human tumors can provide insight into how alterations in chromatin structure are propagated through the pathway of gene expression to result in malignant protein expression. We applied multi-omics profiling of chromatin accessibility, RNA abundance, and protein abundance to 36 human thyroid cancer primary tumors, metastases, and patient-match normal tissue. Through quantification of chromatin accessibility associated with active transcription units and global protein expression, we identify a local chromatin structure that is highly correlated with coordinated RNA and protein expression. In particular, we identify enhancers located within gene-bodies as predictive of correlated RNA and protein expression, that is independent of overall transcriptional activity. To demonstrate the generalizability of these findings we also identify similar results in an independent cohort of human breast cancers. Taken together, these analyses suggest that local enhancers, rather than distal enhancers, are likely most predictive of cancer gene expression phenotypes. This allows for identification of potential targets for cancer therapeutic approaches and reinforces the utility of multi-omics profiling as a methodology to understand human disease.

  View details for DOI 10.1038/s41467-021-25872-1

  View details for PubMedID 34593797

• A phase II clinical trial of talazoparib monotherapy for PALB2 mutation-associated advanced breast cancer. Gruber, J., Gross, W., McMillan, A., Ford, J. M., Telli, M. L. LIPPINCOTT WILLIAMS & WILKINS. 2021

  View details for DOI 10.1200/JCO.2021.39.15_suppl.TPS1109

  View details for Web of Science ID 000708120306163

• Genomic analysis from the talazoparib beyond BRCA clinical trial: Homologous recombination (HR) deficiency scores, loss-of-heterozygosity and mutations in non-BRCA1/2 mutant tumors with other HR mutations Gruber, J. J., Afghahi, A., Hatton, A., Gross, W., Foran, J., McMillan, A., Ford, J. M., Telli, M. L. AMER ASSOC CANCER RESEARCH. 2021

  View details for Web of Science ID 000618737700124

• Developing metabolic intervention strategies to reprogram neuroblastoma epigenome and overcome tumor resistance to differentiation therapy Jiang, H., Li, Y., Yip, M., Gruber, J., Li, A., Ye, J. AMER ASSOC CANCER RESEARCH. 2020

  View details for Web of Science ID 000596811500061

• Deciphering Warburg effect: hypoxia inhibits tumor cell differentiation through reducing acetyl-CoA generation and chromatin accessibility Ye, J., Li, Y., Gruber, J. J., Litzenburger, U. M., Zhou, Y., Miao, Y. R., LaGory, E. L., Li, A. M., Hu, Z., Hart, L. S., Maris, J. M., Chang, H. Y., Giaccia, A. J. AMER ASSOC CANCER RESEARCH. 2020

  View details for DOI 10.1158/1538-7445.AM2020-5708

  View details for Web of Science ID 000590059302011

• Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia. Cell death & disease Li, Y. n., Gruber, J. J., Litzenburger, U. M., Zhou, Y. n., Miao, Y. R., LaGory, E. L., Li, A. M., Hu, Z. n., Yip, M. n., Hart, L. S., Maris, J. M., Chang, H. Y., Giaccia, A. J., Ye, J. n. 2020; 11 (2): 102

  Abstract

  Despite the fact that Otto H. Warburg discovered the Warburg effect almost one hundred years ago, why cancer cells waste most of the glucose carbon as lactate remains an enigma. Warburg proposed a connection between the Warburg effect and cell dedifferentiation. Hypoxia is a common tumor microenvironmental stress that induces the Warburg effect and blocks tumor cell differentiation. The underlying mechanism by which this occurs is poorly understood, and no effective therapeutic strategy has been developed to overcome this resistance to differentiation. Using a neuroblastoma differentiation model, we discovered that hypoxia repressed cell differentiation through reducing cellular acetyl-CoA levels, leading to reduction of global histone acetylation and chromatin accessibility. The metabolic switch triggering this global histone hypoacetylation was the induction of pyruvate dehydrogenase kinases (PDK1 and PDK3). Inhibition of PDKs using dichloroacetate (DCA) restored acetyl-CoA generation and histone acetylation under hypoxia. Knocking down PDK1 induced neuroblastoma cell differentiation, highlighting the critical role of PDK1 in cell fate control. Importantly, acetate or glycerol triacetate (GTA) supplementation restored differentiation markers expression and neuron differentiation under hypoxia. Moreover, ATAC-Seq analysis demonstrated that hypoxia treatment significantly reduced chromatin accessibility at RAR/RXR binding sites, which can be restored by acetate supplementation. In addition, hypoxia-induced histone hypermethylation by increasing 2-hydroxyglutarate (2HG) and reducing α-ketoglutarate (αKG). αKG supplementation reduced histone hypermethylation upon hypoxia, but did not restore histone acetylation or differentiation markers expression. Together, these findings suggest that diverting pyruvate flux away from acetyl-CoA generation to lactate production is the key mechanism that Warburg effect drives dedifferentiation and tumorigenesis. We propose that combining differentiation therapy with acetate/GTA supplementation might represent an effective therapy against neuroblastoma.

  View details for DOI 10.1038/s41419-020-2303-9

  View details for PubMedID 32029721

• Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility. Nature biomedical engineering Stowers, R. S., Shcherbina, A., Israeli, J., Gruber, J. J., Chang, J., Nam, S., Rabiee, A., Teruel, M. N., Snyder, M. P., Kundaje, A., Chaudhuri, O. 2019

  Abstract

  In breast cancer, the increased stiffness of the extracellular matrix is a key driver of malignancy. Yet little is known about the epigenomic changes that underlie the tumorigenic impact of extracellular matrix mechanics. Here, we show in a three-dimensional culture model of breast cancer that stiff extracellular matrix induces a tumorigenic phenotype through changes in chromatin state. We found that increased stiffness yielded cells with more wrinkled nuclei and with increased lamina-associated chromatin, that cells cultured in stiff matrices displayed more accessible chromatin sites, which exhibited footprints of Sp1 binding, and that this transcription factor acts along with the histone deacetylases 3 and 8 to regulate the induction of stiffness-mediated tumorigenicity. Just as cell culture on soft environments or in them rather than on tissue-culture plastic better recapitulates the acinar morphology observed in mammary epithelium in vivo, mammary epithelial cells cultured on soft microenvironments or in them also more closely replicate the in vivo chromatin state. Our results emphasize the importance of culture conditions for epigenomic studies, and reveal that chromatin state is a critical mediator of mechanotransduction.

  View details for DOI 10.1038/s41551-019-0420-5

  View details for PubMedID 31285581

• HAT1 Coordinates Histone Production and Acetylation via H4 Promoter Binding. Molecular cell Gruber, J. J., Geller, B., Lipchik, A. M., Chen, J., Salahudeen, A. A., Ram, A. N., Ford, J. M., Kuo, C. J., Snyder, M. P. 2019

  Abstract

  The energetic costs of duplicating chromatin are large and therefore likely depend on nutrient sensing checkpoints and metabolic inputs. By studying chromatin modifiers regulated by epithelial growth factor, we identified histone acetyltransferase 1 (HAT1) as an induced gene that enhances proliferation through coordinating histone production, acetylation, and glucose metabolism. In addition to its canonical role as a cytoplasmic histone H4 acetyltransferase, we isolated a HAT1-containing complex bound specifically at promoters of H4 genes. HAT1-dependent transcription of H4 genes required an acetate-sensitive promoter element. HAT1 expression was critical for S-phase progression and maintenance of H3 lysine 9 acetylation at proliferation-associated genes, including histone genes. Therefore, these data describe a feedforward circuit whereby HAT1 captures acetyl groups on nascent histones and drives H4 production by chromatin binding to support chromatin replication and acetylation. These findings have important implications for human disease, since high HAT1 levels associate with poor outcomes across multiple cancer types.

  View details for DOI 10.1016/j.molcel.2019.05.034

  View details for PubMedID 31278053

• Talazoparib beyond BRCA: A phase II trial of talazoparib monotherapy in BRCA1 and BRCA2 wild-type patients with advanced HER2-negative breast cancer or other solid tumors with a mutation in homologous recombination (HR) pathway genes. Gruber, J., Afghahi, A., Hatton, A., Scott, D., McMillan, A., Ford, J. M., Telli, M. L. AMER SOC CLINICAL ONCOLOGY. 2019

  View details for DOI 10.1200/JCO.2019.37.15_suppl.3006

  View details for Web of Science ID 000487345804596

• Association of Tumor Infiltrating Lymphocytes with Homologous Recombination Deficiency and BRCA1/2 Status in Patients with Early Triple-Negative Breast Cancer: A Pooled Analysis. Clinical cancer research : an official journal of the American Association for Cancer Research Telli, M. L., Chu, C. n., Badve, S. S., Vinayak, S. n., Silver, D. P., Isakoff, S. J., Kaklamani, V. n., Gradishar, W. n., Stearns, V. n., Connolly, R. M., Ford, J. M., Gruber, J. J., Adams, S. n., Garber, J. n., Tung, N. n., Neff, C. n., Bernhisel, R. n., Timms, K. M., Richardson, A. L. 2019

  Abstract

  Patients with triple-negative breast cancer (TNBC) with homologous recombination deficient tumors achieve significantly higher pathologic complete response (pCR) rates when treated with neoadjuvant platinum-based therapy. Tumor infiltrating lymphocytes (TILs) are prognostic and predictive of chemotherapy benefit in early stage TNBC. The relationship between TILs, BRCA1/2 mutation status and Homologous Recombination Deficiency (HRD) status in TNBC remains unclear.We performed a pooled analysis of 5 phase II studies that included patients with TNBC treated with neoadjuvant platinum-based chemotherapy to evaluate the association of TILs with HRD status (Myriad Genetics) and tumor BRCA1/2 mutation status. Further, the relationship between pathologic response assessed using the residual cancer burden (RCB) index and HRD status with adjustment for TILs was evaluated.Among 161 patients, stromal TIL (sTIL) density was not significantly associated with HRD status (p=0.107) or tumor BRCA1/2 mutation status (p=0.391). In multivariate analyses, sTIL density (OR 1.23, 95% CI 0.94-1.61, p=0.139) was not associated with pCR, but was associated with RCB 0/I status (OR 1.62, 95% CI 1.20-2.28, p=0.001). HRD was significantly associated with both pCR (OR 12.09, 95% CI 4.11-44.29, p= 7.82 x10-7) and RCB 0/I (OR 10.22, 95% CI 4.11-28.75, p= 1.09 x10-7) in these models.In patients with TNBC treated with neoadjuvant platinum-based therapy, TIL density was not significantly associated with either tumor BRCA1/2 mutation status or HRD status. In this pooled analysis, HRD and sTIL density were independently associated with treatment response, with HRD status being the strongest predictor.

  View details for DOI 10.1158/1078-0432.CCR-19-0664

  View details for PubMedID 31796517

• Chromatin Remodeling in Response to BRCA2-Crisis. Cell reports Gruber, J. J., Chen, J. n., Geller, B. n., Jäger, N. n., Lipchik, A. M., Wang, G. n., Kurian, A. W., Ford, J. M., Snyder, M. P. 2019; 28 (8): 2182–93.e6

  Abstract

  Individuals with a single functional copy of the BRCA2 tumor suppressor have elevated risks for breast, ovarian, and other solid tumor malignancies. The exact mechanisms of carcinogenesis due to BRCA2 haploinsufficiency remain unclear, but one possibility is that at-risk cells are subject to acute periods of decreased BRCA2 availability and function ("BRCA2-crisis"), which may contribute to disease. Here, we establish an in vitro model for BRCA2-crisis that demonstrates chromatin remodeling and activation of an NF-κB survival pathway in response to transient BRCA2 depletion. Mechanistically, we identify BRCA2 chromatin binding, histone acetylation, and associated transcriptional activity as critical determinants of the epigenetic response to BRCA2-crisis. These chromatin alterations are reflected in transcriptional profiles of pre-malignant tissues from BRCA2 carriers and, therefore, may reflect natural steps in human disease. By modeling BRCA2-crisis in vitro, we have derived insights into pre-neoplastic molecular alterations that may enhance the development of preventative therapies.

  View details for DOI 10.1016/j.celrep.2019.07.057

  View details for PubMedID 31433991

• High-Resolution Bisulfite-Sequencing of Peripheral Blood DNA Methylation in Early-Onset and Familial Risk Breast Cancer Patients. Clinical cancer research : an official journal of the American Association for Cancer Research Chen, J. n., Haanpää, M. K., Gruber, J. J., Jäger, N. n., Ford, J. M., Snyder, M. P. 2019

  Abstract

  Understanding and explaining hereditary predisposition to cancer has focused on the genetic etiology of the disease. However, mutations in known genes associated with breast cancer, such as BRCA1 and BRCA2, account for less than 25% of familial cases of breast cancer. Recently, specific epigenetic modifications at BRCA1 have been shown to promote hereditary breast cancer, but the broader potential for epigenetic contribution to hereditary breast cancer is not yet well understood.We examined DNA methylation through deep bisulfite sequencing of CpG islands and known promoter or regulatory regions in peripheral blood DNA from 99 familial or early-onset breast or ovarian cancer patients, 6 unaffected BRCA-mutation carriers, and 49 unaffected controls.In 9% of patients, we observed altered methylation in the promoter regions of genes known to be involved in cancer including hypermethylation at the tumor suppressor PTEN and hypomethylation at the proto-oncogene TEX14 These alterations occur in the form of allelic methylation that span up to hundreds of base-pairs in length.Our observations suggest a broader role for DNA methylation in early-onset, familial risk breast cancer. Further studies are warranted to clarify these mechanisms and the benefits of DNA methylation screening for early risk prediction of familial cancers.

  View details for DOI 10.1158/1078-0432.CCR-18-2423

  View details for PubMedID 31175093

• Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid. Scientific reports Liu, Q., Van Bortle, K., Zhang, Y., Zhao, M., Zhang, J. Z., Geller, B. S., Gruber, J. J., Jiang, C., Wu, J. C., Snyder, M. P. 2018; 8 (1): 12960

  Abstract

  13-cis-retinoic acid (isotretinoin, INN) is an oral pharmaceutical drug used for the treatment of skin acne, and is also a known teratogen. In this study, the molecular mechanisms underlying INN-induced developmental toxicity during early cardiac differentiation were investigated using both human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs). Pre-exposure of hiPSCs and hESCs to a sublethal concentration of INN did not influence cell proliferation and pluripotency. However, mesodermal differentiation was disrupted when INN was included in the medium during differentiation. Transcriptomic profiling by RNA-seq revealed that INN exposure leads to aberrant expression of genes involved in several signaling pathways that control early mesoderm differentiation, such as TGF-beta signaling. In addition, genome-wide chromatin accessibility profiling by ATAC-seq suggested that INN-exposure leads to enhanced DNA-binding of specific transcription factors (TFs), including HNF1B, SOX10 and NFIC, often in close spatial proximity to genes that are dysregulated in response to INN treatment. Altogether, these results identify potential molecular mechanisms underlying INN-induced perturbation during mesodermal differentiation in the context of cardiac development. This study further highlights the utility of human stem cells as an alternative system for investigating congenital diseases of newborns that arise as a result of maternal drug exposure during pregnancy.

  View details for PubMedID 30154523

• Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid SCIENTIFIC REPORTS Liu, Q., Van Bortle, K., Zhang, Y., Zhao, M., Zhang, J. Z., Geller, B. S., Gruber, J. J., Jiang, C., Wu, J. C., Snyder, M. P. 2018; 8

  View details for DOI 10.1038/s41598-018-31192-0

  View details for Web of Science ID 000442917500032

• VISTA immune checkpoint deregulation in human triple-negative breast cancer Gruber, J. J., Juntilla, M. M., Yang, S., Geller, B., Jager, N., Lin, C., Lipchik, A. M., Chen, J., Ram, A., Vinayak, S., Telli, M. L., West, R. B., Ford, J. M., Snyder, M. P. AMER ASSOC CANCER RESEARCH. 2018

  View details for DOI 10.1158/1538-7445.AM2018-4749

  View details for Web of Science ID 000468819503369

• Outstanding Questions in the Clinical Management of Triple-Negative Breast Cancer. Journal of oncology practice Gruber, J. J., Telli, M. L. 2017; 13 (5): 305-307

  View details for DOI 10.1200/JOP.2017.023341

  View details for PubMedID 28489983

• Association of AHSG with alopecia and mental retardation (APMR) syndrome. Human genetics Reza Sailani, M., Jahanbani, F., Nasiri, J., Behnam, M., Salehi, M., Sedghi, M., Hoseinzadeh, M., Takahashi, S., Zia, A., Gruber, J., Lynch, J. L., Lam, D., Winkelmann, J., Amirkiai, S., Pang, B., Rego, S., Mazroui, S., Bernstein, J. A., Snyder, M. P. 2017; 136 (3): 287-296

  Abstract

  Alopecia with mental retardation syndrome (APMR) is a very rare autosomal recessive condition that is associated with total or partial absence of hair from the scalp and other parts of the body as well as variable intellectual disability. Here we present whole-exome sequencing results of a large consanguineous family segregating APMR syndrome with seven affected family members. Our study revealed a novel predicted pathogenic, homozygous missense mutation in the AHSG (OMIM 138680) gene (AHSG: NM_001622:exon7:c.950G>A:p.Arg317His). The variant is predicted to affect a region of the protein required for protein processing and disrupts a phosphorylation motif. In addition, the altered protein migrates with an aberrant size relative to healthy individuals. Consistent with the phenotype, AHSG maps within APMR linkage region 1 (APMR 1) as reported before, and falls within runs of homozygosity (ROH). Previous families with APMR syndrome have been studied through linkage analyses and the linkage resolution did not allow pointing out to a single gene candidate. Our study is the first report to identify a homozygous missense mutation for APMR syndrome through whole-exome sequencing.

  View details for DOI 10.1007/s00439-016-1756-5

  View details for PubMedID 28054173

• Differentiated Thyroid Cancer: Focus on Emerging Treatments for Radioactive Iodine-Refractory Patients ONCOLOGIST Gruber, J. J., Colevas, A. D. 2015; 20 (2): 113-126

  Abstract

  The treatment of differentiated thyroid cancer refractory to radioactive iodine (RAI) had been hampered by few effective therapies. Recently, tyrosine kinase inhibitors (TKIs) have shown activity in this disease. Clinical guidance on the use of these agents in RAI-refractory thyroid cancer is warranted.Molecular mutations found in RAI-refractory thyroid cancer are summarized. Recent phase II and III clinical trial data for TKIs axitinib, lenvatinib, motesanib, pazopanib, sorafenib, sunitinib, and vandetinib are reviewed including efficacy and side effect profiles. Molecular targets and potencies of these agents are compared. Inhibitors of BRAF, mammalian target of rapamycin, and MEK are considered.Routine testing for molecular alterations prior to therapy is not yet recommended. TKIs produce progression-free survival of approximately 1 year (range: 7.7-19.6 months) and partial response rates of up to 50% by Response Evaluation Criteria in Solid Tumors. Pazopanib and lenvatinib are the most active agents. The majority of patients experienced tumor shrinkage with TKIs. Common adverse toxicities affect dermatologic, gastrointestinal, and cardiovascular systems.Multiple TKIs have activity in RAI-refractory differentiated thyroid cancer. Selection of a targeted agent should depend on disease trajectory, side effect profile, and goals of therapy.

  View details for DOI 10.1634/theoncologist.2014-0313

  View details for Web of Science ID 000351915500007

  View details for PubMedID 25616432

  View details for PubMedCentralID PMC4319630

• Long-lived microRNA-Argonaute complexes in quiescent cells can be activated to regulate mitogenic responses PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Olejniczak, S. H., La Rocca, G., Gruber, J. J., Thompson, C. B. 2013; 110 (1): 157-162

  Abstract

  Cellular proliferation depends on the integration of mitogenic stimuli with environmental conditions. Increasing evidence suggests that microRNAs play a regulatory role in this integration. Here we show that during periods of cellular quiescence, mature microRNAs are stabilized and stored in Argonaute protein complexes that can be activated by mitogenic stimulation to repress mitogen-stimulated targets, thus influencing subsequent cellular responses. In quiescent cells, the majority of microRNAs exist in low molecular weight, Argonaute protein-containing complexes devoid of essential components of the RNA-induced silencing complex (RISC). For at least 3 wk, this pool of Argonaute-associated microRNAs is stable and can be recruited into RISC complexes subsequent to mitogenic stimulation. Using several model systems, we demonstrate that stable Argonaute protein-associated small RNAs are capable of repressing mitogen-induced transcripts. Therefore, mature microRNAs may represent a previously unappreciated form of cellular memory that allows cells to retain posttranscriptional regulatory information over extended periods of cellular quiescence.

  View details for DOI 10.1073/pnas.1219958110

  View details for Web of Science ID 000313630300043

  View details for PubMedID 23248281

• Ars2 Promotes Proper Replication-Dependent Histone mRNA 3 ' End Formation MOLECULAR CELL Gruber, J. J., Olejniczak, S. H., Yong, J., La Rocca, G., Dreyfuss, G., Thompson, C. B. 2012; 45 (1): 87-98

  Abstract

  Ars2 is a component of the nuclear cap-binding complex that contributes to microRNA biogenesis and is required for cellular proliferation. Here, we expand on the repertoire of Ars2-dependent microRNAs and determine that Ars2 regulates a number of mRNAs, the largest defined subset of which code for histones. Histone mRNAs are unique among mammalian mRNAs because they are not normally polyadenylated but, rather, are cleaved following a 3' stem loop. A significant reduction in correctly processed histone mRNAs was observed following Ars2 depletion, concurrent with an increase in polyadenylated histone transcripts. Furthermore, Ars2 physically associated with histone mRNAs and the noncoding RNA 7SK. Knockdown of 7SK led to an enhanced ratio of cleaved to polyadenylated histone transcripts, an effect dependent on Ars2. Together, the data demonstrate that Ars2 contributes to histone mRNA 3' end formation and expression and these functional properties of Ars2 are negatively regulated by interaction with 7SK RNA.

  View details for DOI 10.1016/j.molcel.2011.12.020

  View details for Web of Science ID 000299301300012

  View details for PubMedID 22244333

  View details for PubMedCentralID PMC3269315

• Hypoxia promotes isocitrate dehydrogenase-dependent carboxylation of alpha-ketoglutarate to citrate to support cell growth and viability PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wise, D. R., Ward, P. S., Shay, J. E., Cross, J. R., Gruber, J. J., Sachdeva, U. M., Platt, J. M., DeMatteo, R. G., Simon, M. C., Thompson, C. B. 2011; 108 (49): 19611-19616

  Abstract

  Citrate is a critical metabolite required to support both mitochondrial bioenergetics and cytosolic macromolecular synthesis. When cells proliferate under normoxic conditions, glucose provides the acetyl-CoA that condenses with oxaloacetate to support citrate production. Tricarboxylic acid (TCA) cycle anaplerosis is maintained primarily by glutamine. Here we report that some hypoxic cells are able to maintain cell proliferation despite a profound reduction in glucose-dependent citrate production. In these hypoxic cells, glutamine becomes a major source of citrate. Glutamine-derived α-ketoglutarate is reductively carboxylated by the NADPH-linked mitochondrial isocitrate dehydrogenase (IDH2) to form isocitrate, which can then be isomerized to citrate. The increased IDH2-dependent carboxylation of glutamine-derived α-ketoglutarate in hypoxia is associated with a concomitant increased synthesis of 2-hydroxyglutarate (2HG) in cells with wild-type IDH1 and IDH2. When either starved of glutamine or rendered IDH2-deficient by RNAi, hypoxic cells are unable to proliferate. The reductive carboxylation of glutamine is part of the metabolic reprogramming associated with hypoxia-inducible factor 1 (HIF1), as constitutive activation of HIF1 recapitulates the preferential reductive metabolism of glutamine-derived α-ketoglutarate even in normoxic conditions. These data support a role for glutamine carboxylation in maintaining citrate synthesis and cell growth under hypoxic conditions.

  View details for DOI 10.1073/pnas.1117773108

  View details for Web of Science ID 000297683800041

  View details for PubMedID 22106302

• Loss of the Birt-Hogg-Dube tumor suppressor results in apoptotic resistance due to aberrant TGF beta-mediated transcription ONCOGENE Cash, T. P., Gruber, J. J., Hartman, T. R., Henske, E. P., Simon, M. C. 2011; 30 (22): 2534-2546

  Abstract

  Birt-Hogg-Dubé (BHD) syndrome is an inherited cancer susceptibility disease characterized by skin and kidney tumors, as well as cystic lung disease, which results from loss-of-function mutations in the BHD gene. BHD is also inactivated in a significant fraction of patients with sporadic renal cancers and idiopathic cystic lung disease, and little is known about its mode of action. To investigate the molecular and cellular basis of BHD tumor suppressor activity, we generated mutant Bhd mice and embryonic stem cell lines. BHD-deficient cells exhibited defects in cell-intrinsic apoptosis that correlated with reduced expression of the BH3-only protein Bim, which was similarly observed in all human and murine BHD-related tumors examined. We further demonstrate that Bim deficiency in Bhd(-/-) cells is not a consequence of elevated mTOR or ERK activity, but results instead from reduced Bim transcription associated with a general loss of TGFβ-mediated transcription and chromatin modifications. In aggregate, this work identifies a specific tumor suppressive mechanism for BHD in regulating TGFβ-dependent transcription and apoptosis, which has implications for the development of targeted therapies.

  View details for DOI 10.1038/onc.2010.628

  View details for Web of Science ID 000291198400005

  View details for PubMedID 21258407

• Imatinib resistance associated with BCR-ABL upregulation is dependent on HIF-1 alpha-induced metabolic reprograming ONCOGENE Zhao, F., Mancuso, A., Bui, T. V., Tong, X., Gruber, J. J., Swider, C. R., Sanchez, P. V., Lum, J. J., Sayed, N., Melo, J. V., Perl, A. E., Carroll, M., Tuttle, S. W., Thompson, C. B. 2010; 29 (20): 2962-2972

  Abstract

  As chronic myeloid leukemia (CML) progresses from the chronic phase to blast crisis, the levels of BCR-ABL increase. In addition, blast-transformed leukemic cells display enhanced resistance to imatinib in the absence of BCR-ABL-resistance mutations. In this study, we show that when BCR-ABL-transformed cell lines were selected for imatinib resistance in vitro, the cells that grew out displayed a higher BCR-ABL expression comparable to the increase seen in accelerated forms of the disease. This enhanced expression of BCR-ABL was associated with an increased rate of glycolysis but with a decreased rate of proliferation. The higher level of BCR-ABL expression in the selected cells correlated with a nonhypoxic induction of hypoxia-inducible factor-1alpha (HIF-1alpha) that was required for cells to tolerate enhanced BCR-ABL signaling. HIF-1alpha induction resulted in an enhanced rate of glycolysis but with reduced glucose flux through both the tricarboxylic acid cycle and the oxidative arm of the pentose phosphate pathway (PPP). The reduction in oxidative PPP-mediated ribose synthesis was compensated by the HIF-1alpha-dependent activation of the nonoxidative PPP enzyme, transketolase, in imatinib-resistant CML cells. In both primary cultures of cells from patients exhibiting blast transformation and in vivo xenograft tumors, use of oxythiamine, which can inhibit both the pyruvate dehydrogenase complex and transketolase, resulted in enhanced imatinib sensitivity of tumor cells. Together, these results suggest that oxythiamine can enhance imatinib efficacy in patients who present an accelerated form of the disease.

  View details for DOI 10.1038/onc.2010.67

  View details for Web of Science ID 000277890400007

  View details for PubMedID 20228846

• The glucose-responsive transcription factor ChREBP contributes to glucose-dependent anabolic synthesis and cell proliferation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Tong, X., Zhao, F., Mancuso, A., Gruber, J. J., Thompson, C. B. 2009; 106 (51): 21660-21665

  Abstract

  Tumor cells are metabolically reprogrammed to fuel cell proliferation. Most transformed cells take up high levels of glucose and produce ATP through aerobic glycolysis. In cells exhibiting aerobic glycolysis, a significant fraction of glucose carbon is also directed into de novo lipogenesis and nucleotide biosynthesis. The glucose-responsive transcription factor carbohydrate responsive element binding protein (ChREBP) was previously shown to be important for redirecting glucose metabolism in support of lipogenesis in nonproliferating hepatocytes. However, whether it plays a more generalized role in reprogramming metabolism during cell proliferation has not been examined. Here, we demonstrated that the expression of ChREBP can be induced in response to mitogenic stimulation and that the induction of ChREBP is required for efficient cell proliferation. Suppression of ChREBP resulted in diminished aerobic glycolysis, de novo lipogenesis, and nucleotide biosynthesis, but stimulated mitochondrial respiration, suggesting a metabolic switch from aerobic glycolysis to oxidative phosphorylation. Cells in which ChREBP was suppressed by RNAi exhibited p53 activation and cell cycle arrest. In vivo, suppression of ChREBP led to a p53-dependent reduction in tumor growth. These results demonstrate that ChREBP plays a key role both in redirecting glucose metabolism to anabolic pathways and suppressing p53 activity.

  View details for DOI 10.1073/pnas.0911316106

  View details for Web of Science ID 000272994200037

  View details for PubMedID 19995986

  View details for PubMedCentralID PMC2799883

• Ars2 Links the Nuclear Cap-Binding Complex to RNA Interference and Cell Proliferation CELL Gruber, J. J., Zatechka, D. S., Sabin, L. R., Yong, J., Lum, J. J., Kong, M., Zong, W., Zhang, Z., Lau, C., Rawlings, J., Cherry, S., Ihle, J. N., Dreyfuss, G., Thompson, C. B. 2009; 138 (2): 328-339

  Abstract

  Here we identify a component of the nuclear RNA cap-binding complex (CBC), Ars2, that is important for miRNA biogenesis and critical for cell proliferation. Unlike other components of the CBC, Ars2 expression is linked to the proliferative state of the cell. Deletion of Ars2 is developmentally lethal, and deletion in adult mice led to bone marrow failure whereas parenchymal organs composed of nonproliferating cells were unaffected. Depletion of Ars2 or CBP80 from proliferating cells impaired miRNA-mediated repression and led to alterations in primary miRNA processing in the nucleus. Ars2 depletion also reduced the levels of several miRNAs, including miR-21, let-7, and miR-155, that are implicated in cellular transformation. These findings provide evidence for a role for Ars2 in RNA interference regulation during cell proliferation.

  View details for DOI 10.1016/j.cell.2009.04.046

  View details for Web of Science ID 000268277000014

  View details for PubMedID 19632182

  View details for PubMedCentralID PMC2717034

• Ars2 Regulates Both miRNA- and siRNA-Dependent Silencing and Suppresses RNA Virus Infection in Drosophila CELL Sabin, L. R., Zhou, R., Gruber, J. J., Lukinova, N., Bambina, S., Berman, A., Lau, C., Thompson, C. B., Cherry, S. 2009; 138 (2): 340-351

  Abstract

  Intrinsic immune responses autonomously inhibit viral replication and spread. One pathway that restricts viral infection in plants and insects is RNA interference (RNAi), which targets and degrades viral RNA to limit infection. To identify additional genes involved in intrinsic antiviral immunity, we screened Drosophila cells for modulators of viral infection using an RNAi library. We identified Ars2 as a key component of Drosophila antiviral immunity. Loss of Ars2 in cells, or in flies, increases susceptibility to RNA viruses. Consistent with its antiviral properties, we found that Ars2 physically interacts with Dcr-2, modulates its activity in vitro, and is required for siRNA-mediated silencing. Furthermore, we show that Ars2 plays an essential role in miRNA-mediated silencing, interacting with the Microprocessor and stabilizing pri-miRNAs. The identification of Ars2 as a player in these small RNA pathways provides new insight into the biogenesis of small RNAs that may be extended to other systems.

  View details for DOI 10.1016/j.cell.2009.04.045

  View details for Web of Science ID 000268277000015

  View details for PubMedID 19632183

  View details for PubMedCentralID PMC2717035

• DR5 knockout mice are compromised in radiation-induced apoptosis MOLECULAR AND CELLULAR BIOLOGY Finnberg, N., Gruber, J. J., Fei, P. W., Rudolph, D., Bric, A., Kim, S. H., Burns, T. F., Ajuha, H., Page, R., Wu, G. S., Chen, Y. H., McKenna, W. G., Bernhard, E., Lowe, S., Mak, T., El-Deiry, W. S. 2005; 25 (5): 2000-2013

  Abstract

  DR5 (also called TRAIL receptor 2 and KILLER) is an apoptosis-inducing membrane receptor for tumor necrosis factor-related apoptosis-inducing ligand (also called TRAIL and Apo2 ligand). DR5 is a transcriptional target of p53, and its overexpression induces cell death in vitro. However, the in vivo biology of DR5 has remained largely unexplored. To better understand the role of DR5 in development and in adult tissues, we have created a knockout mouse lacking DR5. This mouse is viable and develops normally with the exception of having an enlarged thymus. We show that DR5 is not expressed in developing embryos but is present in the decidua and chorion early in development. DR5-null mouse embryo fibroblasts expressing E1A are resistant to treatment with TRAIL, suggesting that DR5 may be the primary proapoptotic receptor for TRAIL in the mouse. When exposed to ionizing radiation, DR5-null tissues exhibit reduced amounts of apoptosis compared to wild-type thymus, spleen, Peyer's patches, and the white matter of the brain. In the ileum, colon, and stomach, DR5 deficiency was associated with a subtle phenotype of radiation-induced cell death. These results indicate that DR5 has a limited role during embryogenesis and early stages of development but plays an organ-specific role in the response to DNA-damaging stimuli.

  View details for DOI 10.1128/MCB.25.5.2000-2003.2005

  View details for Web of Science ID 000227085700036

  View details for PubMedID 15713653

  View details for PubMedCentralID PMC549384