Joydeep Bhadury

All Publications

• BET bromodomain inhibitors synergize with ATR inhibitors in melanoma in melanoma. Cell death & disease Muralidharan, S. V., Einarsdottir, B. O., Bhadury, J., Lindberg, M. F., Wu, J., Campeau, E., Bagge, R. O., Stierner, U., Ny, L., Nilsson, L. M., Nilsson, J. A. 2017; 8 (8): e2982

  Abstract

  Metastatic malignant melanoma continues to be a challenging disease despite clinical translation of the comprehensive understanding of driver mutations and how melanoma cells evade immune attack. In Myc-driven lymphoma, efficacy of epigenetic inhibitors of the bromodomain and extra-terminal domain (BET) family of bromodomain proteins can be enhanced by combination therapy with inhibitors of the DNA damage response kinase ATR. Whether this combination is active in solid malignancies like melanoma, and how it relates to immune therapy, has not previously investigated. To test efficacy and molecular consequences of combination therapies cultured melanoma cells were used. To assess tumor responses to therapies in vivo we use patient-derived xenografts and B6 mice transplanted with B16F10 melanoma cells. Concomitant inhibition of BET proteins and ATR of cultured melanoma cells resulted in similar effects as recently shown in lymphoma, such as induction of apoptosis and p62, implicated in autophagy, senescence-associated secretory pathway and ER stress. In vivo, apoptosis and suppression of subcutaneous growth of patient-derived melanoma and B16F10 cells were observed. Our data suggest that ATRI/BETI combination therapies are effective in melanoma.

  View details for DOI 10.1038/cddis.2017.383

  View details for PubMedID 28796244

  View details for PubMedCentralID PMC5596569

• Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Alaei-Mahabadi, B., Bhadury, J., Karlsson, J. W., Nilsson, J. A., Larsson, E. 2016; 113 (48): 13768-13773

  Abstract

  Tumor genomes are mosaics of somatic structural variants (SVs) that may contribute to the activation of oncogenes or inactivation of tumor suppressors, for example, by altering gene copy number amplitude. However, there are multiple other ways in which SVs can modulate transcription, but the general impact of such events on tumor transcriptional output has not been systematically determined. Here we use whole-genome sequencing data to map SVs across 600 tumors and 18 cancers, and investigate the relationship between SVs, copy number alterations (CNAs), and mRNA expression. We find that 34% of CNA breakpoints can be clarified structurally and that most amplifications are due to tandem duplications. We observe frequent swapping of strong and weak promoters in the context of gene fusions, and find that this has a measurable global impact on mRNA levels. Interestingly, several long noncoding RNAs were strongly activated by this mechanism. Additionally, SVs were confirmed in telomere reverse transcriptase (TERT) upstream regions in several cancers, associated with elevated TERT mRNA levels. We also highlight high-confidence gene fusions supported by both genomic and transcriptomic evidence, including a previously undescribed paired box 8 (PAX8)-nuclear factor, erythroid 2 like 2 (NFE2L2) fusion in thyroid carcinoma. In summary, we combine SV, CNA, and expression data to provide insights into the structural basis of CNAs as well as the impact of SVs on gene expression in tumors.

  View details for DOI 10.1073/pnas.1606220113

  View details for Web of Science ID 000388835700070

  View details for PubMedID 27856756

  View details for PubMedCentralID PMC5137778

• BET and HDAC inhibitors induce similar genes and biological effects and synergize to kill in Myc-induced murine lymphoma Bhadury, J., Nilsson, L. M., Somsundar, M., Green, L. C., Keller, U. B., McLure, K. G., Nilsson, J. A. AMER ASSOC CANCER RESEARCH. 2016

  View details for DOI 10.1158/1557-3125.MYC15-B26

  View details for Web of Science ID 000390241400079

• BET bromodomain inhibitors synergize with ATR inhibitors to induce DNA damage, apoptosis, senescence-associated secretory pathway and ER stress in Myc-induced lymphoma cells ONCOGENE Muralidharan, S. V., Bhadury, J., Nilsson, L. M., Green, L. C., McLure, K. G., Nilsson, J. A. 2016; 35 (36): 4689-4697

  Abstract

  Inhibiting the bromodomain and extra-terminal (BET) domain family of epigenetic reader proteins has been shown to have potent anti-tumoral activity, which is commonly attributed to suppression of transcription. In this study, we show that two structurally distinct BET inhibitors (BETi) interfere with replication and cell cycle progression of murine Myc-induced lymphoma cells at sub-lethal concentrations when the transcriptome remains largely unaltered. This inhibition of replication coincides with a DNA-damage response and enhanced sensitivity to inhibitors of the upstream replication stress sensor ATR in vitro and in mouse models of B-cell lymphoma. Mechanistically, ATR and BETi combination therapy cause robust transcriptional changes of genes involved in cell death, senescence-associated secretory pathway, NFkB signaling and ER stress. Our data reveal that BETi can potentiate the cell stress and death caused by ATR inhibitors. This suggests that ATRi can be used in combination therapies of lymphomas without the use of genotoxic drugs.

  View details for DOI 10.1038/onc.2015.521

  View details for Web of Science ID 000383324700002

  View details for PubMedID 26804177

• Hypoxia-regulated gene expression explains differences between melanoma cell line-derived xenografts and patient-derived xenografts ONCOTARGET Bhadury, J., Einarsdottir, B. O., Podraza, A., Bagge, R. O., Stierner, U., Ny, L., Lopez, M. D., Nilsson, J. A. 2016; 7 (17): 23801-23811

  Abstract

  Cell line-derived xenografts (CDXs) are an integral part of drug efficacy testing during development of new pharmaceuticals against cancer but their accuracy in predicting clinical responses in patients have been debated. Patient-derived xenografts (PDXs) are thought to be more useful for predictive biomarker identification for targeted therapies, including in metastatic melanoma, due to their similarities to human disease. Here, tumor biopsies from fifteen patients and ten widely-used melanoma cell lines were transplanted into immunocompromised mice to generate PDXs and CDXs, respectively. Gene expression profiles generated from the tumors of these PDXs and CDXs clustered into distinct groups, despite similar mutational signatures. Hypoxia-induced gene signatures and overexpression of the hypoxia-regulated miRNA hsa-miR-210 characterized CDXs. Inhibition of hsa-miR-210 with decoys had little phenotypic effect in vitro but reduced sensitivity to MEK1/2 inhibition in vivo, suggesting down-regulation of this miRNA could result in development of resistance to MEK inhibitors.

  View details for DOI 10.18632/oncotarget.8181

  View details for Web of Science ID 000377706200062

  View details for PubMedID 27009863

  View details for PubMedCentralID PMC5029664

• Cancer Differentiating Agent Hexamethylene Bisacetamide Inhibits BET Bromodomain Proteins CANCER RESEARCH Nilsson, L. M., Green, L. C., Muralidharan, S. V., Demir, D., Welin, M., Bhadury, J., Logan, D. T., Walse, B., Nilsson, J. A. 2016; 76 (8): 2376-2383

  Abstract

  Agents that trigger cell differentiation are highly efficacious in treating certain cancers, but such approaches are not generally effective in most malignancies. Compounds such as DMSO and hexamethylene bisacetamide (HMBA) have been used to induce differentiation in experimental systems, but their mechanisms of action and potential range of uses on that basis have not been developed. Here, we show that HMBA, a compound first tested in the oncology clinic over 25 years ago, acts as a selective bromodomain inhibitor. Biochemical and structural studies revealed an affinity of HMBA for the second bromodomain of BET proteins. Accordingly, both HMBA and the prototype BET inhibitor JQ1 induced differentiation of mouse erythroleukemia cells. As expected of a BET inhibitor, HMBA displaced BET proteins from chromatin, caused massive transcriptional changes, and triggered cell-cycle arrest and apoptosis in Myc-induced B-cell lymphoma cells. Furthermore, HMBA exerted anticancer effects in vivo in mouse models of Myc-driven B-cell lymphoma. This study illuminates the function of an early anticancer agent and suggests an intersection with ongoing clinical trials of BET inhibitor, with several implications for predicting patient selection and response rates to this therapy and starting points for generating BD2-selective BET inhibitors. Cancer Res; 76(8); 2376-83. ©2016 AACR.

  View details for DOI 10.1158/0008-5472.CAN-15-2721

  View details for Web of Science ID 000374170700032

  View details for PubMedID 26941288

• Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells - Evidence of unique microRNA cargos RNA BIOLOGY Lunavat, T. R., Cheng, L., Kim, D., Bhadury, J., Jang, S. C., Lasser, C., Sharples, R. A., Lopez, M. D., Nilsson, J., Gho, Y. S., Hill, A. F., Lotvall, J. 2015; 12 (8): 810-823

  Abstract

  Melanoma cells release different types of extracellular vesicles (EVs) into the extracellular milieu that are involved with communication and signaling in the tumor microenvironment. Subsets of EVs include exosomes, microvesicles, and apoptotic bodies that carry protein and genetic (RNA) cargos. To define the contribution of the RNA cargo of melanoma cell derived EVs we performed small RNA sequencing to identify different small RNAs in the EV subsets. Using validated centrifugation protocols, we separated these EV subsets released by the melanoma cell line MML-1, and performed RNA sequencing with the Ion Torrent platform. Various, but different, non-coding RNAs were detected in the EV subsets, including microRNA, mitochondrial associated tRNA, small nucleolar RNA, small nuclear RNA, Ro associated Y-RNA, vault RNA and Y-RNA. We identified in total 1041 miRNAs in cells and EV subsets. Hierarchical clustering showed enrichment of specific miRNAs in exosomes, including hsa-miR-214-3p, hsa-miR-199a-3p and hsa-miR-155-5p, all being associated with melanoma progression. Comparison of exosomal miRNAs with miRNAs in clinical melanoma samples indicate that multiple miRNAs in exosomes also are expressed specifically in melanoma tissues, but not in benign naevi. This study shows for the first time the presence of distinct small RNAs in subsets of EVs released by melanoma cells, with significant similarities to clinical melanoma tissue, and provides unique insights into the contribution of EV associated extracellular RNA in cancer.

  View details for DOI 10.1080/15476286.2015.1056975

  View details for Web of Science ID 000359659700006

  View details for PubMedID 26176991

  View details for PubMedCentralID PMC4615768

• Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions ONCOTARGET Einarsdottir, B. O., Bagge, R. O., Bhadury, J., Jespersen, H., Mattsson, J., Nilsson, L. M., Truve, K., Lopez, M. D., Naredi, P., Nilsson, O., Stierner, U., Ny, L., Nilsson, J. A. 2014; 5 (20): 9609-9618

  Abstract

  The development of novel therapies against melanoma would benefit from individualized tumor models to ensure the rapid and accurate identification of biomarkers of therapy response. Previous studies have suggested that patient-derived xenografts (PDXes) could be useful. However, the utility of PDXes in guiding real-time treatment decisions has only been reported in anecdotal forms. Here tumor biopsies from patients with stage III and IV metastatic malignant melanoma were transplanted into immunocompromised mice to generate PDXes. 23/26 melanoma biopsies generated serially transplantable PDX models, and their histology, mutation status and expression profile resembled their corresponding patient biopsy. The potential treatment for one patient was revealed by an in vitro drug screen and treating PDXes with the MEK inhibitor trametinib. In another patient, the BRAF mutation predicted the response of both the patient and its corresponding PDXes to MAPK-targeted therapy. Importantly, in this unselected group of patients, the time from biopsy for generation of PDXes until death was significantly longer than the time required to reach the treatment phase of the PDXes. Thus, it could be clinically meaningful to use this type of platform for melanoma patients as a pre-selection tool in clinical trials.

  View details for Web of Science ID 000348036500007

  View details for PubMedID 25228592

  View details for PubMedCentralID PMC4259423

• Identification of tumorigenic and therapeutically actionable mutations in transplantable mouse tumor cells by exome sequencing. Oncogenesis Bhadury, J., López, M. D., Muralidharan, S. V., Nilsson, L. M., Nilsson, J. A. 2013; 2

  Abstract

  Cancer development occurs in response to the successive accumulation of mutations that eventually targets key regulators of cell proliferation. As most mutations likely occur randomly, cancer driver mutations can only be found if they are recurrent. Here we use exome sequencing of the mouse cell lines Panc02, L1210 and Colon 26 to identify genetic alterations (single-nucleotide polymorphisms and small insertion and deletions) that occurred in three different strains of mice and that resulted in tumorigenesis. We identify known mutations in genes like Kras, Cdkn2a/b, Smad4 and Trp53 and a large list of genes whose causal link to cancer is unknown. Interestingly, by screening a compound library we find that the identified oncogenic Kras mutation in Colon 26 cells correlates with its sensitivity to MEK inhibitors in vitro and in vivo. Our analysis of these mouse tumor exomes show that their manageable number of mutations could facilitate the identification of novel mutations or pathways driving tumor development. Furthermore, their use as tools is now enhanced as they can be used to create syngenic transplant models for utilization in drug discovery and validation. Finally, by showing that Kras mutant Colon 26 cells are sensitive to MEK inhibitors, we provide one proof-of-principle experiment that a platform containing targeted resequencing and drug screens could be a valuable addition in the clinic to devise anti-cancer drug schemes.

  View details for DOI 10.1038/oncsis.2013.8

  View details for PubMedID 23588493

  View details for PubMedCentralID PMC3641362