About

Dipayan Bose, Ph.D., is a Research Assistant Professor of Otorhinolaryngology: Head and Neck Surgery at the University of Pennsylvania's Perelman School of Medicine. His research focuses on virology, molecular biology, and immunology, with particular attention to the mechanisms of viral reactivation, immune signaling, and virus-associated cancers. Dr. Bose has contributed to understanding how viruses such as Epstein-Barr Virus (EBV) and Kaposi's Sarcoma-Associated Herpesvirus (KSHV) manipulate host cellular processes, including epigenetic reprogramming and epitranscriptomic modifications, to promote viral reactivation and oncogenesis. His work involves investigating the molecular pathways that regulate virus-host interactions, which has implications for developing targeted therapies for virus-related diseases.

Research topics

• Biology
• Chemistry
• Crystallography
• Materials science
• Cell biology

Selected publications

• Novel small non-coding RNAs of Epstein-Barr virus upregulated upon lytic reactivation aid in viral genomic replication and virion production

  mBio · 2025-04-08 · 3 citations

  articleOpen access

  Epstein-Barr virus (EBV) employs various strategies for long-term survival, including the expression of non-coding RNAs (ncRNAs). This study uncovers and characterizes two novel EBV-encoded ncRNAs, p7 and p8, which are upregulated during lytic reactivation and interact with both viral and host genomes. These ncRNAs bind to cellular RNA transcripts, significantly reducing ARMCX3 mRNA levels, while p8 also influences PTPN6 and RPL24 expressions. Although p7 does not directly bind to LMP1 RNA but both ncRNAs found to downregulate LMP1 expression. Furthermore, these ncRNAs interact with the OriLyt region of EBV genome, promoting viral DNA replication. Functional assays indicate that p7 and p8 enhance cell proliferation and inhibit apoptosis by modulating the p53 pathway and suppressing pro-apoptotic proteins. These findings highlight the role of p7 and p8 in supporting EBV persistence by regulating viral replication, cell survival, and immune evasion, making them promising targets for therapeutic strategies in EBV-related diseases.IMPORTANCEEpstein-Barr virus (EBV) employs diverse strategies for long-term persistence in the host, including the expression of viral non-coding RNAs (ncRNAs) that manipulate key cellular pathways to promote viral replication and immune evasion. This study identifies two novel EBV-encoded ncRNAs, p7 and p8, which are upregulated during lytic reactivation and interact with both viral and host genes to regulate viral DNA replication and promote host cellular survival. By modulating apoptotic and proliferative pathways, p7 and p8 facilitate viral reactivation while promoting host cell survival, highlighting their potential as critical regulators in EBV-driven oncogenesis. This discovery expands our understanding of EBV-host interactions, suggesting p7 and p8 as targets for novel therapeutic strategies in EBV-associated malignancies.

  PublisherDOI

• Epigenetic and epitranscriptomic regulation during oncogenic γ-herpesvirus infection

  Frontiers in Microbiology · 2025-01-07 · 6 citations

  reviewOpen access

  Oncogenic gamma herpesviruses, including Epstein-Barr Virus (EBV) and Kaposi's Sarcoma-associated Herpesvirus (KSHV), are opportunistic cancer-causing viruses and induces oncogenesis through complex mechanisms, which involves manipulation of cellular physiology as well as epigenetic and epitranscriptomic reprogramming. In this review, we describe the intricate processes by which these viruses interact with the epigenetic machinery, leading to alterations in DNA methylation, histone modifications, and the involvement of non-coding RNAs. The key viral proteins such as EBNA1 and LMP1 encoded by EBV; LANA and vGPCR encoded by KSHV; play pivotal roles in these modifications by interacting with host factors, and dysregulating signaling pathways. The resultant reprogramming can lead to activation of oncogenes, silencing of tumor suppressor genes, and evasion of the immune response, which ultimately contributes to the oncogenic potential of these viruses. Furthermore, in this review, we explore current therapeutic strategies targeting these epigenetic alterations and discuss future directions for research and treatment. Through this comprehensive examination of the epigenetic and epitranscriptomic reprogramming mechanisms employed by oncogenic gamma herpesviruses, we aim to provide valuable insights into potential avenues for novel therapeutic interventions.

  PublisherOA PDFDOI

• The F-box E3 ligase protein FBXO11 regulates EBNA3C-associated degradation of BCL6

  Journal of Virology · 2024-06-12 · 1 citations

  articleOpen access

  ABSTRACT Most mature B-cell malignancies originate from the malignant transformation of germinal center (GC) B cells. The GC reaction appears to have a role in malignant transformation, in which a major player of the GC reaction is BCL6, a key regulator of this process. We now demonstrate that BCL6 protein levels were dramatically decreased in Epstein-Barr virus (EBV)-positive lymphoblastoid cell lines and Burkitt’s lymphoma cell lines. Notably, BCL6 degradation was significantly enhanced in the presence of both EBNA3C and FBXO11. Furthermore, the amino-terminal domain of EBNA3C, which contains residues 50–100, interacts directly with FBXO11. The expression of EBNA3C and FBXO11 resulted in a significant induction of cell proliferation. Furthermore, BCL6 protein expression levels were regulated by EBNA3C via the Skp Cullin Fbox (SCF) FBXO11 complex, which mediated its ubiquitylation, and knockdown of FBXO11 suppressed the transformation of lymphoblastoid cell lines. These data provide new insights into the function of EBNA3C in B-cell transformation during GC reaction and raise the possibility of developing new targeted therapies against EBV-associated cancers. IMPORTANCE The novel revelation in our study involves the suppression of BCL6 expression by the essential Epstein-Barr virus (EBV) antigen EBNA3C, shedding new light on our current comprehension of how EBV contributes to lymphomagenesis by impeding the germinal center reaction. It is crucial to note that while several EBV latent proteins are expressed in infected cells, the collaborative mechanisms among these proteins in regulating B-cell development or inducing B-cell lymphoma require additional investigation. Nonetheless, our findings carry significance for the development of emerging strategies aimed at addressing EBV-associated cancers.

  PublisherDOI

• Viruses and Carcinogenesis

  Elsevier eBooks · 2024-08-04

  book-chapter
  PublisherDOI

• A minimal presynaptic protein machinery mediating synchronous and asynchronous exocytosis and short-term plasticity

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-04-18

  preprintOpen access1st author

  Abstract Neurotransmitters are released from synaptic vesicles with remarkable precision in response to presynaptic Ca 2+ influx but exhibit significant heterogeneity in exocytosis timing and efficacy based on the recent history of activity. This heterogeneity is critical for information transfer in the brain, yet its molecular basis remains poorly understood. Here, we employ a biochemically-defined fusion assay under physiologically-relevant conditions to delineate the minimal protein machinery sufficient to account for different modes of Ca 2+ -triggered vesicle fusion and short-term facilitation. We find that Synaptotagmin-1, Synaptotagmin-7, and Complexin, synergistically restrain SNARE complex assembly, thus preserving vesicles in a stably docked state at rest. Upon Ca 2+ activation, Synaptotagmin-1 induces rapid vesicle fusion, while Synaptotagmin-7 mediates delayed fusion. Competitive binding of Synaptotagmin-1 and Synaptotagmin-7 to the same SNAREs, coupled with differential rates of Ca 2+ -triggered fusion clamp reversal, govern the kinetics of vesicular fusion. Under conditions mimicking sustained neuronal activity, the Synaptotagmin-7 fusion clamp is destabilized by the elevated basal Ca 2+ concentration, thereby enhancing the synchronous component of fusion. These findings provide a direct demonstration that a small set of proteins is sufficient to account for how nerve terminals adapt and regulate the Ca 2+ -evoked neurotransmitter exocytosis process to support their specialized functions in the nervous system.

  PublisherOA PDFDOI

• Minimal presynaptic protein machinery governing diverse kinetics of calcium-evoked neurotransmitter release

  Nature Communications · 2024-12-30 · 7 citations

  articleOpen access1st authorCorresponding

  Neurotransmitters are released from synaptic vesicles with remarkable precision in response to presynaptic calcium influx but exhibit significant heterogeneity in exocytosis timing and efficacy based on the recent history of activity. This heterogeneity is critical for information transfer in the brain, yet its molecular basis remains poorly understood. Here, we employ a biochemically-defined fusion assay under physiologically relevant conditions to delineate the minimal protein machinery sufficient to account for various modes of calcium-triggered vesicle fusion dynamics. We find that Synaptotagmin-1, Synaptotagmin-7, and Complexin synergistically restrain SNARE complex assembly, thus preserving vesicles in a stably docked state at rest. Upon calcium activation, Synaptotagmin-1 induces rapid vesicle fusion, while Synaptotagmin-7 mediates delayed fusion. Competitive binding of Synaptotagmin-1 and Synaptotagmin-7 to the same SNAREs, coupled with differential rates of calcium-triggered fusion clamp reversal, govern the overall kinetics of vesicular fusion. Under conditions mimicking sustained neuronal activity, the Synaptotagmin-7 fusion clamp is destabilized by the elevated basal calcium concentration, thereby enhancing the synchronous component of fusion. These findings provide a direct demonstration that a small set of proteins is sufficient to account for how nerve terminals adapt and regulate the calcium-evoked neurotransmitter exocytosis process to support their specialized functions in the nervous system.

  PublisherOA PDFDOI

• A minimal presynaptic protein machinery mediating synchronous and asynchronous exocytosis and short-term plasticity

  Research Square · 2024-04-23

  preprintOpen access
  PublisherOA PDFDOI

• Synaptotagmin-1 and synaptotagmin-7 synergistically regulate the timing and plasticity of Ca2+-evoked vesicular release process

  Biophysical Journal · 2024-02-01

  article1st authorCorresponding
  PublisherDOI

• Viruses, cell transformation, and cancer

  Elsevier eBooks · 2024-01-01 · 3 citations

  book-chapter1st authorCorresponding
  PublisherDOI

• List of contributors

  Elsevier eBooks · 2023-01-01

  book-chapter
  PublisherDOI

Frequent coauthors

• B.K. Ghosh

  Janssen (United States)

  19 shared

• Subhadip Das

  18 shared

• Krishna Das Saha

  Indian Institute of Chemical Biology

  16 shared

• Nabanita Chatterjee

  Chittaranjan National Cancer Institute

  13 shared

• Sk Hafijur Rahaman

  13 shared

• Somenath Banerjee

  University of Illinois Chicago

  13 shared

• G. Mostafa

  King Saud University

  12 shared

• Erle S. Robertson

  12 shared

Labs

• Dipayan Bose LaboratoryPI