Biology subjects

Rana, T. M.

Publications and source records attributed to Rana, T. M..

6 recordsLinked to original sources

bioRxiv2026

Cell-type specific impact of opioid use disorder and HIV on the human forebrain and cerebellum

Opioid use disorder (OUD), which frequently co-occurs with HIV infection, causes long-term neurological disease, yet the epigenetic and transcriptomic effects of OUD and HIV on specific cell types and regions of the brain are poorly understood. To assess the cell-type specific impacts of OUD and HIV across the human brain, we measured single cell transcriptomes and epigenomes of 580,353 cells in the prefrontal cortex, amygdala and cerebellum of 44 donors. We cataloged over 750k candidate cis-regulatory elements (cCREs) and identified gene regulatory networks (GRNs) of transcription factor activity across 35 neuronal and non-neuronal cell types. We identified specific neuronal and glial populations whose cCREs were significantly enriched for genetic risk of addiction-related traits. In OUD donors, we found evidence for reduced metabolic function in neurons in the PFC and cerebellum as well as increased gene expression related to voltage-gated calcium channel activity in the cerebellum. Using a cerebellar organoid model, fentanyl treatment reduced metabolic activity while increasing neuronal activity. Across brain regions, HIV activated immune-related pathways in glial populations, while comorbid OUD and HIV exacerbated metabolic changes in cortical glial cells. Cerebellum-specific Bergmann glia, in addition to forebrain microglia and astrocytes, showed expansion of reactive state identity in HIV. These results highlight shared and specific changes to immune, synaptic, and metabolic processes in OUD and HIV across brain regions and reveal that cerebellar cell types are distinctly affected by opioid abuse.

genomics↗

bioRxiv2026

A new mRNA antigen vaccine induces potent B and T cell responses and in vivo protection against SARS-CoV-2

The SARS-CoV-2 mRNA vaccine provides effective protection against viral infection and severe disease by inducing efficient adaptive immunity. However, vaccine efficacy is decreased against emerging variants, and immune memory is relatively short-lived. Here, we added new T cell epitopes to the RBD (receptor-binding domain) mRNA vaccine and identified a SARS-CoV-2 membrane epitope that significantly improved vaccine-induced immunity and protection in vivo. That new vaccine, designated G1-C, induced 8.2-fold higher levels of RBD-specific antibodies than did RBD and enhanced spike-specific T cell and B cell responses. Remarkably, the G1-C modulated hematopoietic stem cell (HSC) differentiation and increased levels of B and NK cells by regulating multiple signaling pathways in bone marrow potentially via Fos, Klf4, and Klf6 transcription factors. Altogether, these findings identify a new vaccine candidate to control viral infection by affecting the lymphoid-myeloid lineage bias and suggest the potential role of T cell epitopes in vaccine design and development.

immunology↗

bioRxiv2025

Investigation of CNS damage following HIV infection and methamphetamine exposure using human iPSC-derived microglia and 3D cerebral assembloid models

HIV-associated neurocognitive disorder (HAND) is characterized by glial activation and neuroinflammation emerging from HIV infection. Moreover, methamphetamine (METH) is a highly addictive psychostimulant whose use is linked to high HIV prevalence, significantly worsening clinical outcomes for people living with HIV and hastening onset of systemic illness. Overall, pathologies associated with HIV infection/METH use comorbidity include neuroinflammation, neurotoxicity, synaptodendritic damage, and resulting cognitive dysfunction. However, mechanisms underlying this neuropathogenesis remain elusive due to the scarcity of human brain-specific experimental model systems. Therefore, we created a next-generation three-dimensional (3D) human brain model derived from human induced pluripotent stem cells (hiPSCs). Specifically, this 3D in vitro cerebral assembloid model integrates functional microglia derived from hiPSCs with cerebral organoids. Microglia are key contributors to HAND symptoms associated with HIV/METH comorbidity. We show that the presence of microglia in this assembloid model allows productive infection with HIV, which is enhanced by METH exposure, resulting in increased glial activation, inflammatory responses (namely IL-1{beta} and IL-6 release), and neurotoxicity marked by neuronal cell death and synaptic protein loss. Importantly, in this model, we observed markedly decreased levels of the microglial receptor TREM2, which is implicated in microglial functions including phagocytosis, apoptosis and inflammatory responses following HIV infection and METH treatment. Analysis of our model showed that decreased TREM2 function may lead to HIV- and METH-associated pathological changes. Overall, our assembloid model could be a valuable tool for future analyses of HIV/METH/CNS interactions and mechanisms underlying HAND, which could lead to novel therapeutic approaches to decreasing the CNS viral reservoir.

neuroscience↗

bioRxiv2024

Interferon-Inducible Guanylate-Binding Protein 5 Inhibits Replication of Multiple Viruses by Binding to the Oligosaccharyltransferase Complex and Inhibiting Glycoprotein Maturation

Viral infection induces production of type I interferons and expression of interferon-stimulated genes (ISGs) that play key roles in inhibiting viral infection. Here, we show that the ISG guanylate-binding protein 5 (GBP5) inhibits N-linked glycosylation of key proteins in multiple viruses, including SARS-CoV-2 spike protein. GBP5 binds to accessory subunits of the host oligosaccharyltransferase (OST) complex and blocks its interaction with the spike protein, which results in misfolding and retention of spike protein in the endoplasmic reticulum likely due to decreased N-glycan transfer, and reduces the assembly and release of infectious virions. Consistent with these observations, pharmacological inhibition of the OST complex with NGI-1 potently inhibits glycosylation of other viral proteins, including MERS-CoV spike protein, HIV-1 gp160, and IAV hemagglutinin, and prevents the production of infectious virions. Our results identify a novel strategy by which ISGs restrict virus infection and provide a rationale for targeting glycosylation as a broad antiviral therapeutic strategy. HighlightsO_LIThe interferon-stimulated gene GBP5 is induced by SARS-CoV-2 infection in vitro and in vivo. C_LIO_LIER-localized GBP5 restricts N-linked glycosylation of SARS-CoV-2 spike protein, leading to protein misfolding and preventing transport to the Golgi apparatus. C_LIO_LIGBP5 binds to OST complex accessory proteins and potentially blocks access of the catalytic subunit to the spike protein. C_LIO_LIGBP5 inhibits N-glycosylation of key proteins in multiple viruses, including SARS-CoV-2 C_LIO_LIPharmacological inhibition of OST blocks host cell infection by SARS-CoV-2, variants of concern, HIV-1, and IAV. C_LI SignificanceViral infection induces production of type I interferons and expression of interferon-stimulated genes (ISGs) that play key roles in inhibiting viral infection. We found that the interferon-stimulated gene GBP5 is induced by SARS-CoV-2 infection in vitro and in vivo. GBP5 inhibits N-glycosylation of key proteins in multiple viruses, including SARS-CoV-2. Importantly, pharmacological inhibition of Oligosaccharyltransferase (OST) Complex blocks host cell infection by SARS-CoV-2, variants of concern, HIV-1, and IAV, indicating future translational application of our findings.

microbiology↗

bioRxiv2023

Redox Regulation of m6A Methyltransferase METTL3 in Human β-cells Controls the Innate Immune Response in Type 1 Diabetes

Type 1 Diabetes (T1D) is characterized by autoimmune-mediated destruction of insulin-producing {beta}-cells. Several observations have renewed interest in the innate immune system as an initiator of the disease process against {beta}-cells. Here, we show that N6-Methyladenosine (m6A) is an adaptive {beta}-cell safeguard mechanism that accelerates mRNA decay of the 2-5-oligoadenylate synthetase (OAS) genes to control the antiviral innate immune response at T1D onset. m6A writer methyltransferase 3 (METTL3) levels increase drastically in human and mouse {beta}-cells at T1D onset but rapidly decline with disease progression. Treatment of human islets and EndoC-{beta}H1 cells with pro-inflammatory cytokines interleukin-1 {beta} and interferon mimicked the METTL3 upregulation seen at T1D onset. Furthermore, m6A-sequencing revealed the m6A hypermethylation of several key innate immune mediators including OAS1, OAS2, and OAS3 in human islets and EndoC-{beta}H1 cells challenged with cytokines. METTL3 silencing in human pseudoislets or EndoC-{beta}H1 cells enhanced OAS levels by increasing its mRNA stability upon cytokine challenge. Consistently, in vivo gene therapy, to prolong Mettl3 overexpression specifically in {beta}-cells, delayed diabetes progression in the non-obese diabetic (NOD) mouse model of T1D by limiting the upregulation of Oas pointing to potential therapeutic relevance. Mechanistically, the accumulation of reactive oxygen species blocked METTL3 upregulation in response to cytokines, while physiological levels of nitric oxide promoted its expression in human islets. Furthermore, for the first time to our knowledge, we show that the cysteines in position C276 and C326 in the zinc finger domain of the METTL3 protein are sensitive to S-nitrosylation (SNO) and are significant for the METTL3 mediated regulation of OAS mRNA stability in human {beta}-cells in response to cytokines. Collectively, we report that m6A regulates human and mouse {beta}-cells to control the innate immune response during the onset of T1D and propose targeting METTL3 to prevent {beta}-cell death in T1D.

molecular biology↗

bioRxiv2022

Induction of neutralizing antibodies against SARS-CoV-2 variants by a multivalent mRNA-lipid nanoparticle vaccine encoding SARS-CoV-2/SARS-CoV Spike protein receptor-binding domains

To address the need for multivalent vaccines against Coronaviridae that can be rapidly developed and manufactured, we compared antibody responses against SARS-CoV, SARS-CoV-2, and several variants of concern in mice immunized with mRNA-lipid nanoparticle vaccines encoding homodimers or heterodimers of SARS-CoV/SARS-CoV-2 receptor-binding domains. All vaccine constructs induced robust anti-viral antibody responses, and the heterodimeric vaccine elicited an IgG response capable of cross-neutralizing SARS-CoV, SARS-CoV-2 Wuhan-Hu-1, B.1.351 (beta), and B.1.617.2 (delta) variants.

immunology↗