Biology subjects

Sreeram, S.

Publications and source records attributed to Sreeram, S..

3 recordsLinked to original sources

bioRxiv2026

Transcriptional Mapping of Neuro-Immune Interactions during Homeostasis and HIV infection using Microglia-containing Human Cerebral Assembloids

BackgroundA significant number of people with HIV-1 still experience neurocognitive impairments (NCI), despite effective antiretroviral treatment. HIV-NCI is diverse and multifactorial, with mechanisms that cause its development and progression still not fully understood. We examined early HIV-related changes in brain stability and studied neuroimmune interactions at the single-cell level to better understand how NCI develops. MethodsTo model changes in brain homeostasis, we developed an advanced human iPSC-derived 3D cerebral assembloid model that includes microglia, by co-developing neural progenitor cells with tdTomato-tagged and CD34+ cell-derived microglial precursors. Assembloids were infected with a macrophage R5-tropic HIV-1 strain NL-AD8. Viral spread was measured using a proviral DNA assay, qPCR for HIV RNA, and 3D immunostaining for Tat protein. Single-cell transcriptomics with tdTomato lineage tracing revealed HIV-1 induced disturbances and cell-type-specific responses. The niche net algorithm was used to identify ligand-receptor interactions between microglia and the brain microenvironment during homeostasis and HIV infection. ResultsHighly ramified tdTomato+ IBA-1+ microglia were evenly distributed throughout the assembloids within 15 days of culture. Single-cell transcriptomics identified microglia, excitatory/inhibitory neurons, astrocytes, and oligodendrocyte precursors within the assembloids. Neurons in microglia-containing assembloids upregulated genes related to neurotransmission, synaptogenesis, and neuronal development compared to neurons in organoids without microglia. Niche net analysis showed microglia-derived neurotropic ligands supported neuronal and astrocytic differentiation. The R5-tropic HIV-1 specifically targeted microglia, inducing a reactive phenotype that transmitted interferon and pro-inflammatory signals to nearby cells and increased MHC-I antigen-presentation genes. Notably, neuroprotective ligands from non-glial cells and bystander microglia in the assembloids attempted to counteract HIV-related inflammation and promote neural repair. ConclusionsOur microglia-containing assembloid model replicates in vivo neurodevelopmental interactions, allowing high-resolution analysis of homeostatic and HIV-induced responses across different brain cell types. Homeostatic microglia support neuronal health, while HIV infection triggers a reactive state that spreads inflammatory signals within the brain environment. The presence of multiple glial and non-glial populations uncovered previously unknown crosstalk, including bystander microglial phenotypes and neuroprotective signaling mechanisms that counteract inflammation. These findings emphasize early HIV responses that balance injury and adaptation, offering insights for developing therapies that target microglial activation, boost neuroprotection, and address HIV reservoirs in the brain.

microbiology↗

bioRxiv2025

HIV infection in microglia leads to senescence, triggering activation of neurotoxicity pathways

HIV-associated neurocognitive disorders (HAND) persist in milder forms despite anti-retroviral therapy, leading to premature and exacerbated aging-related cognitive disorders. We investigated the interplay between HAND and aging in microglia, which constitute the main brain HIV reservoir. We compared the transcriptomic patterns associated with normal aging in healthy humans to those observed following HIV infection in both ex vivo and in vivo models. Single cell and bulk transcriptomic patterns revealed that HIV infection induces a pattern of cellular senescence, with strong parallels to the transcriptomic signature of normal aging. Both processes were characterized by p53 pathway activation, upregulation of inflammatory genes and downregulation of proliferative genes while maintaining mTOR signaling, a pattern characteristic of cellular senescence. Importantly, both actively HIV infected and bystander microglia showed the cellular senescence patterns. Our results provide a mechanistic basis for the observed premature brain aging in HAND, and identify senescence-associated pathways as potential therapeutic targets.

microbiology↗

bioRxiv2021

The Nerve Growth Factor IB-like Receptor Nurr1 (NR4A2) recruits CoREST transcription repressor complexes to silence HIV following proviral reactivation in microglial cells

Human immune deficiency virus (HIV) infection of microglial cells in the brain leads to chronic neuroinflammation, which is antecedent to the development of HIV-associated neurocognitive disorders (HAND) in the majority of patients. Productively HIV infected microglia release multiple neurotoxins including proinflammatory cytokines and HIV proteins such as envelope glycoprotein (gp120) and transactivator of transcription (Tat). However, powerful counteracting silencing mechanisms in microglial cells result in the rapid shutdown of HIV expression to limit neuronal damage. Here we investigated whether the Nerve Growth Factor IB-like nuclear receptor Nurr1 (NR4A2), which is a repressor of inflammation in the brain, acts to directly restrict HIV expression. HIV silencing was substantially enhanced by Nurr1 agonists in both immortalized human microglial cells (h{micro}glia) and induced pluripotent stem cells (iPSC)-derived human microglial cells (iMG). Overexpression of Nurr1 led to viral suppression, whereas by contrast, knock down (KD) of endogenous Nurr1 blocked HIV silencing. Chromatin immunoprecipitation (ChIP) assays showed that Nurr1 mediates recruitment of the CoREST/HDAC1/G9a/EZH2 transcription repressor complex to HIV promoter resulting in epigenetic silencing of active HIV. Transcriptomic studies demonstrated that in addition to repressing HIV transcription, Nurr1 also downregulated numerous cellular genes involved in inflammation, cell cycle, and metabolism, thus promoting HIV latency and microglial homoeostasis. Thus, Nurr1 plays a pivotal role in modulating the cycles of proviral reactivation by cytokines and potentiating the proviral transcriptional shutdown. These data highlight the therapeutic potential of Nurr1 agonists for inducing HIV silencing and microglial homeostasis and amelioration of the neuroinflammation associated with HAND. AUTHOR SUMMARYHIV enters the brain almost immediately after infection where it infects perivascular macrophages, microglia and, to a less extent, astrocytes. In previous work using an immortalized human microglial cell model, we observed that integrated HIV constantly underwent cycles of reactivation and subsequent silencing. In the present study, we found that the Nurr1 nuclear receptor is a key mediator of HIV silencing. The functional activation of Nurr1 by specific agonists, or the over expression of Nurr1, resulted in rapid silencing of activated HIV in microglial cells. Global gene expression analysis confirmed that Nurr1 not only repressed HIV expression but also regulated numerous genes involved in microglial homeostasis and inflammation. Thus, Nurr1 is pivotal for HIV silencing and repression of inflammation in the brain and is a promising therapeutic target for treatment of HAND.

microbiology↗