Spatial Mapping of the HIV Brain Reservoir and Genomic Changes in Health and Neurological Diseases

CONTEXT Over the past two decades, advancements in HIV treatment, particularly antiretroviral therapy (ART), have significantly improved survival and quality of life for people living with HIV (PLWH). While ART enables individuals with undetectable viral loads to manage the virus, HIV reservoirs, particularly in the brain, remain a major barrier to curing the disease. These reservoirs contribute to persistent immune activation and dysregulation, even in aviraemic patients. Despite effective viral control, elevated risk of cerebrovascular disease (CVD) and cognitive impairment, leading to debilitating neurological disease, persists, implicating the HIV brain reservoir. The burden of HIV-related CVD has tripled over the past two decades, and nearly half of ART-treated individuals exhibit signs of cognitive dysfunction, showing little improvement since the pre-ART era. Emerging data have shown Alzheimer's disease is more prevalent in PLWH, though the contribution of CVD remains unclear. This highlights the urgent need to understand the role of the HIV brain reservoir in these conditions. A major challenge is detecting latent form of HIV in brain tissue and understanding its impact on surrounding cells. AIMS AND OBJECTIVES This research aims to investigate the location of HIV in the brain. We will explore how both active and latent infection, which form the HIV brain reservoir, affect brain cells and their surrounding environment, potentially contributing to neurological disease. The specific objectives are: (A) To identify the cell types and brain regions that express HIV genes, and to understand how the brain, including its vasculature, responds on a cellular level to varying degrees of HIV gene expression. (B) To investigate the organisation and cellular responses to HIV gene expression in the brain; in neurological asymptomatic individuals, individuals with neurological diseases, and those who are not people living with HIV (non-PLWH). Traditional research methods have been limited in identifying latent HIV locations and their effects on surrounding cells. Due to a lack of sensitivity, attempts to unravel this question using techniques such as DNA Fluorescence In situ Hybridisation (FISH) have not been successful. Single-cell sequencing is forthcoming but fails to underpin the location of infection to determine the signals to which cells are exposed or how non-exposed neighbouring cells are impacted. To address these limitations, we propose using a powerful high throughput spatial transcriptomics approach, coppaFISH (combinatorial padlock-probe-amplified fluorescence in situ hybridisation). This technique will allow us to simultaneously detect HIV vDNA (indicating latent infection in isolation), vRNA (active infection), and viral proteins potentially involved in neurological disease. It will also enable multiplexing of hundreds of genes to create a detailed map of how the HIV reservoir impacts the organisation and modifications of brain cells. We will use well-characterised human HIV-positive brain tissue to spatially map cell types and describe cell states in response to HIV. POTENTIAL APPLICATIONS This project will drive critical progress in understanding the HIV brain reservoir and its role in neurological diseases, advancing targets for HIV treatment and biomarkers of brain-related complications. Ultimately, this work will provide unparalleled opportunities by establishing multi-omics foundations which we believe is critical to understand the causative relationships between HIV and neurological diseases in PLWH.