Intracellular HIV-1 Tat regulator induces epigenetic changes in the DNA methylation landscape

Andrea Rodriguez-Agustin ^1,2 Rubén Ayala-Suárez ^1,2 Francisco Diez-Fuertes ³ María José Maleno ^1,2 Izar de Villasante ⁴ Angelika Merkel ⁴ Mayte Coiras ^3,5 Victor Casanova ^1,2* José (Pepe) Alcami ^1,2,5* Núria Climent ^1,2,5*

• ¹ Fundació Clínic per a la Recerca Biomèdica, Barcelona, Catalonia, Spain
• ² August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Catalonia, Spain
• ³ National Microbiology Center, Carlos III Health Institute (ISCIII), Madrid, Madrid, Spain
• ⁴ Josep Carreras Leukaemia Research Institute (IJC), Badalona, Catalonia, Spain
• ⁵ Networked Biomedical Research Center for Infectious Diseases (CIBERINFEC), Madrid, Asturias, Spain

The HIV regulatory protein Tat enhances viral transcription but also modifies host gene expression, affecting cell functions like cell cycle and apoptosis. Residual expression of Tat protein is detected in blood and other tissues even under antiretroviral treatment. Cohort studies indicate that, despite virologic suppression, people with HIV (PWH) are at increased risk of comorbidities linked to chronic inflammation, accelerated immune-ageing and cellular senescence, sometimes associated with abnormal genomic methylation patterns. We analysed whether Tat influences DNA methylation and subsequently impact the transcriptional signature, contributing to inflammation and accelerated ageing. Jurkat cells were transfected with full-length Tat (Tat101), Tat’s first exon (Tat72), or an empty vector (TetOFF). DNA methylation modifications were assessed via Infinium MethylationEPIC array, and transcriptomic alterations were evaluated through RNA-seq. Methylation levels in gene promoter or body regions were correlated to their expression data and subsequently we performed an overrepresentation analysis to identify the biological terms containing differentially methylated and expressed genes. Tat101 expression caused significant hyper- and hypomethylations changes at individual CpG sites resulting in a slightly global DNA hypermethylation. Methylation changes at gene promoters and bodies resulted in altered gene expression, specifically regulating gene transcription in 5.1% of DEG in Tat101 expressing cells. In contrast Tat72 had a minimal impact on this epigenetic process. The observed differentially methylated and expressed genes were involved in inflammatory responses, lipid antigen presentation, and apoptosis. Tat expression in HIV infection may constitute a key epigenetic modelling actor that contributes to HIV pathogenesis and chronic inflammation. Clinical interventions targeting Tat blockade may reduce chronic inflammation and cellular senescence related to HIV infection comorbidities.