Interdependent Dynamics of mRNA Expression and HIV-1 Viral Load: Insights from Transcriptomics and Mendelian Randomization

Oreshkov, S.; Thorball, C.; Meylan, J.; Muriset, M.; Calmy, A.; Ciuffi, A.; Elzi, L.; Nemeth, J.; Muhammad, A.; Baumann, L.; Schmid, P.; Stoeckle, M.; Alpern, D.; Fellay, J.; Santoni, F.

doi:10.1101/2025.11.13.688267

bioRxiv · 10.1101/2025.11.13.688267

Interdependent Dynamics of mRNA Expression and HIV-1 Viral Load: Insights from Transcriptomics and Mendelian Randomization

Oreshkov, S.·Thorball, C.·Meylan, J.·Muriset, M.·Calmy, A.·Ciuffi, A.·Elzi, L.·Nemeth, J.·Muhammad, A.·Baumann, L.·Schmid, P.·Stoeckle, M.·Alpern, D.·Fellay, J.·Santoni, F.

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Abstract

The interaction between HIV-1 and the host immune system plays a crucial role in the natural control and progression of the infection. Previous studies have identified APOBEC3G, Tetherin, SAMHD1, and SERINC5 as HIV-1 host restriction factors, which are counteracted by the viral proteins Vif, Vpu, and Nef, respectively. The blood expression levels of some of these host proteins are correlated with HIV load, suggesting that interindividual differences in the spontaneous control of HIV infection might lead to the identification of novel HIV restriction factors. Our study enrolled 150 participants from the Swiss HIV Cohort Study with human genome-wide genotyping data, pre-antiretroviral treatment peripheral blood mononuclear cells (PBMC) aliquots and HIV load measurements. Using BrB-seq, we quantified mRNA expression of all protein-coding genes and found significant associations between 792 genes and HIV load. Pathway analysis revealed that higher viral load associated with the upregulation of innate immune response, proteasome complex, mitochondrial and cell-cycle related activity, and with the downregulation of ribosomal transcripts and genes involved in cytokine-cytokine receptor interaction, including IL4R, IL7R, and TCF7. Mendelian Randomization confirmed the viral restriction activity of TRABD2A and identified new candidates as potential restriction factors. These findings provide novel insights into the host-virus interplay and suggest additional genes that may contribute to the natural control of HIV-1 infection.

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Oreshkov, S., Thorball, C., Meylan, J., Muriset, M., Calmy, A., Ciuffi, A., Elzi, L., Nemeth, J., Muhammad, A., Baumann, L., Schmid, P., Stoeckle, M., Alpern, D., Fellay, J., Santoni, F.. 2025-11-14. Interdependent Dynamics of mRNA Expression and HIV-1 Viral Load: Insights from Transcriptomics and Mendelian Randomization. https://doi.org/10.1101/2025.11.13.688267

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