Elevated m6A RNA modifications associate with immune dysregulation and cancer in people with HIV-1

N6-methyladenosine (m6A) modifications of human immunodeficiency virus type 1 (HIV-1) and cellular RNA contribute to regulation of viral and host gene expression. RNA m6A dysregulation has been implicated in multiple cancers. However, the role of m6A modifications in HIV-1-associated cancers remains unclear. Here, we aim to address this important question using clinical samples. Using enzyme-linked immunosorbent assay (ELISA), RNA m6A levels were quantified in peripheral blood mononuclear cells (PBMCs) from 43 de-identified people living with HIV-1 (PLWH), comparing those with cancer (n = 15) to those without cancer (n = 28). Correlation analyses were performed to evaluate the associations between m6A levels and HIV-1 RNA copies, CD4+ T-cell counts, and age of PLWH. The mRNA and protein expression of m6A regulatory genes was measured by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot, respectively. Furthermore, quantitative transcriptomic profiling of 84 type I interferon (IFN-I)-responsive genes was performed using an RT-qPCR array. We observed that HIV-1 viral load in the cancer group was higher than the non-cancer group. m6A levels of PBMCs were 2.8-fold higher in the cancer group and correlated with the expression of some m6A regulatory genes and proteins. Higher m6A levels were positively associated with HIV-1 RNA copies and negatively associated with CD4+ T-cell counts and age. Transcriptomic analysis of 84 IFN-I-responsive genes revealed upregulation of many pro-inflammatory and interferon-stimulated genes, along with downregulation of some genes in PLWH with cancer. Our findings suggest that HIV-1 infection and cancer-mediated m6A reprogramming may contribute to multifaceted chronic immune activation and malignancy in PLWH. Our results also highlight a post-transcriptional mechanism linking HIV-1 persistence to cancer risk.