Transcriptionally Active HIV Reservoirs Enriched for Interferon-Inducible APOBEC3-Related Mutational Signatures Associate with Reduced Neuroaxonal Integrity

Despite sustained viral suppression with effective antiretroviral therapy (ART), impaired neuroaxonal integrity persist in a subset of people with HIV-1 (PWH). We investigated whether interferon (IFN)-inducible APOBEC3-associated mutational signatures, reflected by premature stop codons (PSCs), and reservoir-associated drug resistance mutations (RS-DRMs) within transcriptionally active HIV-1 reservoirs influence neuroaxonal integrity in fully virally suppressed individuals. Peripheral CD4 T cells from individuals with undetectable plasma HIV-1 RNA (n = 27) were analyzed for long HIV-1 gag/pol transcripts (>4.2 kb), and frontal white matter (FWM) neuroaxonal integrity was assessed using proton magnetic resonance spectroscopy ({superscript 1}H-MRS) measurement of N-acetylaspartate (NAA). Short HIV-1 RNA transcripts, reflecting promoter-associated transcriptional activity, were detected in all participants and were associated with reduced NAA levels in FWM, consistent with a relationship between ongoing reservoir activity and impaired neuroaxonal integrity despite virological suppression. Long gag/pol transcripts (>4.2 kb) were detected in 78% of participants and exhibited marked heterogeneity in APOBEC3-associated PSC burden. PSC-containing long transcripts were associated with higher NAA, whereas long transcripts lacking such inactivating mutations were associated with reduced NAA, suggesting that APOBEC3-associated restriction of viral translational competence may contribute to differences in the downstream neurobiological effects of transcriptionally active reservoir states. RA-DRMs were detected in 43% of participants, including triple-class resistance consistent with archived treatment exposure over more than a decade. Matching gag/pol sequences from reactivated virions confirmed latent reservoir origin; however, RS-DRMs showed no independent association with neuroaxonal outcomes. Across systemic inflammatory markers, vascular risk factors, cerebrospinal fluid immune activation measures, and clinical neurocognitive outcomes (including HAND status), no consistent associations with NAA were observed. Overall, reduced neuroaxonal integrity in the FWM was associated with the interplay between short HIV-1 RNA transcriptional activity and APOBEC3-edited translational states of long HIV-1 RNA transcripts within peripheral reservoirs, suggesting that interferon-inducible APOBEC3-associated mutational signatures may reflect biologically distinct reservoir states that correspond to neurobiological effects during suppressive antiretroviral therapy. Graphical AbstractInterferon-Inducible APOBEC3-Associated Premature Stop Codon Signatures in HIV-1 Reservoirs and Preservation of Neuroaxonal Integrity O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/729658v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1ed98c2org.highwire.dtl.DTLVardef@1c8281eorg.highwire.dtl.DTLVardef@1c1e006org.highwire.dtl.DTLVardef@15adc0d_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIShort HIV-1 RNA transcription within peripheral CD4 T-cell reservoirs was associated with reduced frontal white matter N-acetylaspartate during suppressive ART. C_LIO_LILong HIV-1 gag/pol RNA transcripts exhibited marked heterogeneity in interferon-inducible APOBEC3-associated G-to-A hypermutation, including premature stop codon signatures. C_LIO_LIArchived reservoir-associated drug resistance mutations were identified within transcriptionally active long HIV-1 reservoir-derived RNA during suppressive ART. C_LIO_LIReduced neuroaxonal integrity was associated with the interplay between short HIV-1 transcriptional activity and interferon-inducible APOBEC3-associated editing of long HIV-1 transcripts with reduced predicted translational competence. C_LI