Biology subjects

Brew, B. J.

Publications and source records attributed to Brew, B. J..

4 recordsLinked to original sources

bioRxiv2026

Transcriptionally Active HIV Reservoirs Enriched for Interferon-Inducible APOBEC3-Related Mutational Signatures Associate with Arterial Inflammation

Despite suppressive antiretroviral therapy (ART), people with HIV (PWH) remain at increased risk of cardiovascular disease (CVD), likely driven, at least in part, by persistent immune activation and vascular inflammation. Mechanistic pathways may include ongoing low-level HIV transcription within immune cells, particularly peripheral blood mononuclear cells (PBMCs), which may contribute to chronic inflammatory signaling. Persistent viral transcription and inflammatory signaling may also be associated with an interferon-responsive cellular environment conducive to APOBEC3 activation and mutational editing of viral transcripts. APOBEC3 enzymes, which are interferon (IFN)-inducible cytidine deaminases, generate characteristic premature stop codons (PSCs) within retroviral genomes and may reflect interferon-associated inflammatory states relevant to vascular pathology. We investigated whether APOBEC3-associated PSC signatures and reservoir-associated drug resistance mutations (RA-DRMs) in viral reservoirs, as markers of persistent reservoir transcriptional activity, are associated with vascular inflammation in ART-suppressed individuals. PBMCs from ART-suppressed PWH (n=36) were analyzed for long HIV-1 gag/pol transcripts (>4.2 kb) and PSCs as a surrogate marker of APOBEC3 activity, with RA-DRMs assessed by Oxford Nanopore sequencing. Arterial inflammation was quantified using PET imaging of the aorta and carotid arteries. Additionally, an exploratory panel of >60 cardiometabolic, clinical, and inflammatory biomarkers was profiled to identify host immune signatures associated with reservoir PSC burden, with focused analyses on circulating inflammatory biomarkers sCD14, sCD163, and IP-10. Long HIV-1 transcripts were detected in 67% (24/36) despite ART. Higher PSC frequency within these transcripts was significantly associated with increased aortic inflammation, but not carotid inflammation, in univariable analysis ({beta} = 0.00834, p = 0.013). RA-DRMs were detected in 50% (12/24), including triple-class resistance, but were not associated with vascular inflammation or soluble biomarkers. In multivariable models, PSCs remained independently associated with aortic inflammation after adjustment for sCD14 and sCD163 ({beta} = 0.0075, p = 0.023), and remained the only significant predictor when IP-10 was included ({beta} = 0.0073, p = 0.036). These findings suggest that APOBEC3-associated PSC signatures in long HIV transcripts identify transcriptionally active HIV reservoir states associated with aortic inflammation during suppressive ART. Rather than reflecting ongoing mutational accumulation or direct pathogenic effects of PSCs themselves, these signatures may serve as biomarkers of an interferon-associated inflammatory reservoir state related to cardiovascular risk. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/729898v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@531cb9org.highwire.dtl.DTLVardef@82c53corg.highwire.dtl.DTLVardef@16318aaorg.highwire.dtl.DTLVardef@e87e22_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights: Interferon-inducible APOBEC3-associated PSC signatures in HIV reservoirs and vascular inflammationO_LIAPOBEC3-associated premature stop codon (PSC) signatures were identified in transcriptionally active HIV reservoir-derived RNA despite suppressive ART. C_LIO_LIHigher PSC burden was significantly associated with increased aortic vascular inflammation measured by FDG-PET. C_LIO_LIReservoir-associated drug resistance mutations (RA-DRMs) showed no association with arterial inflammation. C_LIO_LIPSC burden remained independently associated with aortic vascular inflammation in multivariable analyses. C_LIO_LIPSC-enriched reservoir states were associated with inflammatory biomarker patterns consistent with monocyte-macrophage activation and vascular immune activation. C_LIO_LIThese findings are consistent with an interferon-inducible APOBEC3-edited reservoir state associated with persistent arterial inflammation during suppressive ART. C_LIO_LIAPOBEC3-associated mutational signatures may represent a candidate biomarker of vascular inflammation and cardiovascular risk in people with HIV. C_LI

molecular biology↗

bioRxiv2026

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@19c98d8org.highwire.dtl.DTLVardef@1f6c627org.highwire.dtl.DTLVardef@4b33a7org.highwire.dtl.DTLVardef@12c4a54_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

molecular biology↗

bioRxiv2019

Smaller limbic structures are associated with greater immunosuppression in over 1000 HIV-infected adults across five continents: Findings from the ENIGMA-HIV Working Group

BackgroundHuman immunodeficiency virus type-1 (HIV) infection can be controlled with combination antiretroviral therapy (cART), but neurocognitive impairment remains common even in chronic and treated HIV-infected (HIV+) cohorts. Identifying the neuroanatomical pathways associated with infection has the potential to delineate novel neuropathological processes underlying persisting deficits, yet individual neuroimaging studies have yielded inconsistent findings. The ENIGMA-HIV Working Group was established to harmonize data from diverse studies to identify the common effects of HIV-infection on brain structure.\n\nMethodsData were pooled from 12 independent neuroHIV studies from Africa, Asia, Australia, Europe, and North America. Volume estimates for eight subcortical brain regions were extracted from T1-weighted MRI from 1,044 HIV+ adults (aged 22-81 years; 72.4% on cART; 70.3% male; 41.6% with detectable viral load (dVL)), to identify associations with plasma markers reflecting current immunosuppression (CD4+ T-cell count) or dVL. Follow-up analyses stratified data by cART status and sex. Bonferroni correction was used to determine statistical significance.\n\nFindingsLower current CD4+ count was associated with smaller hippocampal ({beta} = 20.3 mm3 per 100 cells/mm3; p = 0.0001) and thalamic volumes ({beta} = 29.3; p = 0.003); in the subset of participants not on cART, it was associated with smaller putamen volumes ({beta} = 65.1; p = 0.0009). On average, a dVL was associated with smaller hippocampal (Cohens d = 0.24; p = 0.0003) and amygdala volumes (d = 0.18; p = 0.0058).\n\nInterpretationIn HIV+ individuals across five continents, smaller limbic volumes were consistently associated with current plasma markers. As we assessed cohorts with different inclusion/exclusion criteria and demographic distributions, these deficits may represent a generalizable brain-signature of HIV infection in the cART era. Our findings support the importance of achieving viral suppression and immune restoration for maintaining brain health.\n\nFundingThis work was supported, in part, by NIH grant U54 EB020403.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSHIV type-1 infection can be managed with antiretroviral therapy, however neurocognitive impairment persists even in treated HIV+ individuals. Given the challenges associated with standardized cognitive testing, there is a need to identify quantitative markers of central nervous system impairment. A number of neuroimaging studies have reported brain abnormalities in HIV-infected patients; however, prior studies investigating associations between CD4+ T-cell count or HIV viral load and subcortical brain volume report variable effect sizes and regional distributions of effects, limiting the generalizability of the conclusions drawn to date. We have conducted a literature search for reports in English language journals published until June 2019, using the following search terms: HIV AND subcortical AND neuroimaging AND brain AND viral load AND RNA AND CD4. After removing studies that were not applicable, there were 30 studies investigating CD4+ T-cell count and viral load associations with subcortical brain structure.\n\nAdded value of the studyThe aim of the current study was to investigate structural brain associations with two biomarkers universally used to monitor immune function and treatment response, namely plasma RNA viral load and CD4+ T-cell counts. Prior analyses have been performed in smaller, heterogeneous cohorts, but by combining data across cohorts, we can identify consistent associations between brain volume and indicators of HIV infection across cohorts. The ENIGMA-HIV Working Group was established to identify common neurobiological signatures of the HIV-infected brain by harmonizing data analysis from HIV neuroimaging studies worldwide. The value of this dataset is that it is well-powered and representative of many HIV+ people living in the cART era.\n\nImplications of all the available evidenceOur results provide robust evidence that despite demographic and clinical heterogeneity among HIV-infected individuals, brain abnormalities are consistently linked to HIV viral load and immunosuppression. This supports the importance of achieving viral suppression and immune system restoration in maintaining brain health in people living with HIV. The vulnerability of limbic regions, found in this study, extends beyond the classically implicated regions of the basal ganglia; this suggests that these regions remain an important target of cART era HIV research, especially given their heightened vulnerability to age-associated atrophy and neurodegeneration.

neuroscience↗

bioRxiv2017

Metagenomics for chronic meningitis: clarifying interpretation and diagnosis

ImportanceIdentifying infectious causes of subacute and chronic meningitis can be challenging. Enhanced, unbiased diagnostic approaches are needed.\n\nObjectiveTo present a case series of patients with diagnostically challenging subacute and chronic meningitis in whom metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF), supported by a statistical framework generated from mNGS sequencing of non-infectious patients and environmental controls, identified a pathogen.\n\nDesignCase series. Using mNGS data from the CSF of 94 non-infectious neuroinflammatory cases and 24 water and reagent controls, we developed and implemented a weighted scoring metric based on z-scores at the species and genus level for both nucleotide and protein databases to prioritize and rank mNGS results. We performed mNGS on total RNA extracted from CSF of patients with subacute or chronic meningitis and highlight seven cases representing a diverse array of pathogens.\n\nSettingA multi-center study of mNGS pathogen discovery in patients with suspected neuroinflammatory conditions.\n\nParticipantsPatients with diagnostically challenging subacute or chronic meningitis enrolled in a research study of mNGS performed on CSF.\n\nInterventionmNGS was performed on total RNA extracted from CSF (0.25-0.5 mL). A weighted z-score was used to filter out environmental contaminants and facilitate efficient data triage and analysis.\n\nMain Outcomes1) Pathogens identified by mNGS and 2) ability of a statistical model to prioritize, rank, and simplify mNGS results.\n\nResultsmNGS identified parasitic worms, fungi and viruses in seven subjects: Taenia solium (n=2), Cryptococcus neoformans, human immunodeficiency virus-1, Aspergillus oryzae, Histoplasma capsulatum, and Candida dubliniensis. Evaluating mNGS data with a weighted z-score based scoring algorithm effectively separated bona fide pathogen sequences from spurious environmental sequences.\n\nConclusions and RelevancemNGS of CSF identified a diversity of microbial pathogens in patients with diagnostically challenging subacute or chronic meningitis, including a case of subarachnoid neurocysticercosis that defied diagnosis for one year, the first case of CNS vasculitis caused by Aspergillus oryzae, and the fourth reported case of Candida dubliniensis meningitis. Filtering metagenomic data with a scoring algorithm greatly clarified data interpretation and highlights the difficulties attributing biological significance to organisms that may be present in control samples used for metagenomic sequencing studies.\n\nKey PointsQuestion: How can metagenomic next-generation sequencing of cerebrospinal fluid be leveraged to aid in the diagnosis of patients with subacute or chronic meningitis?\n\nFindings: Metagenomic next-generation sequencing identified parasitic worms, fungi and viruses in a case series of seven subjects. A database of water-only and healthy patient controls enabled application of a z-score based scoring algorithm to effectively separate bona fide pathogen sequences from spurious environmental sequences.\n\nMeaning: Our scoring algorithm greatly simplified data interpretation in a series of patients with a wide range of challenging infectious causes of subacute or chronic meningitis identified by metagenomic next-generation sequencing.

microbiology↗