Oral diseases are prevalent and linked to systemic health outcomes. People with HIV may face elevated oral disease risk, yet data on dental disease in this population remain limited. In this cross-sectional study, we analyzed oral health data collected from 2927 participants in the MACS/WIHS Combined Cohort Study (968 women with HIV [WWH], 450 women without HIV [WWoH], 941 men with HIV [MWH], 568 men without HIV [MWoH]) who had intraoral photographs collected and evaluated by dentist-researchers. We used log-binomial regression to examine associations between demographic and clinical characteristics and two outcomes: missing teeth and untreated caries or residual roots, stratified by sex. Among 2927 participants (median [interquartile range, IQR] age: WWH, 55.3 years [48.3–61.6]; WWoH, 53.3 [44.8–60.3]; MWH, 55.1 [42.6–62.9]; MWoH, 62.9 [50.1–69.5]), women experienced a higher prevalence of tooth loss and untreated decay than men. Among participants aged 65 years or older, 15

Depression disproportionately affects women living with HIV, yet symptom heterogeneity and the lack of observable biomarkers can impede detection. Accelerated aging of monocytes-key innate immune cells-may contribute to depression, particularly in this population. A DNA methylation clock, MonoDNAmAge, estimates monocyte biological age and has shown evidence of epigenetic age acceleration (EAA) in women with HIV. Here, we examine MonoDNAmAge as a biomarker of depression in women with and without HIV, differentiating non-somatic from somatic symptom domains. DNA methylation data and Center for Epidemiologic Studies Depression Scale (CES-D) scores were available from 440 Women's Interagency HIV Study participants. Two biological age estimates (HorvathDNAmAge and MonoDNAmAge) were calculated and orthogonalized with chronological age. In the total sample and subsamples stratified by HIV status, we used multiple linear regression to assess how EAAMono and EAAHorvath were associated with depressive symptoms. Standardized β coefficients are reported. The sample included 261 women with HIV (mean chronological age = 43.7 (8.9) years; 38% Black; 48% Hispanic) and 179 women without HIV (mean chronological age = 39.5 (10.0) years; 31% Black; 49% Hispanic). In the overall sample, EAAMono was associated with the non-somatic depressive symptom domain (β = 0.125, p = .018), and anhedonia specifically (β = 0.354, p = .007), adjusting for HIV, race, and ethnicity. This pattern persisted in the subsample with HIV (β = 0.112, p = .085). EAAHorvath was not associated with depression severity or symptom domains. Monocyte aging may represent a sensitive biomarker of non-somatic depression symptoms in women with HIV. The dynamics of monocyte aging and depression warrant further study to clarify mechanistic links.

BackgroundWomen living with type 2 diabetes (T2D) face elevated risks for depression and its consequences, including early mortality, yet depression is underrecognized in this population. Depression is a heterogeneous phenotype lacking objective diagnostic biomarkers, with symptoms spanning multiple inconsistently assessed dimensions across various measures. Converging evidence implicates inflammation in depression and links depression with T2D. Here, we explored associations between inflammation and various measures and dimensions of depressive symptoms.MethodsThis cross-sectional pilot study enrolled 38 women with T2D from the MACS/WIHS Combined Cohort Study (MWCCS) Bronx site from 2022-2023. Serum inflammatory biomarkers (hsCRP, INF-γ, IL-1β, IL-1RA, IL-2, IL-4, IL-6, IL-8, IL-10, TNF-α) were measured and analyzed via Luminex. We performed Spearman correlation analysis using log-transformed biomarker levels and the multidimensional Center for Epidemiological Studies Depression scale (CES-D), alongside unidimensional Patient-Reported Outcomes Measurement Information System (PROMIS) measures for depression, fatigue, sleep, and anxiety, in this exploratory analysis.ResultsParticipants were on average 61.4 (SD 4.8) years old, 71% Black, and 32% Hispanic. While all women had T2D, 82% were also living with HIV. Mean BMI of 34.7 kg/m2 (SD 7.4) was high, but HbA1c of 6.5% (SD 1.3%) indicated fairly adequate glycemic control. Among participants with HIV, 94% were taking antiretroviral therapy. Mean high sensitivity C-reactive protein (hsCRP) of 4.1 mg/L (SD 3.7) signaled moderate inflammation in this population. IL-4 demonstrated significant negative associations with PROMIS-Depression (rs= 0.35; 95% CI -0.61, -0.03; p = 0.034) and PROMIS-Anxiety scores (rs = -0.37; 95% CI -0.62, -0.05; p = 0.025), but associations with CES-D were not significant. hsCRP and IL-6 were positively correlated with CES-D and negatively correlated with PROMIS-Depression, although these associations did not reach statistical significance. PROMIS-Sleep was moderately associated with IL-8 (rs = 0.39; 95% CI 0.06, 0.64; p = 0.021).ConclusionsWhile preliminary, our findings suggest that associations between inflammatory biomarkers and depression may not be consistent across all depressive measures or symptom dimensions. Although larger samples with repeated measures are needed, findings from this exploratory study suggest that including inflammatory measures beyond hsCRP and IL-6, together with tools that capture distinct depressive symptom dimensions, may help to inform future precision mental health research.

Abstract Pain is one of the worst symptoms experienced by patients with oral squamous cell carcinoma (OSCC), which impairs patients' function and quality of life. Yet its clinical and molecular determinants remain poorly defined. The objective of this study was to investigate how pain, quality of life (QoL), and tumor biology intersect to improve prognostication and patient-centered care. This prospective multi-institutional study enrolled 196 OSCC patients from Loma Linda University (LLU) and the University of Alabama at Birmingham (UAB). Pain was assessed using the UCSF Oral Cancer Pain Questionnaire and, Brief Pain Inventory (BPI). Functional and symptom disturbance (QoL) were characterized using EORTC QLQ-C30/H&N35. Flash frozen tumors were collected at surgery for RNA-Seq. Data were analyzed using Spearman correlation, Wilcoxon, Kruskal-Wallis tests, ANCOVA, Kaplan-Meier log-rank test, and Cox hazard regression. Our results revealed that patients reporting high pain demonstrated significantly lower overall QoL, including reduced functional scores (physical, role, emotional, cognitive, and social functioning) and higher symptom burden (p<0.05), entirely independent of their cancer stage at diagnosis. Additionally, morphine milligram equivalents (MME/day) were strongly correlated with pain severity and worse QoL metrics (p<0.05). Kaplan-Meier analysis showed that high pain (UCSF and BPI), higher symptom score, and higher H&N35 score, lower global health status score and functional score, and opioid use were associated with worse survival (p<0.05). After adjustment for confounders (age, sex, race, pathologic stage, PNI, LVI, smoking status), Cox hazard regression analysis revealed functional score (HR = 0.5, CI 95% [0.287-0.873]), symptom score (HR = 2.144, CI 95% [1.169-3.934]), HN35 scores (HR = 2.192, CI 95% [1.195-4.023]) and opioid use (HR = 2.665, CI 95% [1.510-4.706]) as independent predictors of survival. RNAseq analysis of 128 patients comparing high- and low-pain tumors identified significant enrichment in GO pathways related to axonogenesis, neuron to neuron synapse, and in KEGG involved pathways of neurodegeneration-multiple disease, Alzheimer’s, and Huntington’s disease pathways. In addition, the top dysregulated GO pathways in patients with low function (low functional score) were cytoplasmic translation, ribosome biogenesis, and regulator of signal transduction by p53 class mediator. In conclusion, these findings demonstrated that pain severity, opioid requirement, and diminished quality of life are tightly linked to aggressive tumor features and poorer survival in OSCC. Molecular analyses highlight the potential of neural-associated dysregulation in OSCC pain. Citation Format: Minh Phuong Dong, Gary Yu, Michele Arambula, Bac An Luong, Paul Walker, Traeden Wilson, Khanh Nguyen, Carissa M. Thomas, Yi Ye, Bradley Aouizerat, Chi Viet. Pain severity is related to molecular pathways underlying aggressive disease and poor survival in OSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1240.

Background Patients with breast cancer undergoing chemotherapy experience multiple symptoms that cause decrements in quality of life. A deeper understanding of serum metabolites as biomarkers may guide in predicting symptom occurrence and severity. This study evaluated change in serum metabolite levels from before chemotherapy (T1) to after the initial first or second cycle of chemotherapy (T2), after the third cycle of chemotherapy (T3) and finally after a month of chemotherapy completion (T4). Change in metabolite levels were analyzed in association with symptom occurrence. Methods Patients with breast cancer (n = 10) completed study measures at four timepoints. Neuropsychological and gastrointestinal (GI) symptoms were evaluated using the Memorial Symptom Assessment Scale. Dietary intake was assessed using the NHANES Dietary Screener Questionnaire. Serum metabolites were analyzed using gas chromatography-mass spectrophotometry. Results Five patients experienced > 3 GI symptoms at T2 and T3. At all 4 timepoints, ≥ 6 patients experienced moderate to severe neuropsychological symptoms severity. Daily mean intake of fiber, whole grain, and calcium were less than the recommended guidelines. Compared to T1, long chain fatty acid and amino acid derivative levels decreased at T2 and T3 (p < 0.05). Increase in metabolite levels of glucose-6-phosphate (p = 0.02) and 6-phosphogluconate (p = 0.05) at T2 were associated with fatigue occurrence. Conclusions Patients experienced several gastrointestinal and neuropsychological symptoms during chemotherapy and early survivorship. Chemotherapy-induced changes in metabolites involved in cellular energy metabolism may explain patient symptom experience. Metabolite level changes overtime may reflect inadequate dietary intake. Larger sample size studies may guide in building metabolic prediction models for symptom burden.

Social relationships are an important social determinant of health. Loneliness, the perceived gap between one's actual and desired relationships, has emerged as an important mechanism through which social relationships impact health. Like other intrapersonal-level factors associated with health, loneliness is influenced by broader social and structural factors, including characteristics of one's neighborhood social environment. Although neighborhood-level protective and risk factors for loneliness and for mental health have been identified, prior studies have often focused solely on self-reported perceptions of the neighborhood environment. Further, few have considered aspects of the neighborhood social environments, such as neighborhood stability (i.e., stability of the community with long or short-term residents), independent of neighborhood socioeconomic conditions. In the current analysis, we explored longitudinal patterns of loneliness in conjunction with neighborhood stability among women with HIV (WWH) enrolled into the MACS/WIHS Combined Cohort Study (MWCCS) from 2014-2019 ( N 2019 =1,394) to examine whether trajectories of loneliness and neighborhood stability were associated with depressive symptoms, non-prescription substance use, past-year cannabis use, number of alcoholic drinks per week, and several domains of quality of life. Loneliness at baseline (Betas = 0.24 - 0.54) and changes in loneliness over time (Betas = 0.11 - 0.26) were associated with each outcome, except for the association between changes in loneliness over time and drinks per week (Beta=0.13, p = 4.14×10 -2 ), which did not persist after correcting for multiple comparisons. Neighborhood stability at baseline was associated with past year cannabis use (Beta=0.26, p = 1.00×10 -2 ), depressive symptoms (Beta=-0.12, p = 1.54×10 -3 ), and overall self-reported health (Beta=-0.08, p = 2.05×10 -2 ). Changes in neighborhood stability across time were not associated with any outcome. Neighborhood stability moderated the association between changes in loneliness and general health perceptions. Our results demonstrate both overall loneliness and changes in loneliness over time have implications for current mental health in WWH, while changes in neighborhood stability did not.

Ferroportin (FPN) disease is a genetically predisposed iron overload driven by over 30 mutations in the FPN gene that increase FPN resistance to degradation by hepcidin. Most of the reported mutations have negligible frequencies, except for the FPN Q248H mutation, which is highly prevalent in Africans (frequency up to 13.4%). A high frequency of the FPN Q248H mutation may be due to a survival advantage and positive selection. Data from combined cohorts comprising over 18,000 African children demonstrated that the FPN Q248H mutation is associated with modest protection against anemia, hemolysis, and iron deficiency, but does not protect against malaria or bacteremia. We hypothesize that the FPN Q248H mutation might protect from HIV-1 infection and possibly other chronic viral infections which have a high burden in Africa, and, thus, be positively selected. Our previous studies showed that the FPN Q248H mutant has reduced sensitivity to hepcidin and facilitated more active iron export in the presence of hepcidin (Nekhai et al., Haematologica, 2013), and that FPN expression inhibits HIV-1 replication (Xu et al., Retrovirology, 2010). We hypothesize that the FPN Q248H mutation might reduce the comorbidities of chronic HIV infection. We genotyped the FPN Q248H mutation in 927 African American male participants from the Multicenter AIDS Cohort Study (MACS, age 26-48 years), including 479 persons with HIV (PWH) and 448 control persons without HIV-1 (PWOH). The FPN Q248H mutation was genotyped by single-nucleotide polymorphism (SNP) assay from Thermo Fisher (rs11568350 SNP ID) using DNA extracted from peripheral blood mononuclear cells. Longitudinal analysis of viral load (VL), CD4+ and CD8+ levels were assessed alongside body weight trends and stratified by the FPN Q248H mutation status. The baseline characteristics between FPN mutants(A/A or A/C) and wild type FPN (C/C) were compared using the Student's t-test. We used mixed-effect models to test the effect of FPN Q248H mutation on the change of CD4, CD8, and weight during the follow-up period in PWH. Models were adjusted for the confounding effect of antiretroviral therapy, the number of male sex partners, and illicit drug use. The frequency of the FPN Q248H mutation was 9.6% in PWH and 9.2% in PWOH. The baseline VL was higher in participants with FPN Q248H (A/A or A/C) mutations (β=0.14, p=0.74), whereas CD4 (β=-1.48, p=0.11), CD8 (β=-1.50, p=0.11), or CD4/CD8 (β=-0.02, p=0.63), levels were lower. The proportion with undetectable VL at the initial visit was higher among PWH with the FPN Q248H (A/A or A/C) mutation (14.3%) compared to WT FPN (C/C) (10.5%). In the 20-year follow-up, there was a statistically significant increase in CD4 (β=0.19, p<0.001), and CD8 (β=0.12, p<0.001), levels in PWH with FPN Q248H mutation compared to those with WT FPN, suggesting better control of HIV-1 infection. Analysis of the longitudinal changes in the body weight of PWH showed a significant increase in participants with the FPN Q248H mutation. PWH with WT FPN gained less than 2% of body weight, whereas PWH who had FPN Q248H mutation gained about 8% of body weight (P for interaction of time and mutation <0.001).PWOH gained about 10% of body weight during the 20-year follow-up period. The findings of this study indicate that PWH with FPN Q248H mutation maintain similar weight trajectories to PWOH as compared to the PWH with WT FPN. Weight loss is a serious complication of HIV infection that increases mortality risks. A substantial proportion of PWH in Sub-Saharan Africa is undernourished, and undernutrition contributes to an increased risk of mortality and other comorbidities. Protection from weight loss (cachexia) in people with chronic infections may contribute to the positive selection of the FPN Q428H mutation in Africa. Future studies will elucidate the mechanism of weight preservation and evaluate the role of iron metabolism modifying treatments in the management of chronic HIV-1 infection. ACKNOWLEDGMENTS: We acknowledge the Genomics Core Facility at the University of Utah for sample processing and genotyping and thank Michael Klein for his assistance. This work was supported by 1R01HL125005, U54MD007597, 2P30AI117970, U01-HL146241, U01-HL146201, U01-HL146204, U01-HL146202, U01-HL146193, U01-HL146245, U01-HL146242, U01-HL146205, U01-HL146203, U01-HL146192, U01-HL146194, UL1-TR000004, P30-AI-050409, P30-AI-050410 and P30-AI-027767.

Metabolic syndrome is a pressing public health issue and risk factor for the development of type 2 diabetes (T2D) and cardiovascular disease (CVD), yet clinical practice is lacking in biomarkers that represent pre-clinical perturbations of the heterogenous subtypes of risk. This study aimed to characterize the baseline metabolome in relation to known clinical characteristics of risk in a sample of obese adults. Untargeted metabolome data from N = 126 plasma samples with baseline data from a previously completed study including obese adults with metabolic syndrome. Metabolites were acquired using validated liquid chromatography mass spectrometry methods with 15–25 internal standards quantified by peak heights. Pearson’s correlations were used to determine relationships between baseline metabolites, sample characteristics (e.g., age, body mass index (BMI)), and atherosclerotic clinical characteristics (e.g., high-density lipoprotein cholesterol (HDL), low-density lipoprotein cholesterol (LDL), triglycerides), adjusting for multiple comparisons using the Benjamini–Hochberg False Discovery Rate (FDR) method. Differences in metabolite levels between clinical classifications of dysglycemia (e.g., normal, prediabetes, diabetes) at baseline were assessed using ANOVA and adjusted for multiple comparisons and adjusted for covariates. The sample consisted primarily of female (74

BACKGROUND:Orofacial pain, affecting 10-15% of adults, is a prevalent form of chronic pain that remains a major clinical challenge. The Schwann cell involvement in this pathophysiology is not fully understood. Low-density lipoprotein receptor-related protein 1 (LRP1) in Schwann cells has an unclear role in orofacial pain mechanisms. FINDINGS:We demonstrate that Schwann cell-specific conditional knockout of Lrp1 (scLrp1-/-) in mice leads to pronounced mechanical and thermal hypersensitivity in the orofacial region. RNA-seq of trigeminal ganglia (TG) from scLrp1-/- mice revealed broad changes in mitochondrial and metabolic pathways, reactive oxygen species (ROS) signaling, calcium homeostasis, and neurodegeneration-related processes. Altered mitochondrial function and ROS production in the TG were further confirmed with Seahorse metabolic flux analysis and biochemical assays. Additionally, mechano- and thermos-sensitive ion channels TRPV1 and TRPA1 are overexpressed and sensitized in the TG isolated from scLrp1-/- mice. Schwann cells isolated from scLrp1-/- mice displayed defective oxLDL uptake and excessive H₂O₂ release. Conditioned medium from LRP1 ablated Schwann cells induced orofacial hypersensitivity in vivo and robustly activated TG neurons in vitro in a TRPV1/TRPA1 dependent manner. CONCLUSIONS:Our results demonstrate that Schwann cell LRP1 safeguards mitochondrial function and supports neuron-glia metabolic coupling in the trigeminal system. The finding that LRP1 deficiency in Schwann cells drives orofacial pain in the absence of external insults highlights Schwann cells as active drivers, rather than passive amplifiers of chronic pain and identifies LRP1 as a promising target for orofacial pain management.

Perineural invasion (PNI), defined by cancer spreading or invading into the nerve, links to severe pain, recurrence, and poor prognosis. PNI contributes to nerve damage, Schwann cell activation, and sensory neuron dysfunction. Soluble tumor necrosis factor α (solTNFα) binds to TNFR1 to drive inflammation and nerve injury, playing a key role in cancer progression and pain. This study, using a mouse sciatic nerve PNI model, explored whether blocking solTNFα-TNFR1 signaling via TNFR1 knockout or pharmacological inhibition by XPro1595 could reduce PNI-associated pain. Data showed that XPro1595, but not TNFR1 knockout, reduced tumor burden, alleviated mechanical allodynia, and improved muscle function and locomotion, primarily in females. Histological analysis in females showed that XPro1595 increased the number of myelin and dendritic cells while reducing axonal damage that resulted from PNI. In the tumor zone outside the nerve truck, XPro1595 reduced T cell and increased macrophage and dendritic cell numbers. Transcriptomic analysis revealed that XPro1595 in females with PNI upregulated mitochondrial, myelination, motor function, and immune regulation gene pathways while it downregulated inflammatory, extracellular matrix, and tumor progression pathways. Overall, we demonstrated that XPro1595 exhibited antitumor, neuroprotective, and analgesic properties in female mice, likely by promoting neuronal regeneration and mitochondrial function, while reducing inflammation and extracellular remodeling.

Objective: This cross-sectional study investigated the associations of neighborhood-level factors with immune activation, systemic inflammation, and leukocyte telomere length in 110 sexual minority men with human immunodeficiency virus. Method: From 2013 to 2017, sexual minority men with human immunodeficiency virus who used stimulants were recruited in San Francisco, California and provided blood samples to measure the markers of immune activation, systemic inflammation, and leukocyte telomere length. To measure neighborhood-level indices, the home address for each participant was geocoded and linked to data from the Centers for Disease Control and Prevention. Hierarchical linear modeling was employed to investigate the associations of neighborhood-level factors with systemic inflammation and leukocyte telomere length. Results: After adjusting for age, stimulant use, self-reported income, level of education, and race and ethnicity, residing in neighborhoods with greater percentages of poverty (beta = .33, p < .001) and a higher proportion of racial/ethnic minority residents (beta = .26, p < .05) were independently associated with higher levels of interleukin-6. Additionally, residing in neighborhoods with higher percentage of uninsured individuals was independently associated with higher tumor necrosis factor-alpha (beta = .24, p < .05). Indices of neighborhood-level adversity were additionally associated with providing a urine sample that was reactive for stimulants (OR = 1.31, p = .002), which was, in turn, associated with shorter leukocyte telomere length (beta = -.31, p < .05). Conclusions: Future longitudinal research should examine the biobehavioral pathways linking neighborhood-level factors and stimulant use with systemic inflammation and cellular aging.

Pancreatic ductal adenocarcinoma (PDAC) is characterized by late-stage diagnosis and poor survival rates. Identifying biomarkers that can aid in early detection and disease characterization is critical. This study leverages a novel ELISA platform to explore IgG reactivity to chemical adducts in the plasma of PDAC patients compared to healthy donors (HD). Plasma samples from 39 PDAC patients and 40 age- and sex-matched HD were analyzed for IgG reactivity to 93 adducts, including phosphorylated amino acids, advanced glycation end products, and coenzymes. Reactivity to phosphoryl-Thr, -Ser, and -Tyr were further validated and characterized using IgG1-4-specific secondary antibodies. Paired tumor and non-tumoral tissues from a subset of cases underwent immunofluorescence and phosphoproteomic analyses to identify phosphorylation changes. Serum IgG reactivity to phosphorylated threonine, serine, and tyrosine was significantly higher in patients with pancreatic ductal adenocarcinoma (PDAC) than in healthy donors (HD). A Boruta-based random forest classifier identified these phosphorylated adducts as the most significant target adducts discriminating between the two groups. High-titer IgG responses to these phosphorylated adducts—predominantly IgG1 and IgG3—were observed for PDAC patients. Moreover, patients with metastatic disease exhibited greater IgG reactivity to phosphorylated adducts than those without metastasis. Immunofluorescence analysis demonstrated the accumulation of phosphorylated adducts in PDAC cells, suggesting that their abundance in the tumor triggered the specific antibody response. Additionally, phosphoproteomics revealed dysregulated phosphorylation pathways in PDAC, with 124 proteins showing significantly higher phosphorylation levels in tumor tissue compared to non-tumoral tissue. Gene ontology analysis linked these proteins to processes involving chromatin organization, transcription regulation, and histone acetylation. Essential molecular functions of these aberrantly expressed proteins included chromatin and RNA binding, evoking altered gene expression. Serum IgG responses to phosphoryl adducts represent a robust biomarker for PDAC detection and may reflect disease progression. These findings highlight the potential of anti-adduct IgG profiles as tools for early cancer detection and therapeutic monitoring. Talita Aguiar, Shunya Mashiko, Kesava Asam, Poulomi Roy, Shikun Wang, Katharina Frank, Max Dietzel, Luca G. Z. Schahadat, Mattea Ausmeier, Andrea Hertel, Zhe Ran S Susan Duan, Bradley Aouizerat, Jeanine M. Genkinger, Helen Remotti, Emmanuel Zorn. Serological responses to phosphorylated adducts in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6145.

Hypermutated proviruses, which arise in a single HIV replication cycle when host antiviral APOBEC3 proteins introduce extensive G-to-A mutations throughout the viral genome, persist in all people living with HIV receiving antiretroviral therapy (ART). But, the within-host evolutionary origins of hypermutated sequences are incompletely understood because phylogenetic inference algorithms, which assume that mutations gradually accumulate over generations, incorrectly reconstruct their ancestor-descendant relationships. Using >1400 longitudinal single-genome-amplified HIV env-gp120 sequences isolated from six women over a median 18 years of follow-up − including plasma HIV RNA sequences collected over a median 9 years between seroconversion and ART initiation, and >500 proviruses isolated over a median 9 years on ART − we evaluated three approaches for removing hypermutation from nucleotide alignments. Our goals were to 1) reconstruct accurate phylogenies that can be used for molecular dating and 2) phylogenetically infer the integration dates of hypermutated proviruses persisting during ART. Two of the tested approaches (stripping all positions containing putative APOBEC3 mutations from the alignment, or replacing individual putative APOBEC3 mutations in hypermutated sequences with the ambiguous base R) consistently normalized tree topologies, eliminated erroneous clustering of hypermutated proviruses, and brought env-intact and hypermutated proviruses into comparable ranges with respect to multiple tree-based metrics. Importantly, these corrected trees produced integration date estimates for env-intact proviruses that were highly concordant with those from benchmark trees that excluded hypermutated sequences, indicating that the corrected trees can be used for molecular dating. Use of these trees to infer the integration dates of hypermutated proviruses persisting during ART revealed that these spanned a wide age range, with the oldest ones dating to shortly after infection. This indicates that hypermutated proviruses, like other provirus types, begin to be seeded into the proviral pool immediately following infection, and can persist for decades. In two of the six participants, hypermutated proviruses differed from env-intact ones in terms of their age distributions, suggesting that different provirus types decay at heterogeneous rates in some hosts. These simple approaches to reconstruct hypermutated provirus' evolutionary histories, allow insights into their in vivo origins and longevity, towards a more comprehensive understanding of HIV persistence during ART.

Objective: Past correlational research has shown that minority stress has direct and indirect effects on the biology of sexual minority people. This pilot randomized controlled trial (RCT) examined the potential of AWARENESS, a nine-session cognitive behavioral intervention to reduce intersectional minority stress, to alter gene expression related to immune function, inflammation, and HIV disease progression. Method: Between 2016 and 2019, 25 sexual minority men living with HIV with recent substance use (n = 12 in AWARENESS and n = 13 in control) were enrolled, a subset with complete gene expression data among the 41 individuals within the parent RCT. Blood samples were taken prior to the intervention, at the 9-week conclusion of the intervention, and at 4 months postrandomization, and leukocyte RNA was sequenced for all samples. The authors examined differential expression analyses of single genes and overrepresentation analysis of gene sets. Results: Neither AWARENESS nor the control condition was related to the differential expression of single genes. Overrepresentation analysis suggested that AWARENESS was related to changes over time in gene expression in leukocyte RNA in 52 gene sets (q < .05), many of which are related to immune function, while the active control condition was related to changes in gene expression among genes in only one gene set. When AWARENESS was compared to the control condition, four gene sets evidenced an overrepresentation of genes reflecting change over time. Conclusions: This RCT suggests that AWARENESS is associated with changes in gene expression, primarily focused on changes in genes associated with immune processes.

Background: Epigenome studies of human HIV-1 (HIV) in whole blood have uncovered a growing list of differentially methylated genes associated with either HIV acquisition, disease progression, or both. Cocaine use is associated with increased disease severity, and methylation changes in some of the HIV-associated genes mediate this effect. Many of these genes are critical players in innate immune response, including both regulators and targets of interferon-alpha and NF-kB activation. However, no study to date has evaluated the gene expression dynamics for these genes in the context of HIV. Methods: Targeted gene expression analyses were performed on 588 people who used illicit drugs within a harmonized cohort comprised of the Vancouver People Who Inject Drugs Study (VPWIDS) using RNAseq in whole blood, including 227 people living with HIV (PLWH). Eighteen genes were selected from six recent epigenome-wide association studies to test for differential expression by HIV status. Both gene-level and transcript-level expression changes were estimated using negative binomial regression models. Results: Nine of the 18 target genes exhibited significant upregulation in PLWH after multiple hypothesis testing correction: EPSTI1, IFI44L, IFIT3, MX1, NLRC5, PARP9, PLSCR1, RIN2, and RSAD2. Transcript-level analysis detected additional upregulation of isoforms for genes CD44, RASSF3, and TAP1. Stratified analysis by cocaine use revealed MX1 and RSAD2 to be exclusively upregulated among PLWH who recently used cocaine. Pathway analysis identified significant dysregulation in the interferon alpha/beta signaling pathway. Conclusions: We confirm the dysregulation of genes previously reported to have differential methylation among PLWH. Results from this study support the model of epigenetic changes altering gene expression for key immune genes such as NLRC5 and MX1, and demonstrate systemic dysregulation of genes involved in innate immune function. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement R01DA038632, R61DA047011, R33DA047011, R01DA051908, U01DA038886, U01DA021525 ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The VIDUS, ACCESS and VPWIDS studies were reviewed and approved by the University of British Columbia/Providence Healthcare research ethics board. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors

The Diabetes Prevention Program (DPP) randomized controlled trial demonstrated that metformin treatment reduced progression to type 2 diabetes (T2D) by 31% compared to placebo in adults with prediabetes. Circulating micro-ribonucleic acids (miRs) are promising biomarkers of T2D risk, but little is known about their associations with metformin regimens for T2D risk reduction. We compared the change in 24 circulating miRs from baseline to 2 years in a subset from DPP metformin intervention (n = 50) and placebo (n = 50) groups using Wilcoxon signed rank tests. Spearman correlations were used to evaluate associations between miR change and baseline clinical characteristics. Multiple linear regression was used to adjust for covariates. The sample was 73% female, 17% Black, 13% Hispanic, and 50 ± 11 years. Participants were obese, normotensive, prediabetic, and dyslipidemic. Change in 12 miR levels from baseline to 2 years was significantly different in the metformin group compared with placebo after adjusting for multiple comparisons: six (let-7c-5p, miR-151a-3p, miR-17-5p, miR-20b-5p, miR-29b-3p, and miR-93-5p) were significantly upregulated and six (miR-130b-3p, miR-22-3p, miR-222-3p, miR-320a-3p, miR-320c, miR-92a-3p) were significantly downregulated in the metformin group. These miRs help to explain how metformin is linked to T2D risk reduction, which may lead to novel biomarkers, therapeutics, and precision health strategies.

Within-host HIV populations continually diversify during untreated infection, and members of these diverse forms persist within infected cell reservoirs, even during antiretroviral therapy (ART). Characterizing the diverse viral sequences that persist during ART is critical to HIV cure efforts, but our knowledge of on-ART proviral evolutionary dynamics remains incomplete, as does our understanding of the differences between the overall pool of persisting proviral DNA (which is largely genetically defective) and the subset of intact HIV sequences capable of reactivating. Here, we reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study (WIHS) who experienced HIV seroconversion. We measured diversity, lineage origins and ages of proviral sequences (env-gp120) sampled up to four times, up to 12 years on ART. We used the same techniques to study HIV sequences emerging from the reservoir in two participants. Proviral clonality generally increased over time on ART, with clones frequently persisting across multiple time points. The integration dates of proviruses persisting on ART generally spanned the duration of untreated infection (though were often skewed towards years immediately pre-ART), while in contrast, reservoir-origin viremia emerging in plasma was exclusively "younger" (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained highly stable during ART in all but one participant in whom, after 12 years, there was evidence that "younger" proviruses had been preferentially eliminated. Analysis of within-host recombinant proviral sequences also suggested that HIV reservoirs can be superinfected with virus reactivated from an older era, yielding infectious viral progeny with mosaic genomes of sequences with different ages. Overall, results underscore the remarkable genetic stability of distinct proviral sequences that persist on ART, yet suggest that replication-competent HIV reservoir represents a genetically-restricted and overall "younger" subset of the overall persisting proviral pool in blood.

PROBLEM:Bacterial vaginosis (BV) disproportionally impacts Black and Hispanic women, placing them at risk for HIV, sexually transmitted infections and preterm birth. It is unknown whether there are differences by genetic ancestry in BV risk or whether polymorphisms associated with BV risk differ by ancestry. METHODS:Women's Interagency HIV Study (WIHS) participants with longitudinal Nugent scores were dichotomized as having (n = 319, Nugent 7-10) or not having BV (n = 367, Nugent 0-3). Genetic ancestry was defined by clustering of principal components from ancestry informative markers and further stratified by BV status. 627 single nucleotide polymorphisms (SNPs) across 41 genes important in mucosal defense were identified in the WIHS GWAS. A logistic regression analysis was adjusted for nongenetic predictors of BV and self-reported race/ethnicity to assess associations between genetic ancestry and genotype. RESULTS:Self-reported race and genetic ancestry were associated with BV risk after adjustment for behavioral factors. Polymorphisms in mucosal defense genes including syndecans, cytokines and toll-like receptors (TLRs) were associated with BV in all ancestral groups. CONCLUSIONS:The common association of syndecan, cytokine and TLR genes and the importance of immune function and inflammatory pathways in BV, suggests these should be targeted for further research on BV pathogenesis and therapeutics.