Faculty Bibliography

OBJECTIVE/UNASSIGNED:This longitudinal study aimed to examine the associations of sexual minority stress and outness with leukocyte telomere length across time among sexually minority men (SMM) with HIV who use methamphetamine. METHODS/UNASSIGNED:A sample of 91 SMM with HIV with biologically confirmed recent methamphetamine use completed measures of sexual minority stress and outness at the baseline visit in a randomized controlled trial. Telomere length was measured over 15 months using extracted leukocyte DNA Statistical analyses were performed using bivariate analyses and generalized estimation equations to examine the independent association between baseline outness and leukocyte telomere length, adjusting for chronological age and recent stimulant use. RESULTS/UNASSIGNED:Greater outness was significantly associated with longer telomere length (estimate = 0.008; CI: 0.001-0.008) after adjusting for chronological age and stimulant use. There was no evidence that stimulant use, intervention assignment, or race/ethnicity moderated the association between outness and greater leukocyte-telomere length. Sexual minority stress was not significantly associated with leukocyte-telomere length. CONCLUSION/UNASSIGNED:Findings are among the first to demonstrate that greater outness is associated with slower biological aging in SMM. Further research is needed to elucidate the bio-behavioral mechanisms linking outness and greater leukocyte-telomere length.

Methylome-wide association studies (MWASs) have identified many 5'-cytosine-phosphate-guanine-3' (CpG) sites associated with complex traits. Several methods have been developed to predict CpG methylation levels from genotypes when the direct measurements of methylation are unavailable. To date, the published methods have mostly used datasets from populations of European ancestry to train prediction models for methylations, which limits the generalizability of methylome-wide association study to non-European populations. To address this gap, we proposed a new model by incorporating local ancestry (LA) information, called LA Methylation Predictor with Preselection (LAMPP), to improve the prediction accuracy of DNA methylation in admixed populations. We showed that LAMPP outperformed the conventional model and other LA models in prediction accuracy using an admixed African American population. We further applied our model to identify significant CpG sites for seven complex traits. Together, our LAMPP model is a valuable tool to reveal epigenetic underpinnings of complex traits in the admixed populations.

BACKGROUND:Opioid addiction is a worldwide public health crisis. In the United States, for example, opioids cause more drug overdose deaths than any other substance. However, opioid addiction treatments have limited efficacy, meaning that additional treatments are needed. METHODS:To help address this problem, we used network-based machine learning techniques to integrate results from genome-wide association studies of opioid use disorder and problematic prescription opioid misuse with transcriptomic, proteomic, and epigenetic data from the dorsolateral prefrontal cortex of people who died of opioid overdose and control individuals. RESULTS:We identified 211 highly interrelated genes identified by genome-wide association studies or dysregulation in the dorsolateral prefrontal cortex of people who died of opioid overdose that implicated the Akt, BDNF (brain-derived neurotrophic factor), and ERK (extracellular signal-regulated kinase) pathways, identifying 414 drugs targeting 48 of these opioid addiction-associated genes. Some of the identified drugs are approved to treat other substance use disorders or depression. CONCLUSIONS:Our synthesis of multiomics using a systems biology approach revealed key gene targets that could contribute to drug repurposing, genetics-informed addiction treatment, and future discovery.

BACKGROUND:Oral squamous cell carcinoma (OSCC) is typically diagnosed at advanced stages, resulting in poor survival rates. Epigenetic alterations, especially DNA methylation, are important early and key contributors to OSCC pathogenesis, but comprehensive epigenetic analysis has traditionally been confounded by cancer tissue availability, with fresh-frozen tissues being the gold standard but difficult to obtain. METHODS:This study established and optimized a new workflow for the use of methylation capture sequencing (MC-seq) to analyze DNA methylation profiles in formalin-fixed paraffin-embedded (FFPE) tissues. Twelve OSCC patients were randomly selected from a prospective, multi-institutional study. Paired fresh-frozen and FFPE tissues were collected and processed for DNA extraction and MC-seq. Data were pre-processed using Bismark and methylKit pipelines. Methylation concordance between FFPE and fresh-frozen samples was assessed by comparing β-value correlation. RESULTS:DNA from FFPE and fresh-frozen OSCC samples showed minimal differences in fragmentation, with FFPE achieving high mapping efficiency (average 71.6%) and retaining an average of about 5 million CpG sites at 10× depth. The distributions of CpG in the methylome region, including promoter, exonic, intronic, and intergenic regions, showed similar patterns between sample types. Additionally, the methylation levels of all matched CpG sites in our 12-gene prognostic panel showed a strong correlation (r ≥ 0.97) between FFPE and fresh-frozen samples. CONCLUSION/CONCLUSIONS:Our findings indicate that FFPE samples are reliable for methylation capture sequencing, offering a new, scalable and reliable alternative to fresh-frozen samples for large-scale OSCC research.

Following peripheral nerve injury, Schwann cell (SC) survival is imperative for successful nerve regeneration. The low-density lipoprotein receptor-related protein-1 (LRP1) has been identified as a pro-survival SC plasma membrane signaling receptor, however, the responsible mechanisms underlying SC homeostasis remain incompletely understood. Herein, we establish that LRP1 largely manages mitochondrial dynamics and bioenergetics in SCs by limiting mitochondria fission, maintaining healthy mitochondria membrane potentials, and reducing lactate production associated with peripheral sensitization. When SC LRP1 is suppressed, inner-mitochondria-linked pathways in peripheral nerve proteome are dramatically altered, and cristae integrity in unmyelinated C-fibers is compromised. SC LRP1 protected sensory neurons from mitochondrial dysfunction and modulated mitochondria-related biological pathways in the DRG transcriptome. Conditional deletion of LRP1 in SCs induces pain-related behaviors in mice without nerve injury. Results point to a significant role for LRP1 in SC mitochondrial homeostasis and advance our understanding of the sensory neuron response to alterations in SC bioenergetics.

Perineural invasion (PNI) frequently occurs in head and neck squamous cell carcinoma (HNSCC), which correlates with poor survival and induces intractable pain and numbness. There is no effective treatment for PNI or associated pain. To gain a better understanding of PNI at the molecular and cellular level, we produced an orthotopic, syngeneic mouse model of PNI by inoculating mouse oral cancer cells into the infraorbital nerve (ION), a nerve that is susceptible to cancer invasion in patients with HNSCC. Mice with PNI in the ION exhibited both evoked and spontaneous nociception and impaired oral function, mimicking human conditions. PNI resulted in a drastic reduction in the proportion and altered mechanical thresholds in mechanically sensitive trigeminal neurons; axon and myelin abnormalities, as well as phagocytic cells, were observed. The tumor bed is marked by CD4⁺ and CD8⁺ T cells, CD68⁺ cells, and F4/80⁺ macrophages, while CD4⁺, CD8⁺, and CD68⁺ immune cells can be found surrounding the nerve. The intraneural niche is predominantly marked by CD68 that does not overlap with F4/80 but instead overlaps with NF200 and MPZ and occasionally with DAPI, suggesting these are likely phagocytic macrophages or Schwann cells. Finally, our RNA sequencing pathway analysis in mouse and human HNSCC found perturbed pathways in neuroinflammation, mitochondrial dysfunction, and cellular metabolism. Additionally, ION-PNI exhibits nerve degenerative features with perturbed pathways that are observed in Alzheimer, Parkinson, and prion diseases. In conclusion, we report a novel, anatomically relevant in vivo model that could be used to study the cellular and molecular mechanisms of PNI-induced neuropathies. Importantly, we found that PNI resembles neurodegenerative diseases with features of altered sensory transduction and conduction, neuroinflammation, and mitochondrial dysfunction, which may underlie peripheral neuropathies, such as pain.

OBJECTIVE:To determine if microbiome differences exist in head and neck squamous cell carcinoma (HNSCC) based on high-risk pathologic features, smoking, and outcomes using The Cancer Microbiome Atlas (TCMA). STUDY DESIGN/METHODS:Database study. SETTING/METHODS:Database review. METHODS:TCMA is a publicly available database containing curated, decontaminated microbial profiles for tumors from 1772 patients. The data were limited to microbiome profiles, survival, and clinicopathologic features for HNSCC patients. Phyloseq objects were created, low-read samples were removed, and differential abundance analysis (DAA) using Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2) was performed. Statistical analysis was done in R (v4.3.1). RESULTS:One hundred fifty-six patients with HNSCC were included from TCMA with a mean age of 59 (std 13, min 19, and max 90), 72% male (n = 113), and 91% white (n = 140). Primary sites encompassed oral cavity (n = 106, 68%), oropharynx (n = 26, 17%), and larynx/hypopharynx (n = 24, 15%). For all HNSCC in TCMA, rates of lymphovascular invasion were 17% (n = 26), perineural invasion, 34% (n = 53), and microscopic or gross extranodal extension (ENE), 19% (n = 30). DAA revealed significant changes in bacterial genera based on high-risk pathologic features, smoking status, vital status, and disease-specific survival (DSS). Genera observed with ANCOM-BC2 include Scardovia, Alloscardovia, Lactobacillus, and Corynebacterium genera for vital status and DSS. CONCLUSION/CONCLUSIONS:Changes in the relative abundance of select intratumoral bacterial genera are associated with adverse pathologic features, DSS, and vital status in HNSCC. Shifts in the microbiome need further investigation to determine if they can provide any mechanistic insight or predictive role.

BACKGROUND:Poor sleep and frailty are prevalent among aging women with HIV (WWH). Although poor sleep quality has been associated with frailty in general aging populations, these relationships are not well characterized among WWH. METHODS:Among 1001 WWH and 371 women without HIV (WWoH) over age 40 years with Pittsburgh Sleep Quality Index (PSQI) and Fried Frailty Phenotype data, we analyzed relationships of poor sleep quality (PSQI>5) and sleep quality components with frailty. Separate hierarchical regression models evaluated associations between sleep and frailty status (prefrail vs. robust, frail vs robust) adjusting for: (1) study site and HIV status, (2) demographics, (3) substance use/Central Nervous System active medications, (4) comorbidities, and (5) depressive symptoms. RESULTS:Median age was 53 years; 9.2% were frail while 52.8% were prefrail. Poor sleep quality was frequent (52% WWH vs. 47% WWoH; p=0.07) and associated with double the frailty odds independent of HIV status, after adjusting for depressive symptoms (fully adjusted odds ratio AOR 1.99, 95% CI:1.14, 3.50, p=0.016). Sleep-associated daytime dysfunction and very poor sleep efficiency were independently associated with being frail. Poor self-rated sleep quality and higher use of sleep medications were independently associated with being prefrail. CONCLUSIONS:Among midlife WWH and WWoH, poor subjective sleep measures are independently associated with higher frailty odds. Longitudinal studies are needed to understand how aspects of sleep may impact progression from prefrailty to frailty after accounting for comorbidities and to elucidate the complex relationships between comorbidities and frailty, with sleep quality among midlife PWH.

BACKGROUND:) pose a major challenge to curing HIV, with many of its mechanisms still unclear. HIV-1 DNA integration and immune responses may alter the host's epigenetic landscape, potentially silencing HIV-1 replication. METHODS:. RESULTS:-associated genes were enriched on the pathways related to immune defence, transcription repression and host-virus interactions. CONCLUSIONS:These findings suggest that HIV-1 reservoir is linked to aberrant DNA methylation in CD4+ T cells, offering new insights into epigenetic mechanisms of HIV-1 latency and potential molecular targets for eradication strategies. KEY POINTS/CONCLUSIONS:Study involved 427 women with HIV. Identified 245 aberrant DNA methylation sites and 85 methylation regions in CD4+ T cells linked to the HIV-1 reservoir. Highlighted genes are involved in viral replication, immune defence, and host genome integration. Findings suggest potential molecular targets for eradication strategies.