Bradley E. Aouizerat

Abstract

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: Database study. Setting: 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: 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.

Abstract

While immunotherapy tends to be ineffective against pancreatic ductal adenocarcinoma (PDAC), this cancer type often elicits B-cell immunity. However, the exact antigens responsible for these spontaneous immune responses are still unclear. This study used a unique high-dimensional ELISA to analyze IgG responses to 93 post-translational modifications and other chemical determinants in PDAC patients at the time of diagnosis and before therapy. Results identified 13 specific targets of serum IgG that distinguished PDAC patients from healthy donors. Phosphorylated-serine, -threonine, and -tyrosine emerged as the primary targets, with most patients showing high-titer IgG, predominantly of the IgG1 and IgG3 subclasses. Moreover, serum reactivity to these phosphorylated residues was higher in patients with metastatic disease, suggesting a relation between B cell immunity and tumor burden. Lastly, immunofluorescence staining and phosphoproteomic analysis provided evidence of the accumulation of phosphorylated amino acids in PDAC cells and identified a series of consensus abnormal phosphosites. Overall, our findings reveal for the first time the development of robust antibody responses targeting phosphorylated residues in PDAC.

Abstract

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.

Abstract

Background: Depression affects 33% of women with type 2 diabetes (T2D) and leads to increased risks of premature mortality. Fluctuation and variation of depressive presentations can hinder clinical identification. Purpose: We aimed to identify and examine subgroups characterized by distinct depressive symptom trajectories among women with T2D. Methods: This retrospective analysis leveraged the Women’s Interagency HIV Study data to identify depressive symptom trajectories based on the Center for Epidemiological Studies Depression scores (2014-2019) among women with and without HIV. Descriptive statistics characterized sample demographics (eg, age, race, income), clinical indices (eg, hemoglobin A1C [HbA1c], BMI, HIV status), and psychosocial experiences (eg, discrimination, social support, anxiety, pain). We used growth mixture modeling to identify groups defined by distinct depressive symptom trajectories and parametric and non-parametric tests to examine demographic, clinical, and psychosocial differences across subgroups. Results: Among the 630 women included, the mean age was 50.4 (SD = 8.3) years, 72.4% identified as Black and non-Hispanic, and 68.2% were living with HIV. Five subgroups were identified and distinguished by severity and symptom type. Participants with lower incomes (P = .01), lower employment (P < .0001), lower social support (P = .0001), and experiences of discrimination (P < .0001) showed greater membership in threshold, moderate, and severe depressive subgroups. Subgroup membership was not associated with metabolic indices (BMI, HbA1c) or HIV status. Anxiety, pain, and loneliness (all P = .0001) were worse in subgroups with higher depressive symptoms. Conclusions: Among women with T2D, depressive symptom trajectories differ across clinical and social contexts. This study advances precision by delineating subgroups within a broad clinical category.

Abstract

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.

Abstract

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.

Abstract

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 (β=.33, p,.001) and a higher proportion of racial/ethnic minority residents (β =.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 (β =.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 (β=−.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.

Abstract

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: 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.

Abstract

Objective: 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: 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: 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: 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.

Abstract

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.