Expression of socially sensitive genes: The multi-ethnic study of atherosclerosis

How community connection, homophobia, and racism shape gene expression in sexual minority men with and without HIV

OBJECTIVE

Although sexual minority men experience substantial discrimination, in addition to increased risk for several serious mental and somatic health problems, the biological mechanisms underlying these effects are unclear. To address this issue, we examined how experiences of social safety (i.e., community connection) and social threat (i.e., discrimination, in the forms of homophobia and racism) were related to conserved transcriptional response to adversity (CTRA) gene expression profiles across time, and whether these associations differed across HIV status, in a well-characterized, racially diverse sample of sexual minority men (Mage = 22.61, SD = 1.90).

METHOD

Experiences of community connection, homophobia, and racism were assessed via self-report, and blood samples were obtained at three timepoints over approximately 2 years. We then used these blood samples to characterize participants' CTRA gene expression, which we quantified using an a priori 53-transcript composite score derived from RNA sequencing data from peripheral blood leukocytes.

RESULTS

As hypothesized, greater community connection was significantly related to decreased CTRA gene expression across time. These effects were similar regardless of HIV status and were robust to statistical adjustment for several potential confounding factors. In contrast, neither homophobia nor racism were related to CTRA gene expression.

CONCLUSION

These results suggest that community connection may be a protective factor that reduces biological processes known to negatively impact health. Consequently, interventions and policies aimed at reducing health disparities in marginalized populations may benefit from increasing community connection and inclusion. (PsycInfo Database Record (c) 2025 APA, all rights reserved).

Genome-wide transcriptome differences associated with perceived discrimination in an urban, community-dwelling middle-aged cohort

Discrimination is a social adversity that is linked to several age-related outcomes. However, the molecular drivers of these observations are poorly understood. Social adverse factors are associated with proinflammatory and interferon gene expression, but little is known about whether additional genes are associated with discrimination among both African American and White adults. In this study, we examined how perceived discrimination in African American and White adults was associated with genome-wide transcriptome differences using RNA sequencing. Perceived discrimination was measured based on responses to self-reported lifetime discrimination and racial discrimination. Differential gene expression and pathway analysis were conducted in a cohort (N = 59) stratified by race, sex, and overall discrimination level. We found 28 significantly differentially expressed genes associated with race among those reporting high discrimination. Several of the upregulated genes for African American versus White adults reporting discrimination were related to immune function IGLV2-11, S100B, IGKV3-20, and IGKV4-1; the most significantly downregulated genes were associated with immune modulation and cancer, LUCAT1, THBS1, and ARPIN. The most enriched gene ontology biological process between African American and White men reporting high discrimination was the regulation of cytokine biosynthetic processes. The immune response biological process was significantly lower for African American women compared to White women reporting high discrimination. Discrimination was associated with the expression of small nucleolar RNAs, long noncoding RNAs, and microRNAs associated with energy homeostasis, cancer, and actin. Understanding the pathways through which adverse social factors like discrimination are associated with gene expression is crucial in advancing knowledge of age-related health disparities.

Proteome-wide association studies for blood lipids and comparison with transcriptome-wide association studies

Blood lipid traits are treatable and heritable risk factors for heart disease, a leading cause of mortality worldwide. Although genome-wide association studies (GWASs) have discovered hundreds of variants associated with lipids in humans, most of the causal mechanisms of lipids remain unknown. To better understand the biological processes underlying lipid metabolism, we investigated the associations of plasma protein levels with total cholesterol (TC), triglycerides (TG), high-density lipoprotein (HDL) cholesterol, and low-density lipoprotein (LDL) cholesterol in blood. We trained protein prediction models based on samples in the Multi-Ethnic Study of Atherosclerosis (MESA) and applied them to conduct proteome-wide association studies (PWASs) for lipids using the Global Lipids Genetics Consortium (GLGC) data. Of the 749 proteins tested, 42 were significantly associated with at least one lipid trait. Furthermore, we performed transcriptome-wide association studies (TWASs) for lipids using 9,714 gene expression prediction models trained on samples from peripheral blood mononuclear cells (PBMCs) in MESA and 49 tissues in the Genotype-Tissue Expression (GTEx) project. We found that although PWASs and TWASs can show different directions of associations in an individual gene, 40 out of 49 tissues showed a positive correlation between PWAS and TWAS signed p values across all the genes, which suggests high-level consistency between proteome-lipid associations and transcriptome-lipid associations.

Structural and social determinants of health: The multi-ethnic study of atherosclerosis

BACKGROUND

Researchers have increasingly recognized the importance of structural and social determinants of health (SSDOH) as key drivers of a multitude of diseases and health outcomes. The Multi-Ethnic Study of Atherosclerosis (MESA) is an ongoing, longitudinal cohort study of subclinical cardiovascular disease (CVD) that has followed geographically and racially/ethnically diverse participants starting in 2000. Since its inception, MESA has incorporated numerous SSDOH assessments and instruments to study in relation to CVD and aging outcomes. In this paper, we describe the SSDOH data available in MESA, systematically review published papers using MESA that were focused on SSDOH and provide a roadmap for future SSDOH-related studies.

METHODS AND FINDINGS

The study team reviewed all published papers using MESA data (n = 2,125) through January 23, 2023. Two individuals systematically reviewed titles, abstracts, and full text to determine the final number of papers (n = 431) that focused on at least one SSDOH variable as an exposure, outcome, or stratifying/effect modifier variable of main interest (discrepancies resolved by a third individual). Fifty-seven percent of the papers focused on racialized/ethnic groups or other macrosocial/structural factors (e.g., segregation), 16% focused on individual-level inequalities (e.g. income), 14% focused on the built environment (e.g., walking destinations), 10% focused on social context (e.g., neighborhood socioeconomic status), 34% focused on stressors (e.g., discrimination, air pollution), and 4% focused on social support/integration (e.g., social participation). Forty-seven (11%) of the papers combined MESA with other cohorts for cross-cohort comparisons and replication/validation (e.g., validating algorithms).

CONCLUSIONS

Overall, MESA has made significant contributions to the field and the published literature, with 20% of its published papers focused on SSDOH. Future SSDOH studies using MESA would benefit by using recently added instruments/data (e.g., early life educational quality), linking SSDOH to biomarkers to determine underlying causal mechanisms linking SSDOH to CVD and aging outcomes, and by focusing on intersectionality, understudied SSDOH (i.e., social support, social context), and understudied outcomes in relation to SSDOH (i.e., sleep, respiratory health, cognition/dementia).

Social Genomic Determinants of Health: Understanding the Molecular Pathways by Which Neighborhood Disadvantage Affects Cancer Outcomes

PURPOSE

Neighborhoods represent complex environments with unique social, cultural, physical, and economic attributes that have major impacts on disparities in health, disease, and survival. Neighborhood disadvantage is associated with shorter breast cancer recurrence-free survival (RFS) independent of individual-level (race, ethnicity, socioeconomic status, insurance, tumor characteristics) and health system-level determinants of health (receipt of guideline-concordant treatment). This persistent disparity in RFS suggests unaccounted mechanisms such as more aggressive tumor biology among women living in disadvantaged neighborhoods compared with advantaged neighborhoods. The objective of this article was to provide a clear framework and biological mechanistic explanation for how neighborhood disadvantage affects cancer survival.

METHODS

Development of a translational epidemiological framework that takes a translational disparities approach to study cancer outcome disparities through the lens of social genomics and social epigenomics.

RESULTS

The social genomic determinants of health, defined as the physiological gene regulatory pathways (ie, neural/endocrine control of gene expression and epigenetic processes) through which contextual factors, particularly one's neighborhood, can affect activity of the cancer genome and the surrounding tumor microenvironment to alter disease progression and treatment outcomes.

CONCLUSION

We propose a novel, multilevel determinants of health model that takes a translational epidemiological approach to evaluate the interplay between political, health system, social, psychosocial, individual, and social genomic determinants of health to understand social disparities in oncologic outcomes. In doing so, we provide a concrete biological pathway through which the effects of social processes and social epidemiology come to affect the basic biology of cancer and ultimately clinical outcomes and survival.

ZIP Code to Genomic Code: Neighborhood Disadvantage, Aggressive Breast Cancer Biology, and Breast Cancer Outcomes

OBJECTIVE

To determine the association between objective (geospatial) and subjective (perceived) measures of neighborhood disadvantage (ND) and aggressive breast cancer tumor biology, defined using validated social adversity-associated transcription factor (TF) activity and clinical outcomes.

BACKGROUND

ND is associated with shorter breast cancer recurrence-free survival (RFS), independent of individual, tumor, and treatment characteristics, suggesting potential unaccounted biological mechanisms by which ND influences RFS.

METHODS

We quantified TF-binding motif prevalence within promoters of differentially expressed genes for 147 tissue samples prospectively collected on the protocol. Covariate-adjusted multivariable regression analyzed objective and subjective ND scores with 5 validated TFs of social adversity and aggressive biology-pro-inflammatory activity [nuclear factor-κB ( NF-kB ), activator protein 1 ( AP-1 )], sympathetic nervous system (SNS) activity [cyclic 3'-5' adenosine monophosphate response element-binding protein ( CREB )], and protective cellular responses [interferon-regulatory factor ( IRF ) and signal transducer and activator of transcription ( STAT )]. To clinically validate these TFs as prognostic biomarkers of aggressive biology, logistic regression and multivariable Cox proportional-hazards models analyzed their association with Oncotype DX scores and RFS, respectively.

RESULTS

Increasing objective ND was associated with aggressive tumor biology (up-regulated NF-kB , activator protein 1, down-regulated IRF , and signal transducer and activator of transcription) and SNS activation (up-regulated CREB ). Increasing subjective ND (eg, threat to safety) was associated with up-regulated NF-kB and CREB and down-regulated IRF . These TF patterns were associated with high-risk Oncotype DX scores and shorter RFS.

CONCLUSIONS

In the largest human social genomics study, objective and subjective ND were significantly associated with TFs of aggressive biology and SNS activation. These TFs also correlated with worse clinical outcomes, implicating SNS activation as one potential mechanism behind ND survival disparities. These findings remain to be validated in a national cohort.

Experiences of racial discrimination and adverse gene expression among black individuals in a level 1 trauma center sample

Up to 40 % of individuals who sustain traumatic injuries are at risk for posttraumatic stress disorder (PTSD) and the conditional risk for developing PTSD is even higher for Black individuals. Exposure to racial discrimination, including at both interpersonal and structural levels, helps explain this health inequity. Yet, the relationship between racial discrimination and biological processes in the context of traumatic injury has yet to be fully explored. The current study examined whether racial discrimination is associated with a cumulative measure of biological stress, the gene expression profile conserved transcriptional response to adversity (CTRA), in Black trauma survivors. Two-weeks (T1) and six-months (T2) post-injury, Black participants (N = 94) provided a blood specimen and completed assessments of lifetime racial discrimination and PTSD symptoms. Mixed effect linear models evaluated the relationship between change in CTRA gene expression and racial discrimination while adjusting for age, gender, body mass index (BMI), smoking history, heavy alcohol use history, and trauma-related variables (mechanism of injury, lifetime trauma). Results revealed that for individuals exposed to higher levels of lifetime racial discrimination, CTRA significantly increased between T1 and T2. Conversely, CTRA did not increase significantly over time in individuals exposed to lower levels of lifetime racial discrimination. Thus, racial discrimination appeared to lead to a more sensitized biological profile which was further amplified by the effects of a recent traumatic injury. These findings replicate and extend previous research elucidating the processes by which racial discrimination targets biological systems.

Proteome-Wide Association Studies for Blood Lipids and Comparison with Transcriptome-Wide Association Studies

Blood lipid traits are treatable and heritable risk factors for heart disease, a leading cause of mortality worldwide. Although genome-wide association studies (GWAS) have discovered hundreds of variants associated with lipids in humans, most of the causal mechanisms of lipids remain unknown. To better understand the biological processes underlying lipid metabolism, we investigated the associations of plasma protein levels with total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL), and low-density lipoprotein cholesterol (LDL) in blood. We trained protein prediction models based on samples in the Multi-Ethnic Study of Atherosclerosis (MESA) and applied them to conduct proteome-wide association studies (PWAS) for lipids using the Global Lipids Genetics Consortium (GLGC) data. Of the 749 proteins tested, 42 were significantly associated with at least one lipid trait. Furthermore, we performed transcriptome-wide association studies (TWAS) for lipids using 9,714 gene expression prediction models trained on samples from peripheral blood mononuclear cells (PBMCs) in MESA and 49 tissues in the Genotype-Tissue Expression (GTEx) project. We found that although PWAS and TWAS can show different directions of associations in an individual gene, 40 out of 49 tissues showed a positive correlation between PWAS and TWAS signed p-values across all the genes, which suggests a high-level consistency between proteome-lipid associations and transcriptome-lipid associations.

Intersectional vulnerability in the relationship between discrimination and inflammatory gene expression

Addressing social disparities in health and well-being requires understanding how the effects of discrimination become biologically embedded, and how embedding processes might vary across different demographic contexts. Emerging research suggests that a threat-related gene expression response may contribute to social disparities in health. We tested a contextual vulnerability model of discrimination embedding using an empirical intersectionality (interaction discovery) analysis of pro-inflammatory gene expression in a national sample of non-institutionalized, English-speaking adults with RNA biomarker data (n = 543). At the time of data collection, the average age of participants was 55 years (SD = 13.26) and approximately half identified as female (50.46%). Most participants identified as White (∼73%) and had some college experience (∼60%). Results showed significant variation in the strength of association between daily discrimination and inflammatory gene expression by race and sex (b = -0.022; 95% CI:-0.038,-0.005, p = .009) with the estimated marginal association larger for racially-minoritized males (b = 0.007; 95% CI:-0.003,0.017, p = .163), compared to White males (b = -0.006; 95% CI:-0.013,0.001, p = .076). This study indicates that the link between daily discrimination and inflammatory gene expression may vary by sociodemographic characteristics. To improve initiatives and policies aimed at ameliorating disparities within populations, greater attention is needed to understand how interlocking systems of inequalities contribute to physiological health.

Social Genomics of Methamphetamine Use, HIV Viral Load, and Social Adversity

Background

Social genomics has demonstrated altered inflammatory and type I interferon (IFN) gene expression among people experiencing chronic social adversity. Adverse social experiences such as discrimination and violence are linked to stimulant misuse and HIV, conditions that dysregulate inflammatory and innate antiviral responses, leading to increased HIV viral replication and risk of chronic diseases.

Purpose

We aimed to determine whether methamphetamine (MA) use, unsuppressed HIV viral load (VL) (≥200 c/mL), and experienced intimate partner violence (IPV) (past 12 months) predicted inflammatory and type I IFN gene expression in HIV-positive Black and Latinx men who have sex with men (MSM).

Methods

Participants were 147 HIV-positive Black and Latinx MSM recruited from the mSTUDY, a cohort of 561 MSM aged 18–45 in Los Angeles, CA, of whom half are HIV-positive and substance-using. Transcriptomic measures of inflammatory and type I IFN activity were derived from RNA sequencing of peripheral blood mononuclear cells and matched to urine drug tests, VL, and survey data across two time points 12 months apart. Analysis used linear random intercept modeling of MA use, unsuppressed VL, and experienced IPV on inflammatory and type I IFN expression.

Results

In adjusted models, MA use predicted 27% upregulated inflammatory and 31% upregulated type I IFN expression; unsuppressed VL predicted 84% upregulated type I IFN but not inflammatory expression; and experienced IPV predicted 31% upregulated inflammatory and 26% upregulated type I IFN expression.

Conclusions

In Black and Latinx MSM with HIV, MA use, unsuppressed VL, and experienced IPV predicted upregulated social genomic markers of immune functioning.

Transcriptomic analyses of black women in neighborhoods with high levels of violence

Chronic stress threatens an individual's capacity to maintain psychological and physiological homeostasis, but the molecular processes underlying the biological embedding of these experiences are not well understood. This is particularly true for marginalized groups, presenting a fundamental challenge to decreasing racial, economic, and gender-based health disparities. Physical and social environments influence genome function, including the transcriptional activity of core stress responsive genes. We studied the relationship between social experiences that are associated with systemic inequality (e.g., racial segregation, poverty, and neighborhood violence) and blood cell (leukocytes) gene expression, focusing on the activation of transcription factors (TF) critical to stress response pathways. The study used data from 68 women collected from a convenience sample in 2013 from the Southside of Chicago. Comparing single, low-income Black mothers living in neighborhoods with high levels of violence (self-reported and assessed using administrative police records) to those with low levels of violence we found no significant differences in expression of 51 genes associated with the Conserved Transcriptional Response to Adversity (CTRA). Using TELiS analysis of promoter TF-binding motif prevalence we found that mothers who self-reported higher levels of neighborhood stress showed greater expression of genes regulated by the glucocorticoid receptor (GR). These findings may reflect increased cortisol output from the hypothalamic-pituitary-adrenal (HPA) axis, or increased GR transcriptional sensitivity. Transcript origin analyses identified monocytes and dendritic cells as the primary cellular sources of gene transcripts up-regulated in association with neighborhood stress. The prominence of GR-related transcripts and the absence of sympathetic nervous system-related CTRA transcripts suggest that a subjective perception of elevated chronic neighborhood stress may be associated with an HPA-related defeat-withdrawal phenotype rather than a fight-or-flight phenotype. The defeat-withdrawal phenotype has been previously observed in animal models of severe, overwhelming threat. These results demonstrate the importance of studying biological embedding in diverse environments and communities, specifically marginalized populations such as low-income Black women.

SARS-CoV-2 morbidity and mortality in racial/ethnic minority populations: A window into the stress related inflammatory basis of health disparities?

Health disparity related to race/ethnicity has been cited as “the most serious and shameful health care issue of our time”(Peterson et al., 2018). A portion of the now recognized disproportionate impact of the COVID-19 pandemic among Black, Indigenous and People of Color (BIPOC) communities is attributable to social determinants such as socioeconomic status (SES), physical living situation, health care access, and the psychosocial factors associated with socioenvironmental circumstances such as bias, victimization, trauma and toxic stress as well as structural factors that reduce the capacity to practice physical distancing (Agurs-Collins et al., 2019).

In this paper, we hypothesize that, prior to the COVID-19 pandemic, disproportionate socio-economic and environmental stressors in the BIPOC population promoted heightened stress-associated neurobiological activity (Stress-NbA). This chronic elevation in Stress-NbA results in down-stream complications of chronic stress including underactivation of anti-viral type I IFN pathway genes. This results in an increase in susceptibility to viral diseases, including coronavirus illnesses. Additionally, Stress-NbA chronically potentiates systemic inflammation (from hematopoietic system activation with myelopoiesis) increasing the prevalence of metabolic syndrome (MetS) and setting the stage for stress-related chronic non-communicable diseases (NCDs).

This process was propelled by overactivation of immune cell gene expression in the nuclear factor κ-light-chain-enhancer of activated B cells (NF-kB) activation pathway and underactivation of gene expression in the anti-viral type I interferon (IFN) pathway. The higher prevalence of MetS and NCDs in minority populations turned out to be predictive of the elevated risk they would face in the presence of a highly contagious viral pandemic. The stress-related generation of a chronic non-pathogen associated molecular pattern (non-PAMP) immunoactivation state led to decreased viral immune defense and increased susceptibility to SARS-CoV-2 infection with increased risk of severe illness induced by cytokine storm syndrome (CSS).

•

There is a disproportionate impact of the COVID-19 pandemic among Black, Indigenous and People of Color (BIPOC) communities.

•

Prior to the COVID-19 pandemic and during the pandemic, existing disproportionate structural, socio-economic and environmental stressors in the BIPOC communities may have resulted in heightened stress-associated neurobiological activity (Stress-NbA).

•

In this paper, we hypothesize that a combination of chronic elevation of stress-NbA, systemic inflammation, stress response and immune response related factors aligned against BIPIC communities are potential drivers of excess morbidity and mortality.

Social regulation of inflammation related gene expression in the multi-ethnic study of atherosclerosis

BACKGROUND

Exposure to adverse social factors has been associated with an altered inflammatory profile, a risk factor for several acute and chronic diseases. Differential gene expression may be a biological mediator in the relationship. In this study, associations between a range of social factors and expression of inflammation-related genes were investigated.

METHODS

Social factor and gene expression data were collected from 1,264 individuals in the Multi-Ethnic Study of Atherosclerosis (MESA). Inflammation-related genes were identified from the Gene Ontology database. The associations between social factors and gene expression were first assessed using the Global Analysis of Covariance (Global ANCOVA) gene set enrichment test. When the global test was significant, linear regression and elastic net penalized regression were employed to identify the individual gene transcripts within each gene set associated with the social factor.

RESULTS

Loneliness (p = 0.003), chronic burden (p = 0.002), and major or lifetime discrimination (p = 0.045) were significantly associated with global expression of the chronic inflammatory gene set. Of the 20 transcripts that comprise this gene set, elastic net selected 12 transcripts for loneliness, 8 for chronic burden, and 3 for major or lifetime discrimination. Major or lifetime discrimination was also associated with the inflammatory response (p = 0.029), regulation of the inflammatory response (p = 0.041), and immune response (p = 0.025) gene sets in global analyses, and 53, 136, and 26 transcripts were selected via elastic net for these gene sets respectively. There were no significant associations in linear regression analyses after adjustment for multiple testing.

CONCLUSIONS

This study highlights gene expression as a biological mechanism through which social factors may affect inflammation.

Experienced homophobia and gene expression alterations in Black and Latino men who have sex with men in Los Angeles County

Men who have sex with men (MSM) experience high rates of homophobic victimization, which is linked to myriad chronic physical and mental health disparities. Social adversity such as rejection, isolation, and racial discrimination can induce a conserved transcriptional response to adversity (CTRA) involving upregulation of proinflammatory genes and downregulation of type I interferon and antibody synthesis genes. This study specifically examines whether homophobic victimization is associated with expression of CTRA profiles in Black and Latino MSM living in Los Angeles. Analyses linked behavioral survey data with quantified RNA from leukocytes from blood samples of 70 participants over 12 months. CTRA gene expression was increased by 3.1-fold in MSM who experienced homophobic victimization while adjusting for major leukocyte subsets and sociodemographics. Accounting for all these factors, CTRA gene expression was significantly enhanced in MSM who identified as Black compared to Latino. Our findings identify experiences of homophobic victimization as drivers of inflammatory and type I interferon gene expression profiles, which can contribute to physical and mental health challenges in Black and Latino MSM.