Multi-omics in stress and health research: study designs that will drive the field forward

Stress tests and biomarkers of resilience: Proceedings of the second state of resilience science conference

The "Stress Tests and Biomarkers of Resilience" conference, hosted by the American Geriatrics Society and the National Institute on Aging, marks the second in a series aimed at advancing the field of resilience science. Held on March 4-5, 2024, in Bethesda, Maryland, this conference built upon the foundational work from the first conference, which focused on defining resilience across various domains-physical, cognitive, and psychosocial. This year's gathering centered around three factors: the biology that underlies resilient outcomes; the social, environmental, genetic, and psychosocial factors that impact that resilience biology; and the biomarker testing and imaging that predicts resilient outcomes for older adults. The presentations and discussions around these topics were underscored by considerations around the many impacts of social determinants of health on resiliency interventions, and by advances in the modern training and research methodologies that influence data collection and experiment design.

Dynamic Lipidome Reorganization in Response to Heat Shock Stress

The heat shock response (HSR) is a conserved cellular mechanism critical for adaptation to environmental and physiological stressors, with broad implications for cell survival, immune responses, and cancer biology. While the HSR has been extensively studied at the proteomic and transcriptomic levels, the role of lipid metabolism and membrane reorganization remains underexplored. Here, we integrate mass spectrometry-based lipidomics with RNA sequencing to characterize global lipidomic and transcriptomic changes in HeLa cells exposed to three conditions: control, heat shock (HS), and HS with eight hours of recovery. Heat shock-induced extensive lipid remodeling, including significant increases in fatty acids, glycerophospholipids, and sphingolipids, with partial normalization during recovery. Transcriptomic analysis identified over 2700 upregulated and 2300 downregulated genes under heat shock, with GO enrichment suggesting potential transcriptional contributions to lipid metabolism. However, transcriptional changes alone did not fully explain the observed lipidomic shifts, suggesting additional layers of regulation. Joint pathway analysis revealed enrichment in glycerophospholipid and sphingolipid metabolism, while network analysis identified lipid transport regulators (STAB2, APOB), stress-linked metabolic nodes (KNG1), and persistent sphingolipid enrichment during recovery. These findings provide a comprehensive framework for understanding lipid-mediated mechanisms of the HSR and highlight the importance of multi-omics integration in stress adaptation and disease biology.

Rethinking Depression-Beyond Neurotransmitters: An Integrated Psychoneuroendocrineimmunology Framework for Depression's Pathophysiology and Tailored Treatment

It is known that the effectiveness of drug treatment for depression, ammine deficit based, is largely unsatisfactory. In this review, we examine the proposal of a precision therapy has emerged and has received a strong push by the identification of the role of inflammation in depression. However, precision psychiatry risks being caught in the reductionist trap of searching for the molecular switch that resets the whole system and switches off the disease. This is an illusion since the human being is complex and depression is a systemic and variable disorder. In this study, we show the inadequacy of the reductionist paradigm, and, at the same time, illustrate the superiority of the systemic paradigm centered on psychoneuroendocrineimmunology (PNEI). According to the PNEI paradigm, depression is a disease of the whole human being, caused by different sources working together: psychological, biological, and behavioral. This means knowing the biological and psychological history of the subject, identifying relational and biological crisis factors, and building personalized treatments targeting those factors with the tools of medicine and psychology, which are not reducible to the combination of drugs and psychotherapy. Our proposal presents a paradigm shift that is both theoretical and practical, which enables clinicians to assess patients experiencing depression in a unified way and treat them in an integrated manner.

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).

Dynamic Lipidome Reorganization in Response to Heat Shock Stress

The heat shock response (HSR) is a conserved cellular mechanism critical for adaptation to environmental and physiological stressors, with broad implications for cell survival, immune responses, and cancer biology. While the HSR has been extensively studied at the proteomic and transcriptomic levels, the role of lipid metabolism and membrane reorganization remains underexplored. Here, we integrate mass spectrometry-based lipidomics with RNA sequencing to characterize global lipidomic and transcriptomic changes in HeLa cells exposed to three conditions: control, heat shock (HS), and HS with eight hours of recovery. Heat shock-induced extensive lipid remodeling, including significant increases in fatty acids, glycerophospholipids, and sphingolipids, with partial normalization during recovery. Transcriptomic analysis identified over 2,700 upregulated and 2,300 downregulated genes under heat shock, with GO enrichment suggesting potential transcriptional contributions to lipid metabolism. However, transcriptional changes alone did not fully explain the observed lipidomic shifts, suggesting additional layers of regulation. Joint pathway analysis revealed enrichment in glycerophospholipid and sphingolipid metabolism, while network analysis identified lipid transport regulators (STAB2, APOB), stress-linked metabolic nodes (KNG1), and persistent sphingolipid enrichment during recovery. These findings provide a comprehensive framework for understanding lipid-mediated mechanisms of the HSR and highlight the importance of multi-omics integration in stress adaptation and disease biology.

The effects of childhood adversity on twenty-five disease biomarkers and twenty health conditions in adulthood: Differences by sex and stressor type

BACKGROUND

Although early adversity is now recognized as a major public health concern, it remains unclear if the effects of early-life stressors on disease biology and health differ by sex or stressor type. Because childhood stressors often covary, examining whether such stressors typically occur together (e.g., cumulative adversity) or in distinct multivariate patterns is needed to determine if and how different life stressors uniquely affect disease biology and health.

METHOD

To investigate, we conducted latent class analyses (LCA) to identify clusters of adults experiencing multiple childhood stressors (N = 2,111, Mage = 53.04, 54.8% female) in the Midlife in the United States (MIDUS) Study. We then tested how latent stressor exposure groups, and individual stressors, related to 25 biomarkers of inflammation, metabolism, and stress, and 20 major health conditions. Multivariate effect sizes were estimated using Mahalanobis's D.

RESULTS

Optimal LCA models yielded three female (Low-, Moderate-, and High-Stress) and two male (Low- and High-Stress) stressor exposure classes. The High-Stress classes had greater inflammation (male: D = 0.43; female: D = 0.59) and poorer metabolic health (male: D = 0.32-0.33; female: D = 0.32-0.47). They also had more cardiovascular (male: HR = 1.56 [1.17, 2.07]; female: HR = 1.97 [1.50, 2.58]), cancer (male: HR = 2.41 [1.52, 3.84]; female: HR = 2.51 [1.45, 4.35]), metabolic (male: HR = 1.54 [1.16, 2.03]; female: HR = 2.01 [1.43, 2.83]), thyroid (male: HR = 3.65 [1.87, 7.12]; female: HR = 2.25 [1.36, 3.74]), arthritis (male: HR = 1.81 [1.30, 2.54]; female: HR = 1.97 [1.41, 2.74]), and mental/behavioral health problems (male: HR = 2.62 [1.90, 3.62]; female; HR = 3.67 [2.72, 4.94]). Moreover, stressors were related to these outcomes in a sex- and stressor-specific manner.

CONCLUSIONS

Childhood adversity portends worse biological health and elevated risk for many major health problems in a sex- and stressor-specific manner. These findings advance stress theory, and may help inform precision interventions for managing stress and enhancing resilience.

RNA Editing Signatures Powered by Artificial Intelligence: A New Frontier in Differentiating Schizophrenia, Bipolar, and Schizoaffective Disorders

Mental health disorders are devastating illnesses, often misdiagnosed due to overlapping clinical symptoms. Among these conditions, bipolar disorder, schizophrenia, and schizoaffective disorder are particularly difficult to distinguish, as they share alternating positive and negative mood symptoms. Accurate and timely diagnosis of these diseases is crucial to ensure effective treatment and to tailor therapeutic management to each individual patient. In this context, it is essential to move beyond standard clinical assessment and employ innovative approaches to identify new biomarkers that can be reliably quantified. We previously identified a panel of RNA editing biomarkers capable of differentiating healthy controls from depressed patients and, among depressed patients, those with major depressive disorder and those with bipolar disorder. In this study, we integrated Adenosine-to-Inosine RNA editing blood biomarkers with clinical data through machine learning algorithms to establish specific signatures for bipolar disorder and schizophrenia spectrum disorders. This groundbreaking study paves the way for the application of RNA editing in other psychiatric disorders, such as schizophrenia and schizoaffective disorder. It represents a first proof-of-concept and provides compelling evidence for the establishment of an RNA editing signature for the diagnosis of these psychiatric conditions.

Adverse childhood experiences (ACEs) and emotion dysregulation phenotypes: An intersectional analysis of race/ethnicity and gender in a nationally representative U.S. sample

BACKGROUND

Adverse childhood experiences (ACEs) are strong, preventable risk factors for emotion dysregulation in adolescence, but whether ACEs-emotion dysregulation associations differ by race/ethnicity or gender remains unclear.

OBJECTIVE

We examined (a) how race/ethnicity and gender jointly impact latent ACEs classes and emotion dysregulation phenotypes, and (b) how these ACEs classes in childhood (by age 9) transition to latent emotion dysregulation phenotypes in adolescence (at age 15).

PARTICIPANTS AND SETTING

Participants were 3,273 children from two waves of data from the Future of Families and Child Wellbeing Study, a large, nationally representative cohort. The sample consisted of 26.6% non-Hispanic (NH) Black boys, 25.4% NH Black girls, 12.9% Hispanic boys, 12.6% Hispanic girls, 11.8% NH White boys, and 10.7% NH White girls.

METHOD

We estimated latent class models to identify ACEs patterns across ten indicators and dysregulation phenotypes across affective, attentional, and behavioral domains. Latent transition analysis was used to examine how ACEs classes transitioned into dysregulation phenotypes from childhood into adolescence.

RESULTS

The findings revealed significant variation in the number and nature of latent classes of both ACEs and emotion dysregulation across the intersection of race/ethnicity and gender. NH Black and Hispanic children were more likely to be in the Poverty and Parental Separation class than NH White children. Hispanic boys had the highest prevalence of Severe Dysregulation (16%), whereas NH White boys had the highest prevalence of Low Symptoms (52%). Individuals in the Poverty and Parental Separation class had a higher probability of transitioning to the Low Symptoms class. In contrast, those in the Abuse and Family Dysfunction class were more likely to transition to the Severe Dysregulation class, with NH White girls showing the highest probability (.34), nearly twice that of NH Black girls (.19). These gender differences in these transition probabilities were observed for Whites but not Blacks.

CONCLUSIONS

These findings thus highlight the need for adopting an intersectional, person-centered approach when studying the effects of ACEs on adolescent development.

AMP-Activated Protein Kinase Treatment Ameliorates Chronic Restraint Stress Induced Memory Impairment in Early Adolescent Rat by Restoring Metabolite Profile and Synaptic Proteins

Recent studies highlight the role of brain metabolites in regulation of neuronal signals and behaviour. To understand the underlying mechanism, brain metabolites and associated signaling molecules were examined in early adolescent rat experienced CRS. Rats were tested for their learning and memory ability, and their metabolite profile was evaluated using Gas chromatography-mass spectrometry (GC-MS). Differences in metabolites were examined by variable importance in projection (VIP) and multivariate analysis. Ingenuity Pathway Analysis (IPA) and KEGG ID were performed for the identified metabolites. We found that CRS altered the metabolites that were involved in biosynthesis of steroid hormone, aminoacyl t-RNA, L-Dopa biosynthesis, and metabolism of tyrosine, fatty acid, and purine. Further analysis showed reduction of 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR, a metabolite involved in purine metabolism) an AMP kinase activator, influenced the hypoxanthine-guanine phosphoribosyltransferase (HPRT), serotonin transporter (SERT), postsynaptic density protein (PSD) -95, its phosphorylation and brain-derived neurotrophic factor (BDNF) in CRS animals, which displayed deficit in memory. The AICAR treated CRS rats showed improved memory and altered metabolites and other molecules (HPRT, SERT, PSD-95 and BDNF) levels were restored. Our analysis revealed that CRS induced changes in metabolites possibly altered synaptic plasticity and memory in which HPRT, SERT-PSD95-BDNF associated pathway involved. Taken together, our observation provides initial insight into how stress differently influences the metabolic pathway, and associated behaviour. Further study will help to develop pharmacological intervention strategies.

Neurobehavioral dysfunction in a mouse model of Down syndrome: upregulation of cystathionine β-synthase, H2S overproduction, altered protein persulfidation, synaptic dysfunction, endoplasmic reticulum stress, and autophagy

Down syndrome (DS) is a genetic condition where the person is born with an extra chromosome 21. DS is associated with accelerated aging; people with DS are prone to age-related neurological conditions including an early-onset Alzheimer's disease. Using the Dp(17)3Yey/ + mice, which overexpresses a portion of mouse chromosome 17, which encodes for the transsulfuration enzyme cystathionine β-synthase (CBS), we investigated the functional role of the CBS/hydrogen sulfide (H2S) pathway in the pathogenesis of neurobehavioral dysfunction in DS. The data demonstrate that CBS is higher in the brain of the DS mice than in the brain of wild-type mice, with primary localization in astrocytes. DS mice exhibited impaired recognition memory and spatial learning, loss of synaptosomal function, endoplasmic reticulum stress, and autophagy. Treatment of mice with aminooxyacetate, a prototypical CBS inhibitor, improved neurobehavioral function, reduced the degree of reactive gliosis in the DS brain, increased the ability of the synaptosomes to generate ATP, and reduced endoplasmic reticulum stress. H2S levels in the brain of DS mice were higher than in wild-type mice, but, unexpectedly, protein persulfidation was decreased. Many of the above alterations were more pronounced in the female DS mice. There was a significant dysregulation of metabolism in the brain of DS mice, which affected amino acid, carbohydrate, lipid, endocannabinoid, and nucleotide metabolites; some of these alterations were reversed by treatment of the mice with the CBS inhibitor. Thus, the CBS/H2S pathway contributes to the pathogenesis of neurological dysfunction in DS in the current animal model.

James German and the Quest to Understand Human RECQ Helicase Deficiencies

James German's work to establish the natural history and cancer risk associated with Bloom syndrome (BS) has had a strong influence on the generation of scientists and clinicians working to understand other RECQ deficiencies and heritable cancer predisposition syndromes. I summarize work by us and others below, inspired by James German's precedents with BS, to understand and compare BS with the other heritable RECQ deficiency syndromes with a focus on Werner syndrome (WS). What we know, unanswered questions and new opportunities are discussed, as are potential ways to treat or modify WS-associated disease mechanisms and pathways.

California Stress, Trauma, and Resilience Study (CalSTARS) protocol: A multiomics-based cross-sectional investigation and randomized controlled trial to elucidate the biology of ACEs and test a precision intervention for reducing stress and enhancing resilience

Adverse Childhood Experiences (ACEs) are very common and presently implicated in 9 out of 10 leading causes of death in the United States. Despite this fact, our mechanistic understanding of how ACEs impact health is limited. Moreover, interventions for reducing stress presently use a one-size-fits-all approach that involves no treatment tailoring or precision. To address these issues, we developed a combined cross-sectional study and randomized controlled trial, called the California Stress, Trauma, and Resilience Study (CalSTARS), to (a) characterize how ACEs influence multisystem biological functioning in adults with all levels of ACE burden and current perceived stress, using multiomics and other complementary approaches, and (b) test the efficacy of our new California Precision Intervention for Stress and Resilience (PRECISE) in adults with elevated perceived stress levels who have experienced the full range of ACEs. The primary trial outcome is perceived stress, and the secondary outcomes span a variety of psychological, emotional, biological, and behavioral variables, as assessed using self-report measures, wearable technologies, and extensive biospecimens (i.e. DNA, saliva, blood, urine, & stool) that will be subjected to genomic, transcriptomic, proteomic, metabolomic, lipidomic, immunomic, and metagenomic/microbiome analysis. In this protocol paper, we describe the scientific gaps motivating this study as well as the sample, study design, procedures, measures, and planned analyses. Ultimately, our goal is to leverage the power of cutting-edge tools from psychology, multiomics, precision medicine, and translational bioinformatics to identify social, molecular, and immunological processes that can be targeted to reduce stress-related disease risk and enhance biopsychosocial resilience in individuals and communities worldwide.