Extreme physiological stress induced by hypobaric hypoxia at high altitude (HA) alters nucleosome organization across the genome, affecting multiple tissues and cell types. Investigating hypoxic responses is essential to understand inter-individual differences in susceptibility, their impact on vital organs, underlying epigenetic modifications, and the clinical consequences of compromised oxygen delivery. Remarkably, the fragmentation pattern of cell-free (cf) DNA in high-altitude pulmonary edema (HAPE), a life-threatening, non-cardiogenic form of pulmonary edema that occurs in susceptible individuals traveling to altitudes >2500m asl, can identify disease-specific changes in nucleosome positioning attributable to hypoxia-induced gene activation or repression. The present case-control study profiled cfDNA fragmentation patterns in 42 healthy HA acclimatized sojourners designated as controls and HAPE patients, further subdivided into mild (n=40), moderate (n=40), and severe (n=37) categories. The windowed protection score employed for tissue deconvolution analysis showed a greater contribution of cfDNA fragments from immune cells, the adrenal gland, spleen, pancreas, liver, and the esophageal muscularis mucosa in HAPE, indicating the systemic impact of the disease, even though its main symptoms are localized in the lungs. In addition, severe HAPE patients exhibited tissue contributions from lung fibroblasts, renal epithelium, and thyroid tissue, suggesting extensive tissue damage in these patients. The positive correlations of cfDNA concentration, peripheral oxygen saturation, respiratory rate, and pulse rate with tissue-specific fragmentation scores enhanced the translational value of the study. Furthermore, motif enrichment analysis, using HAPE-specific open chromatin regions and their integration with in-house RNA-seq data, revealed significant enrichment of oxygen-sensing, inflammatory, and immune-signaling pathways in HAPE.

Estrogens regulate key processes in parturition, yet the specific effects of estradiol (E2) on maternal reproductive tissues in sheep remain unclear. This study investigated the impact of exogenous E2, mimicking physiological prepartum levels, on gene expression in the myometrium, endometrium, cervix, and placental membranes, as well as sex steroid receptor protein expression in uterine compartments of late pregnant ewes. Pregnant ewes (139-142 days gestation) received Silastic implants containing either E2 (200 µg/ewe, n = 6) or control (n = 6), and tissues were collected 26 h post-treatment. Bulk RNA sequencing assessed differential gene expression, while fluorescence immunohistochemistry evaluated nuclear receptor localization and intensity. Transcriptomic analysis (FDR < 0.05) revealed a tissue-specific response, with the cervix showing the most robust transcriptional changes. Gene Ontology enrichment indicated downregulation of extracellular matrix organization pathways associated with cervical dilation at parturition. Targeted analyses revealed regulation of genes related to prostaglandin synthesis, steroid metabolism, immune signaling, and ECM remodeling. The endometrium displayed a moderate response, whereas the myometrium and placental tissues exhibited minimal changes. At the protein level, myometrial progesterone receptor (PR) expression was significantly reduced (P < 0.05), while ERα and ERβ were unaffected. These findings demonstrate that the prepartum rise in E2 is associated with tissue-specific gene expression changes in the ewe uterine tract. In the cervix, the most affected tissue, transcriptomic changes are consistent with cervical ripening. Reduced myometrial PR expression suggests decreased progesterone responsiveness.NEW & NOTEWORTHY Exogenous estradiol treatment in late-gestation ewes induced distinct, tissue-specific transcriptomic changes, with the cervix showing the most pronounced response. In addition, estradiol was associated with reduced progesterone receptor protein expression in the myometrium. Together, these findings suggest that estradiol may play a role in coordinating prepartum changes in reproductive tissues in ewes, consistent with its known actions near term in other species.

Aging is characterized by progressive molecular dysregulation across interconnected biological systems, involving alterations in epigenetic regulation, gene expression, protein homeostasis, and metabolic function. Although physical exercise is widely recognized as one of the most effective nonpharmacological interventions to promote healthy aging, the integrative molecular mechanisms underlying its systemic effects remain incompletely understood. This review proposes a multi-omic framework in which exercise acts as a coordinated biological stimulus capable of remodeling age-associated molecular dysfunction across genomic, epigenomic, transcriptomic, proteomic, and metabolomic layers. We discuss evidence showing that exercise modulates DNA methylation patterns associated with inflammation, oxidative stress, and tissue regeneration. Epigenetically, exercise is associated with attenuation of age-associated hypermethylation in promoter regions and modulation of genes involved in oxidative stress defense and tissue regeneration. Transcriptomic studies further show that exercise is associated with more youthful expression patterns while attenuating inflammatory and senescence-related gene programs. Proteomic studies reveal that training is associated with mitochondrial metabolism, extracellular matrix remodeling, and muscle contractile protein abundance, reducing proteostatic dysfunction. Metabolomic analyses demonstrate that exercise improves metabolic flexibility and remodels cellular energy networks. Importantly, the unique contribution of this review lies in synthesizing emerging evidence that these adaptations are highly cell- and tissue-specific, involving immune cells, skeletal muscle satellite cells, endothelial cells, microglia, and intestinal stem cells. Rather than acting through isolated pathways, exercise may induce convergent adaptations across interconnected molecular systems, supporting the concept that healthy aging is dynamically regulated and that age-associated molecular dysfunction retains a degree of biological plasticity.

Most genetic variants associated with any complex trait are found in noncoding regions. Multiple studies have reported enrichment in single nucleotide polymorphisms (SNPs) found in specific sequences bound by CCCTC-binding factor (CTCF). CTCF binds DNA to establish boundaries, mediate chromatin interactions and topological domains, and recruit factors to regulate local gene expression. Hypertension is one such disease with enrichment of SNPs in CTCF-binding sites; however, it is not clear whether disruption of CTCF binding to any specific site in the genome could be sufficient to alter blood pressure in vivo. We and others have shown the importance of CTCF-binding and local chromatin interactions governing the renal expression of renin, a critical regulator of systemic blood pressure. Here, we developed a model with a mutation to a CTCF-binding motif within the first intron of the Ren gene in the Dahl salt-sensitive (SS) rat. CTCF-binding and local chromatin interactions were disrupted, and plasma renin activity (PRA) was impaired when animals were fed a salt-depleted diet in males, but not females. Consistent with the attenuation of PRA, blood pressure was attenuated in male mutant rats during salt depletion. Isolated kidney tissue culture revealed a transcriptional attenuation of Ren expression, suggesting that disruption of CTCF binding within the first intron is critical for initially stabilizing the expression of Ren in response to an inducing stimulus. This is the first demonstration that a mutation to a CTCF-binding site is sufficient to alter blood pressure regulation in a sex-specific manner.NEW & NOTEWORTHY We mutated a noncoding DNA-binding site for a chromatin architectural protein near a gene critical for blood pressure regulation in the Dahl salt-sensitive rat. This mutation altered chromatin organization, gene expression, and blood pressure, providing the first evidence that disruption of a single regulatory site is sufficient to influence blood pressure in a sex-specific manner. This highlights how chromatin conformation may be altered by noncoding variants to exert whole animal physiological effects.

This systematic review compared genetic evidence of pancreatic steatosis across African and non-African populations to illuminate ancestry-specific mechanisms and precision-prevention opportunities. Following PRISMA guidelines for reporting, a search was conducted across PubMed, Scopus, Web of Science, and NHGRI-EBI GWAS Catalog for studies spanning 2011 to March 31, 2026. Eligible studies included genome-wide association studies (GWAS), polygenic risk score (PRS), and Mendelian randomization (MR) analyses that reported genetic associations with pancreatic fat phenotypes and had explicit ancestry stratification or comparison. Narrative thematic synthesis was performed due to methodological heterogeneity. Six core genetic studies (n > 120,000 participants) were included. The only multi-ethnic GWAS found a strong protective variant of African ancestry, rs73449607 (near PDX1/PLUTO), which reduced pancreatic fat (β = -0.67, P = 4.50 × 10[-8]) and explained 14.3% of the variance in African Americans (vs. 5.3% overall). UK Biobank race-stratified PRS analyses confirmed the lowest pancreatic fat fraction in Black participants, with the strongest HbA1c PRS-fat association in this group (ρ = 0.23, P < 0.0001). European-dominant GWAS highlighted risk loci, including FUT2 rs601338 [higher fat and chronic pancreatitis risk, odds ratio (OR) 1.26]. MR studies demonstrated causal links between genetically predicted intra-pancreatic fat deposition (IPFD) and pancreatic ductal adenocarcinoma (PDAC) (OR 2.46 per SD) but not diabetes. African-ancestry genomes confer substantial protection against pancreatic steatosis, whereas non-African genomes are enriched for risk alleles that amplify the non-alcoholic fatty pancreas disease (NAFPD)-to-PDAC cascade. These ancestry-differentiated mechanisms position NAFPD as a precision medicine target.

Extracellular serine protease, plasmid-encoded (EspP) is a potent serine protease that functions as a cytotoxin and is secreted by enterohemorrhagic Escherichia coli (EHEC). This bacterial toxin can cause significant colonic epithelial damage and mimic the pathophysiology of EHEC infection on human colonic organoids. However, transcriptomic changes within the intestinal epithelial cells and impacts on cell proliferation and differentiation are largely unknown. Here, using human colonic organoids, we defined the molecular and cellular changes that occur in response to acute EspP exposure, independent of microbiota, stroma, and immune cells. We performed droplet-based single-cell RNA sequencing to determine changes in epithelial cell lineages in response to EspP and demonstrated that there is a disruption in proliferation and a preferential differentiation of enteroendocrine cells (EECs). Higher-resolution clustering revealed that the de novo EECs were primarily enterochromaffin or EEC progenitors. Interestingly, EECs induced from EspP treatment displayed an immune profile, expressing cytokines and chemokines associated with macrophage or neutrophil recruitment. These findings demonstrate that EspP, a potent EHEC cytotoxin, stimulates transcriptomic changes previously attributed to the whole bug infection and highlights the significance of crypts-based proliferative cells and secretory cell differentiation as major colonic responses to bacterial pathogens.NEW & NOTEWORTHY EspP, a bacterial serine protease secreted by enterohemorrhagic E. coli, can mimic the intestinal pathophysiology of EHEC in the absence of the bacteria. Using single-cell RNA sequencing, this study identified enteroendocrine cells as early responders to EspP treatment, with preferential hyperplasia of enterochromaffin cells. EspP-induced enteroendocrine cells also expressed immune cytokines and chemokines. This highlights the importance of enteroendocrine cell responses to bacterial pathogens and intestinal pathophysiology during infection.

Nonadditive interactions between environmental stressors, where biological responses to simultaneous stressors do not equal the sum of individual-stressor responses, commonly occur across organisms and environments. To enable predictions of organismal resilience to shifting patterns of environmental stressors, it is important to both identify these interactions and document the mechanisms underlying them. The supratidal copepod Tigriopus californicus demonstrates a nonadditive, antagonistic pattern of increased heat tolerance when simultaneously exposed to high salinities. We investigated salinity's chronic and acute effects on heat tolerance in a northern population and quantified responses in protein abundance to hypersalinity and heat stress, both alone and in combination. The overall proteomic response to multiple stressors was nonadditive and largely reflected that to high temperature. However, 42% of multistressor proteins were absent from either single-stressor response; we refer to these proteins that are only differentially abundant in the multistressor scenario as "emergent." Our results suggest that the increased heat tolerance of T. californicus conferred by hypersalinity may be driven by a combination of these emergent proteins, several proteins induced by hypersalinity in both single- and multistressor conditions that may contribute to cross-tolerance, and four proteins with additive abundance patterns (including a small heat shock protein). These candidate proteins play putative roles in several relevant processes including the heat shock response, protein folding, and regulation of metabolism and oxidative stress responses. Our results connect to prior whole organism findings and highlight promising pathways for future investigation in the context of heat tolerance and multistressor interactions.NEW & NOTEWORTHY Protein abundance responses to single and combined environmental stressors revealed several potential molecular mechanisms that could explain a nonadditive increase in heat tolerance of the intertidal copepod Tigriopus californicus when it is simultaneously exposed to high salinity. Protein abundance also follows a generally nonadditive pattern, with only a few exceptions. Furthermore, a number of proteins with putative roles in stress responses exhibit "emergent" abundance patterns, in which they only respond to the combined stressors.

Sepsis is a life-threatening, infection-triggered syndrome of dysregulated inflammation and immune dysfunction. However, the mechanisms underlying immune escape in sepsis remain poorly understood and merit further investigation. Gene expression data for sepsis were obtained from the Gene Expression Omnibus (GEO) database: GSE65682 was used to construct the training cohort, and GSE95233 served as an independent validation cohort. Feature genes were screened by integrating differential expression profiling with Weighted Gene Co-expression Network Analysis (WGCNA). A diagnostic model was developed and validated using receiver operating characteristic (ROC) analysis, a nomogram, and decision curve analysis (DCA). Functional enrichment, immune infiltration, and competing endogenous RNA (ceRNA) network analyses were also performed. Finally, consensus clustering was applied to identify molecular subtypes of sepsis. Three feature genes were identified by differential expression analysis and WGCNA. Area under the curve (AUC)-based screening selected two diagnostic genes (NXT1 and UXS1), which demonstrated high diagnostic accuracy (AUC > 0.9). Immune infiltration analysis revealed distinct patterns between the Sepsis and Control groups. Regulatory network analysis identified key miRNAs targeting these two genes and lncRNAs that regulate those miRNAs. Two sepsis subtypes with distinct immune and molecular characteristics were further identified. This study systematically explored the association between immune escape and the pathogenesis of sepsis and, through the integration of multiple bioinformatics approaches, elucidated the immune microenvironmental characteristics and molecular regulatory mechanisms of the disease, providing new insights into understanding its pathophysiology and developing targeted diagnostic and therapeutic strategies.NEW & NOTEWORTHY This study identifies NXT1 and UXS1 as novel diagnostic biomarkers for sepsis with high predictive accuracy (AUC > 0.9). By integrating differential expression analysis, Weighted Gene Co-expression Network Analysis (WGCNA), and immune infiltration, we reveal distinct immune microenvironmental characteristics associated with sepsis pathogenesis. We further define two molecular subtypes of sepsis with heterogeneous immune profiles, providing new insights into immune dysfunction and immune escape in sepsis, which may facilitate the development of targeted diagnostic and therapeutic strategies.

Independent of the suprachiasmatic nucleus, peripheral clocks can be strongly entrained by dietary signals. Although feeding time has been widely studied, the effects of food quality-particularly nutrient availability and stress-on peripheral circadian entrainment and metabolic regulation remain less understood. We developed a semimechanistic mathematical model of peripheral clock synchronization and clock-controlled ribosome biogenesis (RiBi) in response to feeding/fasting cycles and rhythms in dietary essential amino acid (EAA) availability. The model integrates EAA-sensitive signaling through mammalian target of rapamycin complex 1 (mTORC1) and the general control nonderepressible 2 (GCN2)-mediated integrated stress response (ISR), together with ribosomal protein expression as a metabolic endpoint. We used the model to examine circadian entrainment under nutrient stress, adaptation during transitions between feeding schedules with EAA insufficiency, and stress-related mechanisms that may restore circadian and metabolic function. Simulations showed that mTORC1 and GCN2-ISR signaling jointly regulate metabolic entrainability and stress adaptation and are required to maintain circadian synchronization and RiBi dynamics during nutrient stress. The model also predicted that differences in homeostatic adaptation can produce individualized recovery trajectories after transient dietary disruption. Finally, appropriate modulation of GCN2-ISR signaling mitigated disruption-associated RiBi hyperactivation by leveraging dietary EAA rhythms to restore clock function. These findings identify dietary EAA stress and its regulatory pathways as important determinants of peripheral circadian entrainment and metabolic adaptation, supporting the development of personalized nutrition-based strategies for circadian disruption-related chronic disease.NEW & NOTEWORTHY This study provides a mechanistic modeling framework linking dietary protein quality, EAA-sensitive mTORC1/GCN2-ISR signaling, peripheral circadian entrainment, and ribosome biogenesis, highlighting how nutrient stress may shape individualized circadian recovery and metabolic regulation.

Incretin-based pharmacotherapies, particularly glucagon-like peptide-1 (GLP-1) receptor agonists, have transformed the treatment of type 2 diabetes, with demonstrated benefits across multiple organ systems. Their success has driven the investigation of related gut-derived hormones, most prominently dual GLP-1/glucose-dependent insulinotropic polypeptide (GIP) receptor agonists, but extend to other targets with similar metabolic functions. For this class of drugs, the extent to which organ health improvements are secondary to improved systemic glycemic control versus direct tissue signaling remains unclear, partly because receptor availability across tissues is poorly annotated. We leveraged data from the Molecular Transducers of Physical Activity Consortium to annotate incretin receptor expression across 17 tissues in Fischer 344 rats and the Genotype-Tissue Expression Portal for human-level receptor expression. Furthermore, given the role of exercise in the preservation of muscle mass during weight loss, we analyzed the effects of 1, 2, 4, or 8 wk of treadmill exercise training on incretin-related signaling at the epigenetic, transcript, and protein levels. Endurance training elicited sex- and tissue-specific changes in incretin receptor expression, including downregulation of Gcgr across brown adipose, adrenal glands, and white adipose tissue (WAT). Training-induced Gipr regulation occurred in the adrenal glands, brain cortex, and hippocampus. Collectively, these findings contribute to the map of incretin receptor biology and identify exercise-responsive regulatory axes that may underlie synergistic effects of exercise and incretin-based therapies on weight management and metabolic health.NEW & NOTEWORTHY This study provides the first multiomic, multitissue description of incretin signaling receptor expression and regulation in response to endurance exercise training. We identify time point and sex-specific changes in incretin signaling across tissues, highlighting training effects on Gcgr, Gipr, and Sctr regulation in the adrenals, WAT, and brain. These findings help establish an exercise-responsive incretin signaling axis that may identify interactions from incretin-based therapies and exercise-based lifestyle interventions.

Increase in mRNA expression following muscle contraction regulates exercise-induced cellular responses associated with exercise adaptation. However, effects of a high-fat diet (HFD) on muscle contraction-induced alterations in transcription and DNA methylation remain unclear. Therefore, this study aimed to identify the effects of a 4-wk HFD on transcriptomic responses to muscle contractions and to examine the association between these transcriptomic changes and DNA methylation in promoter regions. Rats were fed either an HFD or a normal diet (ND) for 4 wk and underwent electrical stimulation-induced muscle contractions (5 sets × 10 contractions of 3 s at 100 Hz) in the right tibialis anterior (TA) muscle. Both TA muscles were harvested 3 h after muscle contractions for transcriptome and DNA methylation analyses. HFD suppressed the expression of 36 genes, and phosphoprotein was enriched as a Gene Ontology (GO) term. These genes were normally upregulated in response to muscle contractions. Furthermore, myosin heavy chain II, and extracellular matrix were enriched as GO terms for 147 genes that decreased after muscle contractions under HFD conditions, whereas their expression remained unchanged under ND conditions. However, genes whose contraction-induced mRNA expression was altered by HFD were not affected and demonstrated no significant inverse correlation between mRNA expression and DNA methylation levels. Collectively, these results indicate that a 4-wk HFD alters the transcriptomic response of specific GOs associated with muscle contractions, whereas these transcriptomic changes were not accompanied by detectable changes in DNA methylation, at least within the regions captured and analyzed in this study.NEW & NOTEWORTHY This study aimed to identify the effects of a 4-wk HFD on transcriptomic responses to muscle contractions and to examine the association between these transcriptomic changes and DNA methylation in promoter regions. A 4-wk HFD altered the transcriptomic response of specific GOs, including phosphoprotein, MHC II, and extracellular matrix, associated with muscle contractions. However, integrative analysis revealed that these mRNA expression changes were not accompanied by detectable DNA methylation within the regions analyzed in this study.

Researchers have posited that increased consumption of tea and coffee may be associated with more favorable treatment outcomes in patients with age-related macular degeneration (AMD). However, there is no clear evidence regarding the causal associations. To delve deeper into this potential connection, scientists used a rigorous method known as Mendelian randomization (MR). This technique was used to explore the causal impact of tea and coffee consumption on the development or progression of AMD. With the aim of investigating the cause-and-effect relationship between 16 tea- and coffee-consuming subtypes and 3 AMD, we designed a two-sample MR study using comprehensive data from genome-wide association studies (GWAS). The major approach adopted was inverse variance weighting (IVW). Furthermore, we implemented complementary methods like the weighted median (WM), weighted mode, and MR-Egger to strengthen our findings. Sensitivity analyses, including MR-Egger, MR-PRESSO, leave-one-out, and Cochran's Q tests, were used to validate results, explore heterogeneity and pleiotropy, and pinpoint potential biases. Two hundred and sixty-eight instrumental variables were selected for MR analysis. The results showed that standard tea intake may be a protective factor for wet AMD [odds ratio (OR) = 0.7076, 95% confidence interval (CI) = 0.5776-0.8668, P = 8 × 10[-4], PFDR = 0.0402]. Sensitivity analysis suggests that the results are robust. Our findings provide genetic evidence that standard tea intake is a protective factor against wet AMD, providing new insights into early risk stratification and prevention strategies for the disease.NEW & NOTEWORTHY This study investigates the potential causal relationship between tea and coffee consumption and age-related macular degeneration (AMD) using Mendelian randomization. Analyzing data from genome-wide association studies, we focused on 16 beverage subtypes and 3 AMD conditions. Our findings suggest that standard tea consumption may protect against wet AMD, with robust evidence supporting this link. The results offer new insights into risk stratification and prevention strategies for AMD, highlighting the importance of dietary factors in eye health.