Physiological genomics最新文献

Preeclampsia is a pregnancy-specific hypertensive disorder and is associated with an increased postpartum risk of cardiovascular morbidity for both women and their offspring. Previous studies have indicated that cord blood endothelial colony-forming cells (ECFCs) are dysfunctional in preeclampsia. The specific mechanisms are not yet fully understood, but dysregulation of alternative splicing has been proposed as one of the pathogenic pathways. To identify specific targets of alternative splicing in fetal ECFCs, we performed transcriptome-wide differential splicing analyses between cord blood ECFCs from preeclamptic (n = 16) and normal pregnancies (n = 13). Selected splicing events were validated using fragment length analysis and Sanger sequencing. In silico transcriptome-wide differential splicing analysis identified a significantly increased abundance of the CADM1 isoform ENST00000542447 in the preeclamptic cohort (P = 0.002), which was confirmed by wet-lab validation. The deleted exon 8 harbors glycosylation sites known to mediate cell-cell adhesion. To investigate the functional impact of alternative splice variants, we induced an in vitro splice switch using antisense morpholino treatment and then monitored cellular effects using migration and angiogenesis assays in ECFCs from six normal pregnancies. The CADM1 exon 8 skipping converted the normal ECFCs to a preeclampsia-like state characterized by a decreased migration ability (P_ANOVA = 0.005) and decreased tubule length (P_ANOVA = 0.02). We propose aberrant splicing of CADM1 and the resulting changes in the adherence properties of ECFCs as a potential contributor to cardiovascular sequelae in the offspring of preeclamptic pregnancies.NEW & NOTEWORTHY We investigated differential splicing between normal and preeclamptic pregnancies in endothelial colony-forming cells (ECFCs) from cord blood. Transcriptome-wide analysis identified exon 8 skipping of CADM1 mRNA to be upregulated in ECFCs from women with preeclampsia. In vitro splice switching studies indicated that induction of this isoform decreases the cell migration and tubule formation abilities of fetal ECFCs. Our findings link a specific splice isoform of CADM1 to preeclampsia, with potential implications for vascular health in the offspring.

Acute cardiorenal syndrome (CRS) represents a critical intersection of cardiac and renal dysfunction with profound clinical implications. Despite its significance, the molecular underpinnings that mediate cellular responses within the kidney during CRS remain inadequately understood. We used single nucleus RNA sequencing (snRNAseq) to dissect the cellular transcriptomic landscape of the kidney following a translational model of CRS, cardiac arrest/cardiopulmonary resuscitation (CA/CPR) in comparison to ischemia-reperfusion injury (IRI). In each dataset, we found that proximal tubule (PT) cells of the kidney undergo significant gene expression changes, with decreased expression of genes critically important for cell identity and function, indicative of dedifferentiation. Based on this, we created a novel score to capture the dedifferentiation state of each kidney cell population and found that certain epithelial cell populations, such as the PT S1 and S2 segments, as well as the distal convoluted tubule, exhibited significant dedifferentiation response. Interestingly, the dedifferentiation response in the distal nephron differed in magnitude between IRI and CA/CPR. Gene set enrichment analysis (GSEA) of PT response to IRI and CA/CPR revealed similarities between the two models and key differences, including enrichment of immune system process genes. Transcriptional changes in both mouse models of acute kidney injury (AKI) highly correlated with a dataset of human biopsies from patients diagnosed with AKI. This comprehensive single-nucleus transcriptomic profiling provides valuable insights into the cellular mechanisms driving CRS.NEW & NOTEWORTHY Cardiac dysfunction is a common cause of acute kidney injury in a malady called acute cardiorenal syndrome. In a mouse model of acute cardiorenal syndrome called cardiac arrest/cardiopulmonary resuscitation, we characterized, for the first time, the kidney transcriptional landscape at the single-cell level. We developed a novel method for quantifying cell response to injury and found that cells adapted through dedifferentiation, the magnitude of which varied depending on cell type.

The study aimed to verify the physiological and metabolic parameters associated with the time to task failure (TTF) during cycling exercise performed within the severe-intensity domain. Forty-five healthy and physically active males participated in two independent experiments. In experiment 1, after a graded exercise test, participants underwent constant work rate (CWR) cycling efforts at 115% of peak power output to assess neuromuscular function (potentiated twitch) pre- and postexercise. Experiment 2 was similar to experiment 1, but with physiological (respiratory parameters, energetic pathway contribution) and metabolic parameters in the blood (gasometry and blood lactate responses) and vastus lateralis muscle tissue (target metabolomic analysis, glycogen content, muscle pH, and buffering capacity in vitro) measured instead of neuromuscular function. Experiment 1 evidenced a significant decrease in muscle force with instauration of peripheral fatigability indices and no change in central fatigue indices. Severe-intensity domain exercise in experiment 2 was accompanied by changes in physiological and metabolic parameters and in blood and muscle parameters. However, the TTF was associated with oxidative contribution (r = 0.811, P < 0.001), as well as anaerobic capacity (r = 0.554, P = 0.027), muscle buffering capacity (r = 0.792, P = 0.035), phosphagen energy contribution (r = 0.583, P = 0.017), and carnitine changes (r = 0.855, P = 0.016), but not correlated with electromyographic response, blood acid-base balance, and muscular glycogen content and pH. TTF during CWR exercise within the severe-intensity domain is likely explained by a combination of interacting mechanisms, with oxidative and phosphagen contributions, and muscle buffering capacity suggested as the main peripheral limiting factors to exercise within this exercise-intensity domain.NEW & NOTEWORTHY For the first time, a metabolomic analysis confirms that the cycling time to task failure (TTF) within the severe-intensity domain can be explained by muscle buffering capacity (62.2%), oxidative pathways contribution (65%), and muscle carnitine changes (71.9%), beyond some correlations with anaerobic capacity, tricarboxylic acid cycle intermediates, and phosphagen pathway contribution. The muscle glycogen content, muscle or blood pH, electromyography, and cardiorespiratory responses were not associated with TTF.

Serum is commonly added to culture medium to improve the production of bovine embryos in vitro. The main goals were to verify the actions of serum to increase blastocyst yield and test the hypothesis that fetal bovine serum alters blastocyst gene expression in a manner that could affect competence to establish pregnancy and dysregulate fetal development. Media used were synthetic oviduct fluid medium bovine embryo 2 (SOF-BE2) and a commercial medium from IVF Biosciences termed here as IVFB. Three experiments were conducted in which either adult or fetal bovine serum (10%, vol/vol) was added at day 1 or 5 of development. Overall, serum increased blastocyst production. Gene expression in blastocysts was measured in the experiment in which fetal bovine serum was added at day 5. Serum resulted in 215 differentially expressed genes for embryos cultured in SOF-BE2 and 194 genes for embryos cultured in IVFB (adjusted P value of <0.05 and a |log₂| fold change >1). Only 24 genes were regulated by serum similarly for both media, including several transcription factors, imprinted genes, PSAT1 implicated in fetal growth in mice, and genes dysregulated in cloned embryos. Serum largely eliminated differences in gene expression between media. Expression data on eight biomarker genes were also used to calculate an embryo competence index previously related to embryo survival. Serum lowered the embryo competence index for both media. In conclusion, actions of fetal bovine serum on the preimplantation embryo include changes in gene expression indicative of reduced embryo competence and possible alterations in fetal development.NEW & NOTEWORTHY Serum is commonly added to the culture medium to improve the production of bovine embryos in vitro, but its molecular consequences for the resultant embryo are unclear. Here, we showed that blastocysts produced in serum experienced changes in gene expression, including transcription factors and imprinted genes. An embryo competence index that predicts embryo's ability to establish pregnancy based on gene expression was reduced by serum, suggesting serum can reduce embryo survivability.

Although the intratumoral microbiota has been discovered to have a close connection with tumor immunity, the specific role played by intratumoral microbiota in regulating the tumor immune microenvironment (TIME) of lung cancer remains largely unexplored. Here, we comprehensively investigated the association between intratumoral microbiota and the TIME in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). First, we found that intratumoral microbiota and host transcriptome profile significantly differed between LUAD and LUSC. Moreover, there were strong associations between the abundance of intratumoral microbes and the expression of host genes in both LUAD and LUSC. Furthermore, we found an association between intratumoral Lachnoclostridium and chemokine expression, suggesting a role for these species of microbiota in modulating tumor immunity. In addition, we found that tumors harbor distinct relative abundance of Lachnoclostridium presented variation in response to immunotherapy and sensitivity to potential drug candidates. Our study provided important insights into the regulation of intratumoral microbiota on the TIME in LUAD and LUSC, which may serve as a precursor for a hypothesis-driven study to better understand the causational relationship of intratumoral microbiota in lung cancer.NEW & NOTEWORTHY LUAD and LUSC exhibited significant differences in intratumoral microbiome and the TIME profile. The relative abundance of intratumoral Lachnoclostridium correlated with the tumor immune infiltration in both LUSC and LUAD. Intratumoral Lachnoclostridium impacted the patients' sensitivity to potential targeted drugs, especially in LUSC.

Ischemia-reperfusion (I/R) injury is an important initiating cause of chronic kidney disease and renal failure. Changes in proximal tubule (PT) morphology, including brush border loss, occur rapidly in response to ischemic stress and I/R injury. Vacuole membrane protein 1 (VMP1) is a compelling target for ischemia-associated renal damage because it is a necessary regulator of autophagy, and the genomic location of hypoxia-responsive microRNA miR-21 lies within an intronic region of the Vmp1 gene. Autophagy is reported to have protective and pathological effects on I/R injury. In this study, we find that VMP1 is rapidly upregulated in renal cortex tissue in response to 15 and 30 min of ischemia. Intravenous delivery of Vmp1-targeting GameR or a scrambled GapmeR was performed on adult male Sprague-Dawley rats for 2 days before either 30 min of renal ischemia, 30 min of ischemia followed by 24 h of reperfusion (I/R), or corresponding control procedures. Autophagy markers and PT morphology were assessed in the renal cortex. Suppression of ischemia-induced upregulation of VMP1 attenuated PT brush border loss following 30 min of ischemia and 24 h post-I/R. Our study reveals a novel and mechanistically important dissociation between VMP1 expression, miR-21-5p expression, autophagy markers, and I/R tubular injury in the renal cortex.NEW & NOTEWORTHY The impact of autophagy on renal ischemia/reperfusion injury (IRI) remains unclear. VMP1 promotes autophagy through interaction with beclin-1 and subsequent localization to the endoplasmic reticulum. In this study, GapmeR-mediated suppression of VMP1 in rats and attenuated proximal tubule damage following 30 min of ischemia or following 24 h of reperfusion, without altering autophagy markers following reperfusion. This new insight suggests that increased VMP1 did not afford autophagy-mediated protection from IRI in proximal tubules.

Decades of artificial selection have markedly enhanced egg production efficiency, yet the epigenetic underpinnings, notably DNA methylation dynamics in the gut, remain largely unexplored. Here, we investigate how breeds and developmental stages influence DNA methylation profiles in laying hens, and their potential relationship to laying performance and gut health. We compared two highly selected laying hen strains, Lohmann Brown-Classic (LB) and Lohmann Selected Leghorn-Classic (LSL), which exhibited similar egg production but divergent physiological, metabolic, and immunological characteristics. Our sampling encompassed key developmental stages: the pullet stage (10 and 16 wk old), peak production (24 and 30 wk old), and later stage (60 wk old) (n = 99; 10 per group), allowing us to elucidate the temporal dynamics of epigenetic regulation. Our findings highlight a crucial window of epigenetic modulation during the prelaying period, characterized by stage-specific methylation alterations and the involvement of predicted transcription factor motifs within methylated regions. This observation was consistent with the expression patterns of DNA methyltransferases (DNMTs), including DNMT1, DNMT3A, and DNMT3B. In addition, a higher methylation level was observed in specific loci or regions in the LSL compared with the LB strain. Notably, we uncover strain-specific differences in methylation levels, particularly pronounced in genomic regions associated with intestinal integrity, inflammation, and energy homeostasis. Our research contributes to the multidisciplinary framework of epigenetics and egg-laying performance, offering valuable implications for poultry production and welfare.NEW & NOTEWORTHY Our study reveals key methylation changes in the jejunum mucosa of laying hens across developmental stages and between strains, with implications for gut health, immune function, and egg production. These findings highlight a crucial role of epigenetic regulation in optimizing performance.

Aspirin (ASA) is a proven chemoprotective agent for colorectal cancer (CRC), though interindividual responses and cellular mechanisms are not well characterized. Human organoids are ideal to study treatment responses across individuals. Here, colonic organoids from African-Americans (AA) and European-Americans (EA) were used to profile genomic and cellular ASA responses. Colonic organoids from 67 participants, 33 AA and 34 EA, were treated with 3 mM ASA or vehicle control for 24 h. Gene expression was assessed by RNA-seq, and differentially responsive genes were analyzed by condition, population, and for gene set enrichment. Top differentially responsive genes were assessed by time and ASA doses in independent organoids. Expression quantitative trait loci (eQTL) mapping was performed to identify variants associated with condition-specific responses. Apoptosis and necrosis assays were performed, and apoptosis gene expression was measured in organoids. Overall, 8,343 genes were differentially responsive to ASA with differences between AA and EA. Significant enrichment for fatty acid oxidation (FAO) and peroxisome proliferator-activated receptor (PPAR) signaling was found. Significant treatment eQTLs were identified for relevant genes involved in FAO, apoptosis, and prostaglandin metabolism. ASA-induced apoptosis and secondary necrosis were confirmed with the identification of significant differential responses of apoptotic genes to ASA. Results demonstrate large transcriptional responses to ASA treatment with differences in responses between individuals. Genomic and cellular results suggest that ASA effects on the mitochondria are key mechanisms of action that could underlie clinical effects. These results could be used to assess clinical treatment responses for chemoprevention in the future.NEW & NOTEWORTHY Aspirin treatment in colonic organoids from diverse individuals revealed significant transcriptome-wide responses, especially for genes in lipid and apoptosis signaling pathways. In normal organoids, apoptosis was induced by aspirin, providing one possible mechanism of colorectal cancer chemoprevention. Our results are a first step toward implementation of personalized medicine for aspirin in colorectal cancer prevention.

"Jiedu Tongluo Tiaoying Formula" (JDTLTYF) is a kind of traditional Chinese medicine (TCM) prescription for treating hyperthyroidism, which can effectively improve the condition of patients. The main active ingredients of JDTLTYF were collected from the traditional Chinese medicine systems pharmacology (TCMSP) database, and the target was predicted. Genes related to hyperthyroidism were identified using DisGeNET, GeneCards, and Online Mendelian Inheritance in Man (OMIM) databases. Protein-protein interaction (PPI) network and interaction network of "formula-herb-active ingredient-target genes" was constructed. Mass spectrometry was used to identify the components. The binding of key components to the target was verified by molecular docking and molecular dynamics (MD) simulations. A hyperthyroidism mouse model was established by using levothyroxine sodium tablets, and the hormone and expression levels of inflammatory factors were examined by ELISA and Western blot. The key genes of JDTLTYF in the treatment of hyperthyroidism were TNF and AKT1. The results of mass spectrometry also showed that quercetin was one of the main components. The results of molecular docking and MD simulation showed that the binding-free energy between AKT1 and quercetin was the lowest, and the binding was stable. In vivo experimental results showed that gastric lavage with JDTLTYF could target AKT1 and TNF-α, effectively alleviate the pathological features of hyperthyroidism in mice, and reduce inflammation response. This study elucidated the key small molecule compounds and their action targets of JDTLTYF in the treatment of hyperthyroidism. It provides a direction for the development of new drugs for clinical hyperthyroidism.NEW & NOTEWORTHY Based on the network pharmacology and molecular dynamics (MD) simulation, this study elucidated the key small molecule compounds and their action targets of JDTLTYF Chinese herbal prescription (debark peony root, common selfheal fruit-spike, figwort root, thunberg fritillary bulb, and oyster shell) in the treatment of hyperthyroidism, preliminarily analyzed its molecular mechanism, and provided a reference direction for subsequent cell experiments.