Physiological genomics最新文献

{"title":"A better way to assess developmental competence of mammalian early embryos?","authors":"Andrew J Watson","doi":"10.1152/physiolgenomics.00055.2025","DOIUrl":"10.1152/physiolgenomics.00055.2025","url":null,"abstract":"","PeriodicalId":20129,"journal":{"name":"Physiological genomics","volume":" ","pages":"447-449"},"PeriodicalIF":2.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144037721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiome and host interactions in catfish: hybridization structures bacterial communities along catfish intestinal tract.","authors":"Xiaoyu Cai, Liqiang Zhong","doi":"10.1152/physiolgenomics.00058.2025","DOIUrl":"10.1152/physiolgenomics.00058.2025","url":null,"abstract":"","PeriodicalId":20129,"journal":{"name":"Physiological genomics","volume":" ","pages":"470-471"},"PeriodicalIF":2.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic responses of equine skeletal muscle to acute exercise in a hot environment.","authors":"Kenya Takahashi, Takanaga Shirai, Kazutaka Mukai, Yusaku Ebisuda, Fumi Sugiyama, Toshinobu Yoshida, Yu Kitaoka","doi":"10.1152/physiolgenomics.00200.2024","DOIUrl":"10.1152/physiolgenomics.00200.2024","url":null,"abstract":"<p><p>While exercise performance deteriorates in hot environments, heat stress may contribute to exercise-induced adaptations in skeletal muscle. In this study, we assessed transcriptional profiles of equine skeletal muscle following 3 min of high-intensity exercise (at the speed eliciting their maximal oxygen uptake) in cool [wet bulb globe temperature (WBGT) 15°C] or hot (WBGT 30°C) conditions. Differential gene expression was identified using DESeq2 (false discovery rate cutoff: 0.05, minimal fold change: 1.5). At 4 h after exercise, RNA-seq identified 176 and 156 genes that were differentially expressed in the middle gluteal muscle in hot and cool conditions, respectively. Of these genes, 110 genes were altered in both conditions, whereas 66 genes were only responsive to exercise in the hot condition. Between the two environmental conditions, the expression of only one gene (<i>KANK1</i>) was higher in the hot condition compared with the cool condition. Pathway analysis revealed that the response to temperature stimulus was upregulated only after exercise in the hot condition. Although the overall transcriptional response to exercise was similar in both environmental conditions, our results provide insights into the molecular mechanisms of equine skeletal muscle adaptation to heat acclimation.<b>NEW & NOTEWORTHY</b> Exercise in hot environments raises pulmonary artery temperature to a greater extent than in cool environments in horses. Pathway analysis of RNA-seq revealed expression of genes related to response to temperature stimulus was upregulated only after exercise in a hot environment in equine skeletal muscle.</p>","PeriodicalId":20129,"journal":{"name":"Physiological genomics","volume":" ","pages":"450-455"},"PeriodicalIF":2.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic mapping of electrocardiographic parameters in BXD strains reveals Chromosome 3 loci to be associated with cardiac repolarization abnormalities.","authors":"Buyan-Ochir Orgil, Fuyi Xu, Ning Li, Akhilesh K Bajpai, Neely R Alberson, Jason N Johnson, Qingqing Gu, Glenn T Wetzel, Jeffrey A Towbin, Lu Lu, Enkhsaikhan Purevjav","doi":"10.1152/physiolgenomics.00183.2024","DOIUrl":"10.1152/physiolgenomics.00183.2024","url":null,"abstract":"<p><p>Risk factors for cardiac arrhythmias that can cause sudden death and heart failure include genetics, age, lifestyle, and other environmental factors. The study assessed electrocardiography (ECG) traits in BXD mice and explored associated quantitative trait loci (QTLs). Five-minute electrocardiograms were recorded in 44 BXD strains at 4-5 mo of age (<i>n</i> ≥ 5 mice/sex/strain). ECG and arrhythmia traits were associated with echocardiography, blood pressure, genome, and heart transcriptome data followed by expression QTL mapping. A significant variability in ECG parameters and arrhythmias was recorded among BXDs. Among male BXDs, QRS duration was significantly associated with increased left ventricular internal diameter (LVID) and reduced ejection fraction and fractional shortening, whereas premature ventricular contractions (PVCs) were correlated with LVID, left ventricular (LV) volumes, and pulmonary vein peak pressure. In female BXDs, PVCs and premature atrial contractions (PACs) were significantly related with right ventricular ID and cardiac output. One significant QTL associated with QTc and JT durations was identified on Chromosome (Chr) 3 in male BXDs, whereas Chr 9 locus was suggestive for association with QTc and QT intervals in female mice. <i>Gon4l</i> was predicted as a strong candidate gene associated with repolarization abnormalities including short or long QT syndromes in humans. Study results suggested an influence of genetic background on expression of ECG parameters and arrhythmias based on significant variations of those traits between mouse strains of the BXD family. We conclude that murine BXD family can serve as a valuable reference for systems biology and comparative predictions of arrhythmia disorders.<b>NEW & NOTEWORTHY</b> Our study identified significant variances in ECG phenotypes and arrhythmias segregation in BXD mice. A significant quantitative trait locus (QTL) on Chromosome (Chr) 3 in the mouse genome was associated with increased QTc and JT intervals in male BXD mice. A suggestive QTL on Chr 9 associated with QT and QTc intervals was determined in female BXD mice. We identified a strong candidate gene, <i>Gon4l</i>, that may underlie cardiac repolarization abnormalities such as long and short QT syndromes.</p>","PeriodicalId":20129,"journal":{"name":"Physiological genomics","volume":" ","pages":"456-469"},"PeriodicalIF":2.5,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptional activation of FGL1 by KDM1A promotes immune evasion in lung cancer.","authors":"Jianhua Jiang, Sumei Luo, Xiaoyu Chen, Dandan Liu, Pengchao Zheng, Fanmin Kong, Lei Li","doi":"10.1152/physiolgenomics.00195.2024","DOIUrl":"https://doi.org/10.1152/physiolgenomics.00195.2024","url":null,"abstract":"<p><p><b>Background:</b> Immunotherapy is often thwarted by the innate ability of cancer to evade immune detection. Lysine-specific demethylase 1A (KDM1A) has been implicated in the development of various cancers, yet its specific influence on immune evasion in lung cancer and the mechanisms at play are not well defined in the current scientific discourse. <b>Methods:</b> Through bioinformatics, we probed the expression patterns of KDM1A and fibrinogen-like protein 1 (FGL1) in lung cancer. continues with cellular validation. Lactate Dehydrogenase (LDH) and enzyme-linked immunosorbent assay were utilized for the assessments of CD8⁺ T cell responses to tumor cells. To uncover the molecular underpinnings, we employ a suite of techniques including bioinformatics, luciferase reporter assays, chromatin immunoprecipitation, and qRT-PCR. <b>Results:</b> Bioinformatics pointed to a positive relationship between KDM1A and FGL1, with both markers highly expressed in lung cancer. KDM1A was found to dampen the cytotoxicity of CD8⁺ T cells towards lung cancer cells through its transcriptional activation of FGL1. <b>Conclusion:</b> Our work reveals the role of KDM1A in lung cancer immune evasion by transcriptionally activating FGL1, which could inform the design of new immunotherapies.</p>","PeriodicalId":20129,"journal":{"name":"Physiological genomics","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144601247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vacuole membrane protein 1 and miRNA-21: are they reliable partners to rescue acute kidney injury?","authors":"Utpal Sen","doi":"10.1152/physiolgenomics.00050.2025","DOIUrl":"10.1152/physiolgenomics.00050.2025","url":null,"abstract":"","PeriodicalId":20129,"journal":{"name":"Physiological genomics","volume":" ","pages":"406-408"},"PeriodicalIF":2.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Myocardial transcriptomic and proteomic landscapes across the menopausal continuum in a murine model of chemically induced accelerated ovarian failure.","authors":"Marissa A Lopez-Pier, Vito A Marino, Andrea C Vazquez-Loreto, Rinku S Skaria, Danielle K Cannon, Christina H Hoyer-Kimura, Alice E Solomon, Yulia Lipovka, Kevin Doubleday, Maricela Pier, Meinsung Chu, Rachel Mayfield, Samantha M Behunin, Tianjing Hu, Paul R Langlais, Timothy A McKinsey, John P Konhilas","doi":"10.1152/physiolgenomics.00133.2024","DOIUrl":"10.1152/physiolgenomics.00133.2024","url":null,"abstract":"<p><p>Risk of cardiovascular disease (CVD) in women increases with the menopausal transition. Using a chemical model (4-vinylcyclohexene diepoxide; VCD) of accelerated ovarian failure, we previously demonstrated that menopausal females are more susceptible to CVD compared with peri- or premenopausal females like humans. Yet, the cellular and molecular mechanisms underlying this shift in CVD susceptibility across the pre- to peri- to menopause continuum remain understudied. In this work using the VCD mouse model, we phenotyped cellular and molecular signatures from hearts at each hormonally distinct stage that included transcriptomic, proteomic, and cell biological analyses. The transcriptional profile of premenopausal hearts clustered separately from perimenopausal and menopausal hearts, which clustered more similarly. Proteomics also revealed hormonal clustering; perimenopausal hearts grouped more closely with premenopausal than menopausal hearts. Both proteomes and transcriptomes showed similar trends in genes associated with atherothrombosis, contractility, and impaired nuclear signaling between pre-, peri-, and menopausal murine hearts. Further analysis of posttranslational modifications (PTMs) showed hormone-dependent shifts in the phosphoproteome and acetylome. To further interrogate these findings, we triggered pathological remodeling using angiotensin II (Ang II). Phosphorylation of AMP-activated protein kinase (AMPK) signaling and histone deacetylase (HDAC) activity were found to be dependent on hormonal status and Ang II stimulation. Finally, knockdown of anti-inflammatory regulatory T cells (Treg) exacerbated Ang II-dependent fibrosis implicating HDAC-mediated epigenetic suppression of Treg activity. Taken together, we demonstrated unique cellular and molecular profiles underlying the cardiac phenotype of pre-, peri-, and menopausal mice supporting the necessity to study CVD in females across the hormonal transition.<b>NEW & NOTEWORTHY</b> Cycling and perimenopausal females are protected from cardiovascular disease (CVD) whereas menopausal females are more susceptible to CVD and other pathological sequalae. The cellular and molecular mechanisms underlying loss of CVD protection across the pre- to peri- to menopause transition remain understudied. Using the murine 4-vinylcyclohexene diepoxide (VCD) model of menopause we highlight cellular and molecular signatures from hearts at each hormonally distinct stage that included transcriptomic, proteomic, and cell biological analyses.</p>","PeriodicalId":20129,"journal":{"name":"Physiological genomics","volume":" ","pages":"409-430"},"PeriodicalIF":2.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12212010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alternative splicing of CADM1 in preeclampsia: implications for endothelial dysfunction and offspring cardiovascular risk.","authors":"Brandon M Schickling, Mark K Santillan, Donna A Santillan","doi":"10.1152/physiolgenomics.00047.2025","DOIUrl":"10.1152/physiolgenomics.00047.2025","url":null,"abstract":"","PeriodicalId":20129,"journal":{"name":"Physiological genomics","volume":" ","pages":"403-405"},"PeriodicalIF":2.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the male mouse cortex.","authors":"Alexander Popescu, Caitlin Ottaway, Kaitlyn Ford, Elizabeth Medina, Taylor Wintler Patterson, Ashley Ingiosi, Stephanie C Hicks, Kristan Singletary, Lucia Peixoto","doi":"10.1152/physiolgenomics.00128.2024","DOIUrl":"10.1152/physiolgenomics.00128.2024","url":null,"abstract":"<p><p>Sleep is an essential, tightly regulated biological function. Sleep is also a homeostatic process, with the need to sleep increasing as a function of being awake. Acute sleep deprivation (SD) increases sleep need, and subsequent recovery sleep (RS) discharges it. SD is known to alter brain gene expression in rodents, but it remains unclear which changes are linked to sleep homeostasis. To investigate this question, we analyzed RNA-seq data from adult male mice subjected to 3 and 5-6 h of SD and 2 and 6 h of subsequent RS. We hypothesized that molecular changes associated with sleep homeostasis would mirror sleep pressure dynamics as defined by brain electrical activity, peaking at 5-6 h of SD and no longer differentially expressed after 2 h of RS. We report that 5-6 h of SD produces the largest effect on gene expression, and the majority of differentially expressed genes normalize after 2 h of RS. These genes are involved in cellular redox homeostasis, DNA damage/repair, and chromatin regulation and may underlie the molecular basis of sleep homeostasis. Genes associated with cellular stress do not normalize within 6 h of RS and may underlie non-sleep-specific effects of SD. In addition, RS affects gene expression related to energy metabolism and Wnt-signaling, potentially contributing to its restorative effects. Finally, our study also points to the regulation of expression of a subset of circadian transcription factors as a function of sleep need. Overall, our results offer novel insights into the molecular mechanisms underlying sleep homeostasis and the broader effects of SD.<b>NEW & NOTEWORTHY</b> This study investigates different time points of sleep deprivation and recovery sleep to better understand the molecular processes influenced by sleep and lack of sleep. This study highlights redox metabolism, chromatin regulation, and DNA damage/repair as molecular mechanisms linked to sleep homeostasis while showing the effects of stress are probably non-sleep-specific based on transcriptional dynamics.</p>","PeriodicalId":20129,"journal":{"name":"Physiological genomics","volume":" ","pages":"431-445"},"PeriodicalIF":2.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12140865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143974390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-dimensional characterization of the tumor microenvironment profiles in lung squamous cell carcinoma.","authors":"Yi Zhou, Lixun Chai, Yuyao Wang, Hongguang Zhang","doi":"10.1152/physiolgenomics.00042.2025","DOIUrl":"https://doi.org/10.1152/physiolgenomics.00042.2025","url":null,"abstract":"<p><p>Tumor microenvironment (TME) plays an important role in tumorigenesis, development, metastasis and drug sensitivity, but little is known about it in lung squamous cell carcinoma (LUSC). Here, the RNA-sequencing data, clinical and survival data of patients with LUSC in The Cancer Genome Atlas and six independent datasets were collected. Based on the unsupervised clustering of knowledge-based functional gene expression signatures, LUSC was classified into four subtypes. Cluster1 and cluster3 exhibited substantial tumor immune infiltration, suggesting a better response to immunotherapy. Relatively worse survival was observed in cluster4, probably due to higher angiogenesis. Besides, differentially expressed genes in cluster1, cluster2 and cluster3 were prominently enriched in immune-related pathways, while extracellular matrix-related pathways were enriched for cluster4. Genomic data analyses showed significant variations in tumor mutational burden and mutational frequency of several genes, such as <i>TP53</i>, among the four subtypes. Additionally, the four subtypes exhibited heterogeneity in the sensitivity of commonly used chemotherapy drugs for lung cancer and the intratumor microbiome profile. Finally, a prognostic model was developed and its performance and generalization ability were independently validated in multiple datasets. Overall, our study advances the understanding of the TME in LUSC and proposes a prognostic model that facilitates clinical decision-making.</p>","PeriodicalId":20129,"journal":{"name":"Physiological genomics","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}