Pub Date : 2025-01-16DOI: 10.1016/j.ygeno.2025.110996
Zhifang Tang , Xiaoyan Xu , Wei Shi , Xianzhen Ren , Huan Luo , Yongqing Xu , Chuan Li
Osteonecrosis of the femoral head (ONFH) is a destructive bone disease, and overuse of alcohol is one of the major contributing factors. Although mesenchymal stem cells (MSCs) and their exosomes have been reported to attenuate ONFH, the potential mechanisms of alcohol-induced ONFH (AONFH) are unclear. Here, we isolated and identified human umbilical cord MSCs-derived exosomal (hucMSCs-exos) miR-25-3p. We observed that hucMSCs-exos transferred miR-25-3p into bone marrow stem cells (BMSCs). HucMSCs-exos miR-25-3p increased cell viability, osteogenic differentiation, and inhibited apoptosis of alcohol-treated BMSCs and AONFH rat model. Mechanically, hucMSCs-exos upregulated miR-25-3p expression in BMSCs by repressing miR-25-3p DNA methylation, and DNA methylation inhibitor 5-Aza-2-deoxycytidine (DAC) ameliorated AONFH. Besides, miR-25-3p suppressed gremlin 1 (GREM1) expression, and upregulation of GREM1 restored the inhibition of hucMSCs-exos on AONFH. Therefore, we determined that hucMSCs-exos miR-25-3p alleviated AONFH by inhibiting miR-25-3p DNA methylation and GREM1 expression, which may help identify novel biomarkers, diagnostic and therapeutic targets.
{"title":"Huc-MSC-derived exosomes alleviates alcohol-induced osteonecrosis of the femoral head through targeting the miR-25-3p/GREM1 axis","authors":"Zhifang Tang , Xiaoyan Xu , Wei Shi , Xianzhen Ren , Huan Luo , Yongqing Xu , Chuan Li","doi":"10.1016/j.ygeno.2025.110996","DOIUrl":"10.1016/j.ygeno.2025.110996","url":null,"abstract":"<div><div>Osteonecrosis of the femoral head (ONFH) is a destructive bone disease, and overuse of alcohol is one of the major contributing factors. Although mesenchymal stem cells (MSCs) and their exosomes have been reported to attenuate ONFH, the potential mechanisms of alcohol-induced ONFH (AONFH) are unclear. Here, we isolated and identified human umbilical cord MSCs-derived exosomal (hucMSCs-exos) miR-25-3p. We observed that hucMSCs-exos transferred miR-25-3p into bone marrow stem cells (BMSCs). HucMSCs-exos miR-25-3p increased cell viability, osteogenic differentiation, and inhibited apoptosis of alcohol-treated BMSCs and AONFH rat model. Mechanically, hucMSCs-exos upregulated miR-25-3p expression in BMSCs by repressing miR-25-3p DNA methylation, and DNA methylation inhibitor 5-Aza-2-deoxycytidine (DAC) ameliorated AONFH. Besides, miR-25-3p suppressed gremlin 1 (GREM1) expression, and upregulation of GREM1 restored the inhibition of hucMSCs-exos on AONFH. Therefore, we determined that hucMSCs-exos miR-25-3p alleviated AONFH by inhibiting miR-25-3p DNA methylation and GREM1 expression, which may help identify novel biomarkers, diagnostic and therapeutic targets.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110996"},"PeriodicalIF":3.4,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-14DOI: 10.1016/j.ygeno.2025.110994
Guoying Wang , Huihui Tao , Lingling Zhou , Junning Zhang , Wenjun Pu , Tiantian Xu , Chunmei Wen , Yali Peng , Mengyao Wu , Xuejia Zheng , Yong Dai
Background
Systemic Lupus Erythematosus (SLE) is a typical autoimmune disease characterized by a complex pathogenesis and a strong genetic predisposition. The study of inflammatory response in SLE monocytes is not very clear, and exploring the inflammatory factors of monocytes is beneficial to discover new diagnostic targets.
Results
Using scRNA-seq technology, we obtained the quantitative changes in circulating immune cells and various cellular immune metabolic profiles between SLE patients and healthy volunteers. A significant increase in monocytes was observed in peripheral blood of SLE patients. Flow cytometry was employed to validate the types and quantities of circulating immune cells in SLE, corroborating the scRNA-seq results. Monocyte highly expressed IRF1 (interferon regulatory factor 1) in SLE. Previous research proves that IRF1 is widely involved in immune regulation and inflammatory response, and can promote the transcription of a variety of pro-inflammatory cytokines. Additionally, Inflammatory factors secreted by monocytes in serum were measured. The results demonstrated a significant upregulation of IFN-γ, TNF-α, IL-2, IL-6, IL-8, IL-10, IL-1β in the sera of SLE patients compared to healthy controls.
Conclusion
Our results demonstrate upregulation of monocyte inflammation in circulating immune cells in SLE patients and expands the current understanding of circulating immune cells in SLE.
Our study provides a blueprint for future exploration of SLE monocytes, revealing the pathogenesis and inventing new immunotherapies.
{"title":"scRNA-seq reveals involvement of monocytes in immune response in SLE patients","authors":"Guoying Wang , Huihui Tao , Lingling Zhou , Junning Zhang , Wenjun Pu , Tiantian Xu , Chunmei Wen , Yali Peng , Mengyao Wu , Xuejia Zheng , Yong Dai","doi":"10.1016/j.ygeno.2025.110994","DOIUrl":"10.1016/j.ygeno.2025.110994","url":null,"abstract":"<div><h3>Background</h3><div>Systemic Lupus Erythematosus (SLE) is a typical autoimmune disease characterized by a complex pathogenesis and a strong genetic predisposition. The study of inflammatory response in SLE monocytes is not very clear, and exploring the inflammatory factors of monocytes is beneficial to discover new diagnostic targets.</div></div><div><h3>Results</h3><div>Using scRNA-seq technology, we obtained the quantitative changes in circulating immune cells and various cellular immune metabolic profiles between SLE patients and healthy volunteers. A significant increase in monocytes was observed in peripheral blood of SLE patients. Flow cytometry was employed to validate the types and quantities of circulating immune cells in SLE, corroborating the scRNA-seq results. Monocyte highly expressed IRF1 (interferon regulatory factor 1) in SLE. Previous research proves that IRF1 is widely involved in immune regulation and inflammatory response, and can promote the transcription of a variety of pro-inflammatory cytokines. Additionally, Inflammatory factors secreted by monocytes in serum were measured. The results demonstrated a significant upregulation of IFN-γ, TNF-α, IL-2, IL-6, IL-8, IL-10, IL-1β in the sera of SLE patients compared to healthy controls.</div></div><div><h3>Conclusion</h3><div>Our results demonstrate upregulation of monocyte inflammation in circulating immune cells in SLE patients and expands the current understanding of circulating immune cells in SLE.</div><div>Our study provides a blueprint for future exploration of SLE monocytes, revealing the pathogenesis and inventing new immunotherapies.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110994"},"PeriodicalIF":3.4,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-13DOI: 10.1016/j.ygeno.2025.110995
Smahane Chalabi , Linda Loonen , Jos Boekhorst , Houcheng Li , Lingzhao Fang , Peter W. Harrison , Wassim Lakhal , Jerome Lluch , Alexey Sokolov , Sarah Djebali , Andrea Rau , Elisabetta Giuffra , Jerry Wells
This study investigates the impact of maternal gestation diets with varying fiber contents on gene expression and chromatin accessibility in fetuses and piglets fed a low fiber diet post weaning. High-fiber maternal diets, enriched with sugar beet pulp or pea internal fiber, were compared to a low-fiber maternal diet to evaluate their effects on liver and muscle tissues. The findings demonstrate that maternal high-fiber diets significantly alter chromatin accessibility, predicted transcription factor activity and transcriptional landscape in both fetuses and piglets. A gene set enrichment analysis revealed over-expression of gene ontology terms related to metabolic processes and under-expression of those linked to immune responses in piglets from sows given the high-fiber diets during gestation. This suggests better metabolic health and immune tolerance of the fetus and offspring, in line with the documented epigenetic effects of short chain fatty acids on immune and metabolic pathways. A deconvolution analysis of the bulk RNA-seq data was performed using cell-type specific markers from a single cell transcriptome atlas of adult pigs. These results confirmed that the transcriptomic and chromatin accessibility data do not reflect different cell type compositions between maternal diet groups but rather phenotypic changes triggered by maternal nutrition in shaping the epigenetic and transcriptional environment of fetus and offspring. Our findings have implications for improving animal health and productivity as well as broader implications for human health, suggesting that optimizing maternal diet with high-fiber content could enhance metabolic health and immune function in the formative years after birth and potentially to adulthood.
{"title":"Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets","authors":"Smahane Chalabi , Linda Loonen , Jos Boekhorst , Houcheng Li , Lingzhao Fang , Peter W. Harrison , Wassim Lakhal , Jerome Lluch , Alexey Sokolov , Sarah Djebali , Andrea Rau , Elisabetta Giuffra , Jerry Wells","doi":"10.1016/j.ygeno.2025.110995","DOIUrl":"10.1016/j.ygeno.2025.110995","url":null,"abstract":"<div><div>This study investigates the impact of maternal gestation diets with varying fiber contents on gene expression and chromatin accessibility in fetuses and piglets fed a low fiber diet post weaning. High-fiber maternal diets, enriched with sugar beet pulp or pea internal fiber, were compared to a low-fiber maternal diet to evaluate their effects on liver and muscle tissues. The findings demonstrate that maternal high-fiber diets significantly alter chromatin accessibility, predicted transcription factor activity and transcriptional landscape in both fetuses and piglets. A gene set enrichment analysis revealed over-expression of gene ontology terms related to metabolic processes and under-expression of those linked to immune responses in piglets from sows given the high-fiber diets during gestation. This suggests better metabolic health and immune tolerance of the fetus and offspring, in line with the documented epigenetic effects of short chain fatty acids on immune and metabolic pathways. A deconvolution analysis of the bulk RNA-seq data was performed using cell-type specific markers from a single cell transcriptome atlas of adult pigs. These results confirmed that the transcriptomic and chromatin accessibility data do not reflect different cell type compositions between maternal diet groups but rather phenotypic changes triggered by maternal nutrition in shaping the epigenetic and transcriptional environment of fetus and offspring. Our findings have implications for improving animal health and productivity as well as broader implications for human health, suggesting that optimizing maternal diet with high-fiber content could enhance metabolic health and immune function in the formative years after birth and potentially to adulthood.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110995"},"PeriodicalIF":3.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sesame (Sesamum indicum L., 2n = 2× = 26) from the Pedaliaceae family is primarily grown for its high oil content, rich in unsaturated fatty acids like linoleic acid (LA) and alpha-linolenic acid (ALA). However, the molecular mechanisms of sesame oil accumulation remain poorly understood. This study analyzed transcriptomes at two seed development stages: Young Stage (YS, pods 1.5–2.5 cm) and Mature Stage (MS, brown pods >2.5 cm), to explore regulatory mechanisms and identify key genes involved in lipid biosynthesis.
From 25,173 genes, 18,820 with expression values >10 CPM in at least 70 % of replicates were included in differential expression (DE) analysis. Active expression (LFC > 0) was observed in 9372 and 9448 genes at YS and MS, respectively. DEGs were annotated, revealing roles in various biological processes, (e.g., mRNA metabolic process, reproduction-related developmental processes, seed development), molecular functions (e.g., aminoacyltransferase activity, ubiquitin-like protein and ubiquitin-protein transferase activities), and cellular components (e.g., peroxisome, microbody, lipid droplet).
KEGG analysis highlighted genes involved in fatty acid synthesis (e.g., fabG, fabZ), TAG biosynthesis (DGAT1, GPAT), and alpha-linolenic acid metabolism (AOS, LCAT3). Key genes upregulated at MS included SIN_1025205 (protein transport), SIN_1006853 (acetylajmalan esterase), and SIN_1003267 (gamma-cadinene synthase). The study generated a valuable transcriptome dataset and gene list for seed development and lipid biosynthesis, which will be validated through functional studies. An interactive webpage is provided for data exploration.
{"title":"Decoding gene expression dynamics during seed development in sesame (Sesamum indicum L.) through RNA-Seq analysis","authors":"Bantayehu Bekele , Mebeaselassie Andargie , Miguel Gallach , Dereje Beyene , Kassahun Tesfaye","doi":"10.1016/j.ygeno.2025.110997","DOIUrl":"10.1016/j.ygeno.2025.110997","url":null,"abstract":"<div><div>Sesame (<em>Sesamum indicum</em> L., 2n = 2× = 26) from the Pedaliaceae family is primarily grown for its high oil content, rich in unsaturated fatty acids like linoleic acid (LA) and alpha-linolenic acid (ALA). However, the molecular mechanisms of sesame oil accumulation remain poorly understood. This study analyzed transcriptomes at two seed development stages: Young Stage (YS, pods 1.5–2.5 cm) and Mature Stage (MS, brown pods >2.5 cm), to explore regulatory mechanisms and identify key genes involved in lipid biosynthesis.</div><div>From 25,173 genes, 18,820 with expression values >10 CPM in at least 70 % of replicates were included in differential expression (DE) analysis. Active expression (LFC > 0) was observed in 9372 and 9448 genes at YS and MS, respectively. DEGs were annotated, revealing roles in various biological processes, (e.g., mRNA metabolic process, reproduction-related developmental processes, seed development), molecular functions (e.g., aminoacyltransferase activity, ubiquitin-like protein and ubiquitin-protein transferase activities), and cellular components (e.g., peroxisome, microbody, lipid droplet).</div><div>KEGG analysis highlighted genes involved in fatty acid synthesis (e.g., <em>fabG</em>, <em>fabZ</em>), TAG biosynthesis (<em>DGAT1</em>, <em>GPAT</em>), and alpha-linolenic acid metabolism (<em>AOS</em>, <em>LCAT3</em>). Key genes upregulated at MS included <em>SIN_1025205</em> (protein transport), <em>SIN_1006853</em> (acetylajmalan esterase), and <em>SIN_1003267</em> (gamma-cadinene synthase). The study generated a valuable transcriptome dataset and gene list for seed development and lipid biosynthesis, which will be validated through functional studies. An interactive webpage is provided for data exploration.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110997"},"PeriodicalIF":3.4,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-10DOI: 10.1016/j.ygeno.2025.110992
Xinran Li, Liu Luo, Xuying Wang , Miao Zhu
Cultivation of edible mushrooms on straw can significantly reduce production costs, provide notable environmental and ecological benefits. However, the molecular mechanisms via which mushrooms utilize straw are not well understood. We conducted a comparative transcriptomic analysis of oyster mushrooms cultivated on two different biomass substrates, namely, corncob and tobacco straw at various developmental stages. The results revealed that the biomass substrates induced distinct transcriptomic changes during mycelium and fruiting body development. Straw affected the metabolism of pyruvate and acetyl-CoA, with significant downregulation of pyruvate decarboxylase expression, and upregulation of acetyl-CoA hydrolase during mycelial growth. Genes associated with cell wall and carbohydrate metabolism were significantly upregulated, and the PLD-PA-mTOR pathway was activated during the fruiting body development stage in mushrooms grown on straw. These findings reveal the transcriptomic adaptations of oyster mushrooms to tobacco straw, and enhance our understanding of the molecular mechanisms underlying biomass conversion by edible fungi using straw.
{"title":"Further insights into the molecular mechanisms underlying tobacco straw cultivation of Pleurotus ostreatus by comparative transcriptome analyses","authors":"Xinran Li, Liu Luo, Xuying Wang , Miao Zhu","doi":"10.1016/j.ygeno.2025.110992","DOIUrl":"10.1016/j.ygeno.2025.110992","url":null,"abstract":"<div><div>Cultivation of edible mushrooms on straw can significantly reduce production costs, provide notable environmental and ecological benefits. However, the molecular mechanisms via which mushrooms utilize straw are not well understood. We conducted a comparative transcriptomic analysis of oyster mushrooms cultivated on two different biomass substrates, namely, corncob and tobacco straw at various developmental stages. The results revealed that the biomass substrates induced distinct transcriptomic changes during mycelium and fruiting body development. Straw affected the metabolism of pyruvate and acetyl-CoA, with significant downregulation of pyruvate decarboxylase expression, and upregulation of acetyl-CoA hydrolase during mycelial growth. Genes associated with cell wall and carbohydrate metabolism were significantly upregulated, and the PLD-PA-mTOR pathway was activated during the fruiting body development stage in mushrooms grown on straw. These findings reveal the transcriptomic adaptations of oyster mushrooms to tobacco straw, and enhance our understanding of the molecular mechanisms underlying biomass conversion by edible fungi using straw.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110992"},"PeriodicalIF":3.4,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-09DOI: 10.1016/j.ygeno.2025.110993
Yifan Xu , Rong Zhang , Xinzhe Du , Yangxi Huang , Yao Gao , Yujiao Wen , Dan Qiao , Ning Sun , Zhifen Liu
Background
Major depressive disorder (MDD) during adolescence significantly jeopardizes both mental and physical health. However, the etiology underlying MDD in adolescents remains unclear.
Methods
A total of 74 adolescents with MDD and 40 health controls (HCs) who underwent comprehensive clinical and cognitive assessments were enrolled. Differential expression analysis was conducted on plasma extracellular vesicles (EVs) carrying long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) by microarray analysis. Two possible lncRNA-miR-mRNA networks were established and candidate regulatory axes were generated using the StarBase, miRDB, and TargetScan bioinformatics databases. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the candidate molecules and signaling axes in a clinical cohort.
Results
A total of 3752 dysregulated lncRNAs and 1789 dysfunctional mRNAs were identified. Two candidate regulatory axes (AC156455.1/miR-126-5p/AAK1 and CCDC18-AS1/miR-6835-5p/CCND2) with potential connections with MDD were selected. The candidate molecules exhibit differential expression patterns among adolescents with MDD and HCs, as well as before and after treatment with sertraline in adolescents with MDD. Furthermore, AAK1, CCDC18-AS1, and miR-6835-5p expressions exhibited significant differences between the response and non-response groups. Baseline expression of CCDC18-AS1, miR-6835-5p, and CCND2 could predict the therapeutic effect of sertraline, which may be associated with reducing suicidal ideation and improving cognitive function.
Conclusion
Our study may provide insights into the understanding of the underlying pathological mechanisms in adolescents with MDD.
{"title":"Identification of aberrant plasma vesicles containing AAK1 and CCDC18-AS1 in adolescents with major depressive disorder and preliminary exploration of treatment efficacy","authors":"Yifan Xu , Rong Zhang , Xinzhe Du , Yangxi Huang , Yao Gao , Yujiao Wen , Dan Qiao , Ning Sun , Zhifen Liu","doi":"10.1016/j.ygeno.2025.110993","DOIUrl":"10.1016/j.ygeno.2025.110993","url":null,"abstract":"<div><h3>Background</h3><div>Major depressive disorder (MDD) during adolescence significantly jeopardizes both mental and physical health. However, the etiology underlying MDD in adolescents remains unclear.</div></div><div><h3>Methods</h3><div>A total of 74 adolescents with MDD and 40 health controls (HCs) who underwent comprehensive clinical and cognitive assessments were enrolled. Differential expression analysis was conducted on plasma extracellular vesicles (EVs) carrying long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) by microarray analysis. Two possible lncRNA-miR-mRNA networks were established and candidate regulatory axes were generated using the StarBase, miRDB, and TargetScan bioinformatics databases. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the candidate molecules and signaling axes in a clinical cohort.</div></div><div><h3>Results</h3><div>A total of 3752 dysregulated lncRNAs and 1789 dysfunctional mRNAs were identified. Two candidate regulatory axes (AC156455.1/miR-126-5p/AAK1 and CCDC18-AS1/miR-6835-5p/CCND2) with potential connections with MDD were selected. The candidate molecules exhibit differential expression patterns among adolescents with MDD and HCs, as well as before and after treatment with sertraline in adolescents with MDD. Furthermore, AAK1, CCDC18-AS1, and miR-6835-5p expressions exhibited significant differences between the response and non-response groups. Baseline expression of CCDC18-AS1, miR-6835-5p, and CCND2 could predict the therapeutic effect of sertraline, which may be associated with reducing suicidal ideation and improving cognitive function.</div></div><div><h3>Conclusion</h3><div>Our study may provide insights into the understanding of the underlying pathological mechanisms in adolescents with MDD.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110993"},"PeriodicalIF":3.4,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-05DOI: 10.1016/j.ygeno.2025.110989
Jiayi Wu , Mengya Wang , Xin Gao , Mingyi Wang , Chaofan Jin , Da Zheng , Jiangping Yan , Zhenmin Bao , Bo Wang , Jingjie Hu
Antarctic krill (Euphausia superba), which is rich in astaxanthin, has been widely utilized as a dietary supplement in fish aquaculture. Our study was to feed juvenile leopard coral grouper (Plectropomus leopardus) a diet containing 50 % Antarctic krill, revealing significant body color differentiation between a reddened group (BKR) and a non-reddened group (BKB), followed by comparative analysis with the control group (BCon) without krill supplementation. Histological analysis and carotenoid content in the liver and intestine were differentially regulated in color-differentiated individuals. Transcriptomic profiling revealed differentially expressed genes (DEGs) among color-differentiated individuals, with up-regulated DEGs in BKR being linked to carotenoid uptake, metabolism, and transport. Key DEGs (acss2l, insig1, fabp7, and bco1) were validated through qRT-PCR and FISH. Additionally, WGCNA identified potential gene regulatory networks in the liver and intestine that were responsive to the body coloration. This study elucidates the molecular mechanisms by which Antarctic krill influences carotenoid-based body coloration, offering new insights into the application of Antarctic krill in aquaculture.
{"title":"Hepatic and intestinal insights into the molecular mechanisms of dietary Antarctic krill-induced body color differentiation in Plectropomus leopardus","authors":"Jiayi Wu , Mengya Wang , Xin Gao , Mingyi Wang , Chaofan Jin , Da Zheng , Jiangping Yan , Zhenmin Bao , Bo Wang , Jingjie Hu","doi":"10.1016/j.ygeno.2025.110989","DOIUrl":"10.1016/j.ygeno.2025.110989","url":null,"abstract":"<div><div>Antarctic krill (<em>Euphausia superba</em>), which is rich in astaxanthin, has been widely utilized as a dietary supplement in fish aquaculture. Our study was to feed juvenile leopard coral grouper (<em>Plectropomus leopardus</em>) a diet containing 50 % Antarctic krill, revealing significant body color differentiation between a reddened group (BKR) and a non-reddened group (BKB), followed by comparative analysis with the control group (BCon) without krill supplementation. Histological analysis and carotenoid content in the liver and intestine were differentially regulated in color-differentiated individuals. Transcriptomic profiling revealed differentially expressed genes (DEGs) among color-differentiated individuals, with up-regulated DEGs in BKR being linked to carotenoid uptake, metabolism, and transport. Key DEGs (<em>acss2l</em>, <em>insig1</em>, <em>fabp7</em>, and <em>bco1</em>) were validated through qRT-PCR and FISH. Additionally, WGCNA identified potential gene regulatory networks in the liver and intestine that were responsive to the body coloration. This study elucidates the molecular mechanisms by which Antarctic krill influences carotenoid-based body coloration, offering new insights into the application of Antarctic krill in aquaculture.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110989"},"PeriodicalIF":3.4,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-04DOI: 10.1016/j.ygeno.2025.110988
Wenxin Li , Xinyu Zhang , Jiamin Song , Ling Yang , Dong Wang , Guoyue Yuan , Li Zhao
Background
GLP-1 receptor agonists (GLP-1RA) have been extensively utilized in the management of body weight in individuals with obesity. Circular RNA (circRNA), a class of covalently closed RNA molecules, has garnered increasing attention for its potential role in the pathogenesis of obesity. However, the specific mechanisms through which circRNA contributes to GLP-1RA-induced weight loss remains elusive.
Methods
High-throughput sequencing analyzed epididymal adipose tissue from obese mice under high-fat, and GLP-1RA intervention (600 μg/kg/d). The functions of differentially expressed (DE) genes were enriched and analyzed. The circRNA-miRNA-mRNA interaction network was constructed in Cytoscape, and KEGG pathway gene enrichment was validated via western blotting.
Results
A total of 644 DEcircRNAs, 186 DEmiRNAs, and 3474 DEmRNAs were identified. Based on ceRNA score calculations, network diagrams were constructed. Gene Ontology (GO) analysis revealed that DERNAs were linked to lipid and fatty acid metabolism. DE genes within ceRNA pairs were enriched in lipid metabolism pathways, especially the PI3K-Akt and AMPK signaling pathways. GLP-1RA induced the phosphorylation of AKT and AMPK, which subsequently led to a reduction of SREBP-1, ACC, and FAS.
Conclusion
GLP-1RA might activate PI3K-Akt and AMPK signaling pathways to combat obesity through the ceRNA network of circRNAs.
{"title":"Mechanistic insights into GLP-1 receptor agonist-induced weight loss through ceRNA network analysis","authors":"Wenxin Li , Xinyu Zhang , Jiamin Song , Ling Yang , Dong Wang , Guoyue Yuan , Li Zhao","doi":"10.1016/j.ygeno.2025.110988","DOIUrl":"10.1016/j.ygeno.2025.110988","url":null,"abstract":"<div><h3>Background</h3><div>GLP-1 receptor agonists (GLP-1RA) have been extensively utilized in the management of body weight in individuals with obesity. Circular RNA (circRNA), a class of covalently closed RNA molecules, has garnered increasing attention for its potential role in the pathogenesis of obesity. However, the specific mechanisms through which circRNA contributes to GLP-1RA-induced weight loss remains elusive.</div></div><div><h3>Methods</h3><div>High-throughput sequencing analyzed epididymal adipose tissue from obese mice under high-fat, and GLP-1RA intervention (600 μg/kg/d). The functions of differentially expressed (DE) genes were enriched and analyzed. The circRNA-miRNA-mRNA interaction network was constructed in Cytoscape, and KEGG pathway gene enrichment was validated via western blotting.</div></div><div><h3>Results</h3><div>A total of 644 DEcircRNAs, 186 DEmiRNAs, and 3474 DEmRNAs were identified. Based on ceRNA score calculations, network diagrams were constructed. Gene Ontology (GO) analysis revealed that DERNAs were linked to lipid and fatty acid metabolism. DE genes within ceRNA pairs were enriched in lipid metabolism pathways, especially the PI3K-Akt and AMPK signaling pathways. GLP-1RA induced the phosphorylation of AKT and AMPK, which subsequently led to a reduction of SREBP-1, ACC, and FAS.</div></div><div><h3>Conclusion</h3><div>GLP-1RA might activate PI3K-Akt and AMPK signaling pathways to combat obesity through the ceRNA network of circRNAs.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110988"},"PeriodicalIF":3.4,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-04DOI: 10.1016/j.ygeno.2025.110986
Shaofang Huang , Xinran Wang , Feifan Zhou
Though widely consumed, current research on the neural mechanisms of arecoline, caffeine, and nicotine remains limited, and the similarities and differences of these substances on the nervous system are still not clear. This study used RNA-seq to analyze the gene expression in the nucleus accumbens (NAc) of mice, and compared the behavioral changes through open field and conditioned place preference (CPP), exploring the effects of different psychoactive substances at transcriptional and behavioral levels. Gene Ontology enrichment analysis revealed that nicotine and caffeine significantly alter biological processes related to synaptic function, and KEGG pathway analysis showed that the differentially expressed genes in the nicotine-treated group were significantly more enriched in pathways related to substance dependence, with arecoline showing the least enrichment. Furthermore, only acute caffeine treatment significantly increased mouse activity, and only nicotine induced CPP. These results provided a scientific basis for evaluating arecoline, caffeine, and nicotine on the nervous system.
{"title":"Comparative effects of arecoline, caffeine, and nicotine on transcription level in the nucleus accumbens of mice","authors":"Shaofang Huang , Xinran Wang , Feifan Zhou","doi":"10.1016/j.ygeno.2025.110986","DOIUrl":"10.1016/j.ygeno.2025.110986","url":null,"abstract":"<div><div>Though widely consumed, current research on the neural mechanisms of arecoline, caffeine, and nicotine remains limited, and the similarities and differences of these substances on the nervous system are still not clear. This study used RNA-seq to analyze the gene expression in the nucleus accumbens (NAc) of mice, and compared the behavioral changes through open field and conditioned place preference (CPP), exploring the effects of different psychoactive substances at transcriptional and behavioral levels. Gene Ontology enrichment analysis revealed that nicotine and caffeine significantly alter biological processes related to synaptic function, and KEGG pathway analysis showed that the differentially expressed genes in the nicotine-treated group were significantly more enriched in pathways related to substance dependence, with arecoline showing the least enrichment. Furthermore, only acute caffeine treatment significantly increased mouse activity, and only nicotine induced CPP. These results provided a scientific basis for evaluating arecoline, caffeine, and nicotine on the nervous system.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110986"},"PeriodicalIF":3.4,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-04DOI: 10.1016/j.ygeno.2025.110990
Hao Yang , Mingxing Chu , Naominggaowa , Xiaoxu Zhang , Mingzhu Shan , Xiaoning Lu , Zhangyuan Pan , Jianning He
Horn is a defensive weapon of sheep, consisting of a horny sheath and a bony core. The KRT2 gene is related to keratinization of the epidermis, so it is likely to be one of the contributor genes affecting horn type in sheep. In this study, we first analyzed the species-specific and tissue-specific expression of the KRT2 gene using transcriptome sequencing data. Then, by comparing the protein sequences of 20 species, we identified 28 specific amino acid sites in Artiodactyla animals, constructed a phylogenetic tree of the KRT2 gene, and predicted its three-dimensional protein structure. Finally, whole genome sequencing data was used and mined 4 functional SNP sites of KRT2 gene, and use KASP assay to verify the loci. In addition, we explored the relationship between the KRT2 gene and the evolution of Artiodactyla animals, and predicted the possible mechanism by which the KRT2 gene affects the horn type of sheep.
{"title":"Tissue-specific expression, functional analysis, and polymorphism of the KRT2 gene in sheep horn","authors":"Hao Yang , Mingxing Chu , Naominggaowa , Xiaoxu Zhang , Mingzhu Shan , Xiaoning Lu , Zhangyuan Pan , Jianning He","doi":"10.1016/j.ygeno.2025.110990","DOIUrl":"10.1016/j.ygeno.2025.110990","url":null,"abstract":"<div><div>Horn is a defensive weapon of sheep, consisting of a horny sheath and a bony core. The <em>KRT2</em> gene is related to keratinization of the epidermis, so it is likely to be one of the contributor genes affecting horn type in sheep. In this study, we first analyzed the species-specific and tissue-specific expression of the <em>KRT2</em> gene using transcriptome sequencing data. Then, by comparing the protein sequences of 20 species, we identified 28 specific amino acid sites in <em>Artiodactyla</em> animals, constructed a phylogenetic tree of the <em>KRT2</em> gene, and predicted its three-dimensional protein structure. Finally, whole genome sequencing data was used and mined 4 functional SNP sites of <em>KRT2</em> gene, and use KASP assay to verify the loci. In addition, we explored the relationship between the <em>KRT2</em> gene and the evolution of <em>Artiodactyla</em> animals, and predicted the possible mechanism by which the <em>KRT2</em> gene affects the horn type of sheep.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110990"},"PeriodicalIF":3.4,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号