The maternal microbiome during pregnancy influences maternal and neonatal health, yet its dynamics and cross-site relationships in the third trimester remain unclear.
Methods
Oral, fecal, and vaginal samples were collected from 22 healthy pregnant women and analyzed using 16S rRNA gene sequencing.
Results
As pregnancy progressed, gut microbial richness significantly increased, while vaginal richness significantly declined. Source tracking showed that the majority of microbes originated from their respective niches, although low-level cross-site contributions were also observed. Correlation-based network analysis revealed complex associations among microbial communities across sites. The oral microbiome exhibited distinct relative contributions and network relationships to the gut and vaginal microbiomes. Moreover, some low-abundance genera (relative abundance <1 %) played a critical role in maintaining ecological balance compared to high-abundance genera.
Conclusions
This study demonstrates dynamic, site-specific microbial changes and highlights potential microbial connections across body sites during late pregnancy, offering new ecological insights relevant to maternal–fetal health.
{"title":"Temporal shifts and cross-site relationships of oral, gut, and vaginal microbiota during the third trimester of pregnancy","authors":"Lulu Meng , Haishan Xie , Xia Duan , Xinyuan Liang , Xiaomei Tang , Huijuan Luo , Xiaomin Xiao , Zhe Li","doi":"10.1016/j.ygeno.2025.111123","DOIUrl":"10.1016/j.ygeno.2025.111123","url":null,"abstract":"<div><h3>Background</h3><div>The maternal microbiome during pregnancy influences maternal and neonatal health, yet its dynamics and cross-site relationships in the third trimester remain unclear.</div></div><div><h3>Methods</h3><div>Oral, fecal, and vaginal samples were collected from 22 healthy pregnant women and analyzed using 16S rRNA gene sequencing.</div></div><div><h3>Results</h3><div>As pregnancy progressed, gut microbial richness significantly increased, while vaginal richness significantly declined. Source tracking showed that the majority of microbes originated from their respective niches, although low-level cross-site contributions were also observed. Correlation-based network analysis revealed complex associations among microbial communities across sites. The oral microbiome exhibited distinct relative contributions and network relationships to the gut and vaginal microbiomes. Moreover, some low-abundance genera (relative abundance <1 %) played a critical role in maintaining ecological balance compared to high-abundance genera.</div></div><div><h3>Conclusions</h3><div>This study demonstrates dynamic, site-specific microbial changes and highlights potential microbial connections across body sites during late pregnancy, offering new ecological insights relevant to maternal–fetal health.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111123"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-11-22DOI: 10.1016/j.ygeno.2025.111156
Jun Xiang , Jingyi Cheng , Yidan Fan , Jiawen Wu , Zhaoyuan Lyu , Jiayu Gu , Jianjiang Xu , Ning Lyu
Purpose
Pterygium was a common progressive ocular disease with unclear pathogenesis. The aim of this study was to identify biomarkers associated with the integrated stress response (ISR) in pterygia and explore the underlying molecular mechanisms.
Methods
Differentially expressed genes (DEGs) were identified using transcriptome sequencing. ISR-related genes (IRGs) and DEGs were integrated to identify candidate genes, and biomarkers were identified by machine learning. A nomogram was generated using these biomarkers. Enrichment analysis, immune infiltration analysis, correlation analysis, construction of transcription-factor (TF)-mRNA-miRNA regulatory networks, drug prediction, and molecular docking were performed to assess the functional mechanisms underlying these biomarkers.
Results
EGLN3, HSPA8, and NDRG1 were identified as ISR-related biomarkers. EGLN3, HSPA8, and NDRG1 were associated with oxidative phosphorylation, cellular response to hypoxia, and decreased oxygen levels according to enrichment analysis. EGLN3 and NDRG1 were significantly and negatively correlated with immune cells, including immature B cells, but not HSPA8. ARNTL-EGLN3-hsa-miR-520a-3p, ARNTL-HSPA8-hsa-miR-520a-3p, and SNAPC4-NDRG1-hsa-miR-518a-5p played regulatory roles in pterygium development. Drug prediction and molecular docking analyses suggested Metribolone and Valproic Acid as potential therapeutic targets for pterygium. According to qRT-PCR, the expressions of EGLN3, HSPA8, and NDRG1 significantly differed between control and pterygium tissues.
Conclusions
EGLN3, HSPA8, and NDRG1 were identified as biomarkers associated with ISR in pterygium. The regulatory networks composed of differed expressions of ISR-related genes, miRNA-mRNA-TF regulatory axes, and immune response played crucial roles in the development of pterygium.
{"title":"Unveiling the role of integrated stress response in pterygium: EGLN3, HSPA8, and NDRG1 as novel biomarkers and therapeutic targets","authors":"Jun Xiang , Jingyi Cheng , Yidan Fan , Jiawen Wu , Zhaoyuan Lyu , Jiayu Gu , Jianjiang Xu , Ning Lyu","doi":"10.1016/j.ygeno.2025.111156","DOIUrl":"10.1016/j.ygeno.2025.111156","url":null,"abstract":"<div><h3>Purpose</h3><div>Pterygium was a common progressive ocular disease with unclear pathogenesis. The aim of this study was to identify biomarkers associated with the integrated stress response (ISR) in pterygia and explore the underlying molecular mechanisms.</div></div><div><h3>Methods</h3><div>Differentially expressed genes (DEGs) were identified using transcriptome sequencing. ISR-related genes (IRGs) and DEGs were integrated to identify candidate genes, and biomarkers were identified by machine learning. A nomogram was generated using these biomarkers. Enrichment analysis, immune infiltration analysis, correlation analysis, construction of transcription-factor (TF)-mRNA-miRNA regulatory networks, drug prediction, and molecular docking were performed to assess the functional mechanisms underlying these biomarkers.</div></div><div><h3>Results</h3><div><em>EGLN3</em>, <em>HSPA8</em>, and <em>NDRG1</em> were identified as ISR-related biomarkers. <em>EGLN3</em>, <em>HSPA8</em>, and <em>NDRG1</em> were associated with oxidative phosphorylation, cellular response to hypoxia, and decreased oxygen levels according to enrichment analysis. <em>EGLN3</em> and <em>NDRG1</em> were significantly and negatively correlated with immune cells, including immature B cells, but not <em>HSPA8</em>. ARNTL-EGLN3-hsa-miR-520a-3p, ARNTL-HSPA8-hsa-miR-520a-3p, and SNAPC4-NDRG1-hsa-miR-518a-5p played regulatory roles in pterygium development. Drug prediction and molecular docking analyses suggested Metribolone and Valproic Acid as potential therapeutic targets for pterygium. According to qRT-PCR, the expressions of <em>EGLN3</em>, <em>HSPA8</em>, and <em>NDRG1</em> significantly differed between control and pterygium tissues.</div></div><div><h3>Conclusions</h3><div><em>EGLN3, HSPA8,</em> and <em>NDRG1</em> were identified as biomarkers associated with ISR in pterygium. The regulatory networks composed of differed expressions of ISR-related genes, miRNA-mRNA-TF regulatory axes, and immune response played crucial roles in the development of pterygium.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111156"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145596392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-10-01DOI: 10.1016/j.ygeno.2025.111130
Zhonglong Zhao , Hong Yang , Yong Zhang , Shijun Li , Zhaobi Ai , Runqian Yang , Yixing Ou , Tian Wang , Li Ye , Chang Shu
Muscle growth is a crucial economic trait in poultry, influenced by a combination of environmental, nutritional, and genetic factors. N6-methyladenosine (m6A) modification, the most abundant form of RNA modification, has been identified in various poultry tissues. However, the m6A modification profiles during goose muscle development remain poorly understood. In this study, we characterized m6A modification profiles in breast (n = 5) and leg (n = 5) muscles of Zhijin white geese using MeRIP-seq and RNA-seq. Samples were collected from healthy 6-month-old male geese of similar body weight after euthanasia. Compared to breast muscles, leg muscles exhibited significant differences in muscle fiber morphology (cross-sectional area, diameter, and density), intramuscular fat content, and overall m6A levels (P < 0.001). Leg muscles exhibited upregulation of m6A regulators (including ALKBH5, METTL14, METTL16, and ZC3H13) (P < 0.05) and showed predominant m6A peaks in coding sequences (CDS) and 3′UTRs, with conserved RRACH motifs. Compared with breast muscles, 78 differentially methylated genes (DMGs) were identified by MeRIP-seq, including 43 hyper-methylated and 35 hypo-methylated genes in leg muscles. Integrated analysis with RNA-seq revealed 11 overlapping DMGs, comprising 7 hypo-methylated and 4 hyper-methylated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these DMGs were significantly enriched in neuroactive ligand–receptor interaction, glycosaminoglycan biosynthesis, and regulation of actin cytoskeleton. Furthermore, we identified LGI1, CDK18, and LPAR2 from the significantly enriched pathways as potential candidate genes influencing muscle development. This study provides a theoretical foundation for further investigation into the regulatory role of m6A modification in goose muscle development.
{"title":"Differential m6A methylation landscapes in breast and leg muscles of Zhijin white geese: Epigenetic insights into muscle development","authors":"Zhonglong Zhao , Hong Yang , Yong Zhang , Shijun Li , Zhaobi Ai , Runqian Yang , Yixing Ou , Tian Wang , Li Ye , Chang Shu","doi":"10.1016/j.ygeno.2025.111130","DOIUrl":"10.1016/j.ygeno.2025.111130","url":null,"abstract":"<div><div>Muscle growth is a crucial economic trait in poultry, influenced by a combination of environmental, nutritional, and genetic factors. N<sup>6</sup>-methyladenosine (m6A) modification, the most abundant form of RNA modification, has been identified in various poultry tissues. However, the m6A modification profiles during goose muscle development remain poorly understood. In this study, we characterized m6A modification profiles in breast (<em>n</em> = 5) and leg (n = 5) muscles of Zhijin white geese using MeRIP-seq and RNA-seq. Samples were collected from healthy 6-month-old male geese of similar body weight after euthanasia. Compared to breast muscles, leg muscles exhibited significant differences in muscle fiber morphology (cross-sectional area, diameter, and density), intramuscular fat content, and overall m6A levels (<em>P</em> < 0.001). Leg muscles exhibited upregulation of m6A regulators (including <em>ALKBH5</em>, <em>METTL14</em>, <em>METTL16</em>, and <em>ZC3H13</em>) (<em>P</em> < 0.05) and showed predominant m6A peaks in coding sequences (CDS) and 3′UTRs, with conserved RRACH motifs. Compared with breast muscles, 78 differentially methylated genes (DMGs) were identified by MeRIP-seq, including 43 hyper-methylated and 35 hypo-methylated genes in leg muscles. Integrated analysis with RNA-seq revealed 11 overlapping DMGs, comprising 7 hypo-methylated and 4 hyper-methylated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these DMGs were significantly enriched in neuroactive ligand–receptor interaction, glycosaminoglycan biosynthesis, and regulation of actin cytoskeleton. Furthermore, we identified <em>LGI1</em>, <em>CDK18</em>, and <em>LPAR2</em> from the significantly enriched pathways as potential candidate genes influencing muscle development. This study provides a theoretical foundation for further investigation into the regulatory role of m6A modification in goose muscle development.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111130"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-09-26DOI: 10.1016/j.ygeno.2025.111111
Shuqi Zhang , Wei Cheng , Tiandan Li , Zimu Zhang , Juanjuan Yu , Wanyan Jiao , Xiaomei Wan , Yumeng Wu , Ling Xu , Tongting Ji , Yang Yang , Jian Pan , Jun Lu
Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy, with T-cell acute lymphoblastic leukemia (T-ALL) accounting for 10–25 % of cases. We identified ELOVL5 as a super-enhancer–driven oncogene that is highly expressed in T-ALL and associated with poor overall survival. Through H3K27ac ChIP-seq analysis of patient samples and cellular models, we confirmed that ELOVL5 is transcriptionally regulated by super-enhancers. Functional studies demonstrated that ELOVL5 knockdown suppressed proliferation and induced apoptosis in T-ALL cells, both in vitro and in vivo. In mouse xenograft models, silencing ELOVL5 reduced tumor burden and prolonged survival. RNA-seq analysis further revealed that ELOVL5 promotes T-ALL progression by activating MYC signaling and upregulating SERBP1, a critical downstream effector. Consistently, SERBP1 silencing also inhibited proliferation and induced apoptosis in T-ALL cells. Collectively, these findings establish ELOVL5 as a super-enhancer–associated oncogenic regulator that drives T-ALL progression through the ELOVL5–SERBP1–MYC axis, highlighting its potential as a therapeutic target.
{"title":"Super-enhancer-driven ELOVL5 promotes T-ALL progression through the MYC-SERBP1 pathway","authors":"Shuqi Zhang , Wei Cheng , Tiandan Li , Zimu Zhang , Juanjuan Yu , Wanyan Jiao , Xiaomei Wan , Yumeng Wu , Ling Xu , Tongting Ji , Yang Yang , Jian Pan , Jun Lu","doi":"10.1016/j.ygeno.2025.111111","DOIUrl":"10.1016/j.ygeno.2025.111111","url":null,"abstract":"<div><div>Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy, with T-cell acute lymphoblastic leukemia (T-ALL) accounting for 10–25 % of cases. We identified ELOVL5 as a super-enhancer–driven oncogene that is highly expressed in T-ALL and associated with poor overall survival. Through H3K27ac ChIP-seq analysis of patient samples and cellular models, we confirmed that ELOVL5 is transcriptionally regulated by super-enhancers. Functional studies demonstrated that ELOVL5 knockdown suppressed proliferation and induced apoptosis in T-ALL cells, both in vitro and in vivo. In mouse xenograft models, silencing ELOVL5 reduced tumor burden and prolonged survival. RNA-seq analysis further revealed that ELOVL5 promotes T-ALL progression by activating MYC signaling and upregulating SERBP1, a critical downstream effector. Consistently, SERBP1 silencing also inhibited proliferation and induced apoptosis in T-ALL cells. Collectively, these findings establish ELOVL5 as a super-enhancer–associated oncogenic regulator that drives T-ALL progression through the ELOVL5–SERBP1–MYC axis, highlighting its potential as a therapeutic target.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111111"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145185349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-10-11DOI: 10.1016/j.ygeno.2025.111137
Jun Wang , Yishuang Cui , Yexuan Liu , Yanlei Ge , Weinan Yao , Junqing Gan , Yanna Bi , Guogui Sun
Single-walled carbon nanotubes (SWCNT), as emerging nanomaterials, possess unclear potential carcinogenic mechanisms. This study established a model of malignant transformation using human lung epithelial cells chronically treated with SWCNT, and applied integrated multi-omics analysis to identify key regulatory factors.
Chronic exposure to SWCNT promoted cellular growth, motility, invasive potential, and oncogenic capacity, and activated the PI3K/AKT pathway, facilitating malignant transformation of the cells. Among the upregulated genes, Transforming Growth Factor Alpha (TGFA) was identified as a core regulatory factor. It was significantly overexpressed in malignant transformed cells, lung cancer cells of the non-small cell type (NSCLC), and patient-derived cancer tissues. Further investigation revealed that high TGFA expression was closely associated with poor prognosis and an immune-suppressive microenvironment in patients with lung adenocarcinoma and squamous cell carcinoma. Knockdown of TGFA inhibited the epithelial-mesenchymal transition (EMT) process and the activation of the PI3K/AKT signaling pathway, significantly weakening the malignant phenotype of the cells. Additionally, drug sensitivity analysis suggested that TGFA might be involved in regulating drug responses. In conclusion, TGFA functions as an essential regulator in the carcinogenic effects of SWCNT and holds potential diagnostic, prognostic, and therapeutic value for NSCLC.
{"title":"The role of transforming growth factor alpha in mediating the malignant transformation of human lung epithelial cells induced by single-walled carbon nanotubes and its role in the progression of non-small cell lung cancer","authors":"Jun Wang , Yishuang Cui , Yexuan Liu , Yanlei Ge , Weinan Yao , Junqing Gan , Yanna Bi , Guogui Sun","doi":"10.1016/j.ygeno.2025.111137","DOIUrl":"10.1016/j.ygeno.2025.111137","url":null,"abstract":"<div><div>Single-walled carbon nanotubes (SWCNT), as emerging nanomaterials, possess unclear potential carcinogenic mechanisms. This study established a model of malignant transformation using human lung epithelial cells chronically treated with SWCNT, and applied integrated multi-omics analysis to identify key regulatory factors.</div><div>Chronic exposure to SWCNT promoted cellular growth, motility, invasive potential, and oncogenic capacity, and activated the PI3K/AKT pathway, facilitating malignant transformation of the cells. Among the upregulated genes, Transforming Growth Factor Alpha (TGFA) was identified as a core regulatory factor. It was significantly overexpressed in malignant transformed cells, lung cancer cells of the non-small cell type (NSCLC), and patient-derived cancer tissues. Further investigation revealed that high TGFA expression was closely associated with poor prognosis and an immune-suppressive microenvironment in patients with lung adenocarcinoma and squamous cell carcinoma. Knockdown of TGFA inhibited the epithelial-mesenchymal transition (EMT) process and the activation of the PI3K/AKT signaling pathway, significantly weakening the malignant phenotype of the cells. Additionally, drug sensitivity analysis suggested that TGFA might be involved in regulating drug responses. In conclusion, TGFA functions as an essential regulator in the carcinogenic effects of SWCNT and holds potential diagnostic, prognostic, and therapeutic value for NSCLC.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111137"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145285918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-09-11DOI: 10.1016/j.ygeno.2025.111103
Jianqun Ding , Tian Xia , Shuhong Li , Xiaodong Gao , Zhicheng Yao , Shengyang Zhou , Lei Zhang , Zhihao Zhang , Shunting Chen , Mingke Han , Honghai Zhang
Background
Aythya nyroca (Ferruginous Duck), a small to medium-sized chestnut-colored diving duck, is mainly distributed in central, western, and southern Asia, southern Europe, and central Africa. We employed Oxford Nanopore sequencing and Hi-C technique to assemble the first chromosome-level genome of A. nyroca. The assembled genome had a scaffold N50 of 86,001,877 bp, with 35 pseudochromosomes mounted. Repeat sequences accounted for approximately 14.84 % of the genome.
Results
To uncover the molecular mechanisms of diving adaptations in A. nyroca, we conducted separate enrichment analyses on species-unique genes, expanded and contracted gene families, and positively selected genes. The results indicated the enrichment of pathways related to blood oxygen concentration regulation and energy metabolism. The enrichment of related pathways and the positive selection of related genes may reveal the adaptive evolutionary mechanism of A. nyroca in the diving environment.
Conclusions
This high-quality genome provides a valuable resource for studying the evolution of the diving adaptation mechanism in birds. Whole-genome assemblies are crucial for comprehensively understanding various aspects of A. nyroca biology, including morphology, ecology, and physiology, and thus play an essential role in its conservation.
{"title":"Chromosome-level assembly of the genome of the Aythya nyroca provides insights into diving adaptations","authors":"Jianqun Ding , Tian Xia , Shuhong Li , Xiaodong Gao , Zhicheng Yao , Shengyang Zhou , Lei Zhang , Zhihao Zhang , Shunting Chen , Mingke Han , Honghai Zhang","doi":"10.1016/j.ygeno.2025.111103","DOIUrl":"10.1016/j.ygeno.2025.111103","url":null,"abstract":"<div><h3>Background</h3><div><em>Aythya nyroca</em> (Ferruginous Duck), a small to medium-sized chestnut-colored diving duck, is mainly distributed in central, western, and southern Asia, southern Europe, and central Africa. We employed Oxford Nanopore sequencing and Hi-C technique to assemble the first chromosome-level genome of <em>A. nyroca</em>. The assembled genome had a scaffold N50 of 86,001,877 bp, with 35 pseudochromosomes mounted. Repeat sequences accounted for approximately 14.84 % of the genome.</div></div><div><h3>Results</h3><div>To uncover the molecular mechanisms of diving adaptations in <em>A. nyroca</em>, we conducted separate enrichment analyses on species-unique genes, expanded and contracted gene families, and positively selected genes. The results indicated the enrichment of pathways related to blood oxygen concentration regulation and energy metabolism. The enrichment of related pathways and the positive selection of related genes may reveal the adaptive evolutionary mechanism of <em>A. nyroca</em> in the diving environment.</div></div><div><h3>Conclusions</h3><div>This high-quality genome provides a valuable resource for studying the evolution of the diving adaptation mechanism in birds. Whole-genome assemblies are crucial for comprehensively understanding various aspects of <em>A. nyroca</em> biology, including morphology, ecology, and physiology, and thus play an essential role in its conservation.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111103"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-09-30DOI: 10.1016/j.ygeno.2025.111126
Hongwei Jin , Bin Feng , Wenxiao Gong, Xiaoliang Chen, Dongli Wang, Yan Li, Weijun Huang, Wenting Peng
•
With the proposal of the concept of “metagenomics” and the development of sequencing technology, 16S rRNA gene profiling has been widely applied in the survey of microbial diversity. This study explored the gut microbiota of children with hand, foot and mouth disease (HFMD). This study investigated the gut microbiota of 24 children with asymptomatic and symptomatic hand, foot, and mouth disease (HFMD) and 19 healthy controls using 16S rRNA sequencing. The gut microbiota, both in asymptomatic and symptomatic HFMD patients, was distinct from the controls, with the composition of gut microbiota in the HFMD cases represented a significant difference. The dysbiosis of gut microbiota of the HFMD cases included a reduction of butyrate-producing bacteria and an up-regulation of inflammation-inducing bacteria. These may have impaired the intestinal biological mucosal barrier and host immune functions, promoting the invasion of the enterovirus.
{"title":"Evaluation of gut microbial diversity and correlation in asymptomatic and symptomatic patients with hand, foot and mouth disease","authors":"Hongwei Jin , Bin Feng , Wenxiao Gong, Xiaoliang Chen, Dongli Wang, Yan Li, Weijun Huang, Wenting Peng","doi":"10.1016/j.ygeno.2025.111126","DOIUrl":"10.1016/j.ygeno.2025.111126","url":null,"abstract":"<div><div><ul><li><span>•</span><span><div>With the proposal of the concept of “metagenomics” and the development of sequencing technology, 16S rRNA gene profiling has been widely applied in the survey of microbial diversity. This study explored the gut microbiota of children with hand, foot and mouth disease (HFMD). This study investigated the gut microbiota of 24 children with asymptomatic and symptomatic hand, foot, and mouth disease (HFMD) and 19 healthy controls using 16S rRNA sequencing. The gut microbiota, both in asymptomatic and symptomatic HFMD patients, was distinct from the controls, with the composition of gut microbiota in the HFMD cases represented a significant difference. The dysbiosis of gut microbiota of the HFMD cases included a reduction of butyrate-producing bacteria and an up-regulation of inflammation-inducing bacteria. These may have impaired the intestinal biological mucosal barrier and host immune functions, promoting the invasion of the enterovirus.</div></span></li></ul></div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111126"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Idiopathic congenital nystagmus (ICN) is characterized by involuntary horizontal eye oscillations and is frequently associated with X-linked FRMD7 mutations. Despite over 150 FRMD7 variants have been reported, their pathogenic mechanisms remain poorly understood. In this study, we identified a novel FRMD7 deletion (c.742-211_1050+59del p.Leu249_Val351del) in an ICN-affected family. Minigenes analysis demonstrated that this FRMD7 mutation caused skipping of exon 9– 11. RT-qPCR and western blotting revealed unchanged FRMD7 mRNA levels but a significantly upregulated in protein expression. Structural modeling indicated the loss of a crucial amino acid segment in the mutated FRMD7 protein (FRMD7-m1). These findings suggest that this FRMD7 deletion disrupts protein translation and stability, contributing to ICN pathogenesis, and expand our understanding of FRMD7-related molecular mechanisms.
{"title":"Functional analysis of a novel segment deletion in the FRMD7 gene causing X-linked idiopathic congenital nystagmus","authors":"Xiaoli Zhao , Xinyang Li , Jian Yuan, Xiaolei Wang, Qinxue Meng, Xinwen Zhang","doi":"10.1016/j.ygeno.2025.111138","DOIUrl":"10.1016/j.ygeno.2025.111138","url":null,"abstract":"<div><div>Idiopathic congenital nystagmus (ICN) is characterized by involuntary horizontal eye oscillations and is frequently associated with X-linked <em>FRMD7</em> mutations. Despite over 150 <em>FRMD7</em> variants have been reported, their pathogenic mechanisms remain poorly understood. In this study, we identified a novel <em>FRMD7</em> deletion (c.742-211_1050+59del p.Leu249_Val351del) in an ICN-affected family. Minigenes analysis demonstrated that this <em>FRMD7</em> mutation caused skipping of exon 9– 11. RT-qPCR and western blotting revealed unchanged <em>FRMD7</em> mRNA levels but a significantly upregulated in protein expression. Structural modeling indicated the loss of a crucial amino acid segment in the mutated FRMD7 protein (<em>FRMD7</em>-m1). These findings suggest that this <em>FRMD7</em> deletion disrupts protein translation and stability, contributing to ICN pathogenesis, and expand our understanding of <em>FRMD7</em>-related molecular mechanisms.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111138"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145354375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-09-21DOI: 10.1016/j.ygeno.2025.111115
Zhenzhen Pan , Cengceng He , Xuena Xu , Yuting Jin , Mingyi Xu , Suwan Xiong , Ling Li , Chuangli Hao
Background
Obese asthma is a specific phenotype of childhood asthma characterized by increased severity, decreased quality of life, and reduced treatment response. Herein, we applied transcriptomics to investigate biomarkers of obese asthma.
Methods
Mouse models of obesity and asthma were induced through high-fat diet (HFD) feeding and ovalbumin inhalation, respectively. RNA was extracted from lung samples from HFD-fed asthma, HFD-fed control, normal-fat diet (NFD)-fed asthma, and NFD-fed control mice. Transcriptome sequencing data were analyzed for quality control (QC), and differentially expressed genes (DEGs) were identified. From this list, candidate genes were obtained through intersections, followed by the construction of protein-protein interaction (PPI) networks to identify key genes. Subsequently, immune cell infiltration was analyzed across the different subgroups. Key genes were validated using Quantitative Polymerase Chain Reaction (PCR).
Results
Overall, 86 candidate genes were identified from the intersection of different DEG sets. PPI networks were constructed using three algorithms, revealing nine key genes (ITGM, Slc11a1, Nos2, PirB, IL1RN, LCN2, CD33, MSR1, and CXCL2). Immune infiltration analysis revealed distinct responses in immune cells, including naïve B cells and plasma cells. Following verification by qPCR, ITGAM, Nos2, LCN2, CD33, MSR1, and CXCL2 were confirmed to be significantly higher in the HFD-fed asthma group than in the NFD-fed asthma group. Slc11a1 was significantly downregulated, while PirB and IL1RN showed no significant differences. The expression levels of ITGAM, Nos2, and LCN2 demonstrated a consistent trend in human peripheral blood samples. However, to further substantiate their roles in obesity-associated asthma, an expanded sample size is required for confirmation.
Conclusion
This study systematically investigated the molecular mechanisms underlying the associated obesity and metabolic disorders, identified biomarkers, and provided new directions for future therapeutic and clinical studies on obese asthma.
{"title":"Exploration of novel biomarkers of obese asthma using RNA sequencing in high-fat-fed asthmatic model mice","authors":"Zhenzhen Pan , Cengceng He , Xuena Xu , Yuting Jin , Mingyi Xu , Suwan Xiong , Ling Li , Chuangli Hao","doi":"10.1016/j.ygeno.2025.111115","DOIUrl":"10.1016/j.ygeno.2025.111115","url":null,"abstract":"<div><h3>Background</h3><div>Obese asthma is a specific phenotype of childhood asthma characterized by increased severity, decreased quality of life, and reduced treatment response. Herein, we applied transcriptomics to investigate biomarkers of obese asthma.</div></div><div><h3>Methods</h3><div>Mouse models of obesity and asthma were induced through high-fat diet (HFD) feeding and ovalbumin inhalation, respectively. RNA was extracted from lung samples from HFD-fed asthma, HFD-fed control, normal-fat diet (NFD)-fed asthma, and NFD-fed control mice. Transcriptome sequencing data were analyzed for quality control (QC), and differentially expressed genes (DEGs) were identified. From this list, candidate genes were obtained through intersections, followed by the construction of protein-protein interaction (PPI) networks to identify key genes. Subsequently, immune cell infiltration was analyzed across the different subgroups. Key genes were validated using Quantitative Polymerase Chain Reaction (PCR).</div></div><div><h3>Results</h3><div>Overall, 86 candidate genes were identified from the intersection of different DEG sets. PPI networks were constructed using three algorithms, revealing nine key genes (ITGM, Slc11a1, Nos2, PirB, IL1RN, LCN2, CD33, MSR1, and CXCL2). Immune infiltration analysis revealed distinct responses in immune cells, including naïve B cells and plasma cells. Following verification by qPCR, ITGAM, Nos2, LCN2, CD33, MSR1, and CXCL2 were confirmed to be significantly higher in the HFD-fed asthma group than in the NFD-fed asthma group. Slc11a1 was significantly downregulated, while PirB and IL1RN showed no significant differences. The expression levels of ITGAM, Nos2, and LCN2 demonstrated a consistent trend in human peripheral blood samples. However, to further substantiate their roles in obesity-associated asthma, an expanded sample size is required for confirmation.</div></div><div><h3>Conclusion</h3><div>This study systematically investigated the molecular mechanisms underlying the associated obesity and metabolic disorders, identified biomarkers, and provided new directions for future therapeutic and clinical studies on obese asthma.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111115"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145130571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-09-30DOI: 10.1016/j.ygeno.2025.111128
Shanshan Gao , Mengyi Guo , Enlu Zhang , Zupei Yi , Kui Liu , Shuang Xue , Ruimin Li , Kunpeng Zhang
Aldehyde oxidase in insects participates in the degradation of various aldehyde insecticides and toxic plant-derived aldehydes, increasing the resistance of pests to these agents. However, the specific mechanism underlying this resistance remains unclear. In this study, we examined the differentially expressed genes in Tribolium castaneum, a global stored-grain pest, before and after knockdown of aldehyde oxidase TcAOX3. We found decreased expression levels of chymotrypsin-like proteinase 5B precursor and serine protease P40, which are involved in immunity and digestion, indicating that TcAOX3 may be involved in immune and digestive functions of larvae. Reduction of TcAOX3 expression also significantly decreased the resistance of T. castaneum larvae to benzaldehyde, with an increase of about 20 % in the killing effect of benzaldehyde against T. castaneum. Molecular docking and isothermal titration calorimetry results showed that benzaldehyde bound to TcAOX3 via Val761, Tyr558, Met562, Ile559, Gln557, Arg763, and Arg762, with a binding energy of ΔG = −24.23 kJ/mol. These results provide a theoretical basis for analysis of the detoxification mechanism of aldehyde oxidase in insects and offer a reference for screening of green insecticides targeting aldehyde oxidase.
{"title":"RNA-seq analysis combined with insecticidal efficacy assays reveal the insecticidal molecular mechanism of benzaldehyde against Tribolium castaneum","authors":"Shanshan Gao , Mengyi Guo , Enlu Zhang , Zupei Yi , Kui Liu , Shuang Xue , Ruimin Li , Kunpeng Zhang","doi":"10.1016/j.ygeno.2025.111128","DOIUrl":"10.1016/j.ygeno.2025.111128","url":null,"abstract":"<div><div>Aldehyde oxidase in insects participates in the degradation of various aldehyde insecticides and toxic plant-derived aldehydes, increasing the resistance of pests to these agents. However, the specific mechanism underlying this resistance remains unclear. In this study, we examined the differentially expressed genes in <em>Tribolium castaneum</em>, a global stored-grain pest, before and after knockdown of aldehyde oxidase <em>TcAOX3</em>. We found decreased expression levels of chymotrypsin-like proteinase 5B precursor and serine protease P40, which are involved in immunity and digestion, indicating that <em>TcAOX3</em> may be involved in immune and digestive functions of larvae. Reduction of <em>TcAOX3</em> expression also significantly decreased the resistance of <em>T. castaneum</em> larvae to benzaldehyde, with an increase of about 20 % in the killing effect of benzaldehyde against <em>T. castaneum</em>. Molecular docking and isothermal titration calorimetry results showed that benzaldehyde bound to TcAOX3 via Val761, Tyr558, Met562, Ile559, Gln557, Arg763, and Arg762, with a binding energy of ΔG = −24.23 kJ/mol. These results provide a theoretical basis for analysis of the detoxification mechanism of aldehyde oxidase in insects and offer a reference for screening of green insecticides targeting aldehyde oxidase.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111128"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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