Pub Date : 2025-11-01DOI: 10.1016/j.ygeno.2025.111155
Huihui Guo , Xiaoli Gao , Xiao'an Li , Lan Wang , Wenhua Liao , Xue Bai , Qi Wu
Heat stress has deleterious effects on flowering and yield of Tartary buckwheat. In this study, we compared the transcriptomes between thermo-sensitive MQ and adaptive KQ and XQ, in leaves and inflorescences. Compared with adaptive KQ and XQ, flowering genes like FtFT1, FtFT3 and MADS-Box, and developmental genes like PIF3, CIB1, CLAVATA3, YABBY, and HY5 were repressed in thermo-sensitive MQ leaf and inflorescence. Higher proportions of HSPs and HSFs were induced in thermo-sensitive MQ leaf and inflorescence. By using long-read sequencing, we identified DAS events on circadian clock, floral development and heat stress related genes between thermo-sensitive MQ and adaptive XQ. We found the DAS events on PIF, LHY, MADS-Box AGAMOUS and HSF genes generated malfunctional proteins. We speculated that the DAS events on key floral development and heat stress related genes may influence expressions of downstream flowering genes, thus leading to the flowering retardation in thermo-sensitive rice Tartary buckwheat.
{"title":"Combined short- and long-read sequencing reveals the important regulators and alternative splicing events associated with the thermo-sensitive flowering retardation of rice Tartary buckwheat","authors":"Huihui Guo , Xiaoli Gao , Xiao'an Li , Lan Wang , Wenhua Liao , Xue Bai , Qi Wu","doi":"10.1016/j.ygeno.2025.111155","DOIUrl":"10.1016/j.ygeno.2025.111155","url":null,"abstract":"<div><div>Heat stress has deleterious effects on flowering and yield of Tartary buckwheat. In this study, we compared the transcriptomes between thermo-sensitive MQ and adaptive KQ and XQ, in leaves and inflorescences. Compared with adaptive KQ and XQ, flowering genes like <em>FtFT1</em>, <em>FtFT3</em> and <em>MADS-Box</em>, and developmental genes like <em>PIF3</em>, <em>CIB1</em>, <em>CLAVATA3</em>, <em>YABBY</em>, and <em>HY5</em> were repressed in thermo-sensitive MQ leaf and inflorescence. Higher proportions of <em>HSP</em>s and <em>HSF</em>s were induced in thermo-sensitive MQ leaf and inflorescence. By using long-read sequencing, we identified DAS events on circadian clock, floral development and heat stress related genes between thermo-sensitive MQ and adaptive XQ. We found the DAS events on <em>PIF</em>, <em>LHY</em>, MADS-Box <em>AGAMOUS</em> and <em>HSF</em> genes generated malfunctional proteins. We speculated that the DAS events on key floral development and heat stress related genes may influence expressions of downstream flowering genes, thus leading to the flowering retardation in thermo-sensitive rice Tartary buckwheat.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111155"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145573379","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 : 2025-10-17DOI: 10.1016/j.ygeno.2025.111140
Hongyu Wu , Yu Zhang , Xin Ma , Zenghua Mi , Zhijun Yang
The invasiveness of pituitary adenomas is closely related to the tumour immune microenvironment. This study aimed to identify immune-related genes associated with IPAs. Transcriptomic data from 32 patient-derived samples were analysed to screen immune-related differentially expressed genes between IPAs and non-invasive pituitary adenomas. Weighted gene co-expression network analysis of merged datasets (GSE26966 and GSE51618) was performed to identify hub genes, which were then intersected with immune-related DEGs. Least absolute shrinkage and selection operator regression and support vector machine algorithms consistently identified tissue inhibitor of metalloproteinases 1 (TIMP1) as a key immune-associated invasive gene. Multi-omics validation confirmed significant downregulation of TIMP1 in IPAs. Functional enrichment, single-sample gene set enrichment analysis, CIBERSORT, and immune checkpoint profiling linked TIMP1 to macrophage infiltration and immune regulation. Immunohistochemistry and in vitro experiments further demonstrated that TIMP1 overexpression inhibited tumour-cell proliferation, invasion, and migration. Collectively, these findings suggest that TIMP1 downregulation may promote IPA progression through immune dysregulation.
{"title":"TIMP1: A novel immune-related signature associated with invasiveness and inhibition of pituitary adenoma","authors":"Hongyu Wu , Yu Zhang , Xin Ma , Zenghua Mi , Zhijun Yang","doi":"10.1016/j.ygeno.2025.111140","DOIUrl":"10.1016/j.ygeno.2025.111140","url":null,"abstract":"<div><div>The invasiveness of pituitary adenomas is closely related to the tumour immune microenvironment. This study aimed to identify immune-related genes associated with IPAs. Transcriptomic data from 32 patient-derived samples were analysed to screen immune-related differentially expressed genes between IPAs and non-invasive pituitary adenomas. Weighted gene co-expression network analysis of merged datasets (GSE26966 and GSE51618) was performed to identify hub genes, which were then intersected with immune-related DEGs. Least absolute shrinkage and selection operator regression and support vector machine algorithms consistently identified tissue inhibitor of metalloproteinases 1 (<em>TIMP1</em>) as a key immune-associated invasive gene. Multi-omics validation confirmed significant downregulation of <em>TIMP1</em> in IPAs. Functional enrichment, single-sample gene set enrichment analysis, CIBERSORT, and immune checkpoint profiling linked TIMP1 to macrophage infiltration and immune regulation. Immunohistochemistry and in vitro experiments further demonstrated that TIMP1 overexpression inhibited tumour-cell proliferation, invasion, and migration. Collectively, these findings suggest that TIMP1 downregulation may promote IPA progression through immune dysregulation.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111140"},"PeriodicalIF":3.0,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145328733","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 : 2025-10-17DOI: 10.1016/j.ygeno.2025.111144
Kristina Santucci, Yuning Cheng, Si-Mei Xu, Michael Janitz
Advancements in the accuracy of long-read sequencing technologies and bioinformatic approaches have broadened the applications of RNA sequencing (RNA-seq). This review covers such developments across various aspects of genomics, transcriptomics, and proteomics, focussing on the discovery and characterisation of new genes, transcriptional isoforms, and proteins. This review also explores the different approaches to characterise transcript isoforms that transcribed from both annotated and unannotated novel genes, such as determining protein-coding potential, functional domains, and conserved regions. Finally, the long-read RNA-seq (lrRNA-seq) based approaches for analysing co-transcriptional and post-transcriptional events, such as alternative splicing, polyadenylation, and RNA modifications, are elaborated. Conflicting recommendations, limitations, and priorities for future research for such methods reported by previous studies are also addressed. Overall, this review intends to demonstrate how integrated analyses can be achieved with lrRNA-seq in various areas of molecular biology.
{"title":"Computational methods for the analysis of long-read RNA-seq data","authors":"Kristina Santucci, Yuning Cheng, Si-Mei Xu, Michael Janitz","doi":"10.1016/j.ygeno.2025.111144","DOIUrl":"10.1016/j.ygeno.2025.111144","url":null,"abstract":"<div><div>Advancements in the accuracy of long-read sequencing technologies and bioinformatic approaches have broadened the applications of RNA sequencing (RNA-seq). This review covers such developments across various aspects of genomics, transcriptomics, and proteomics, focussing on the discovery and characterisation of new genes, transcriptional isoforms, and proteins. This review also explores the different approaches to characterise transcript isoforms that transcribed from both annotated and unannotated novel genes, such as determining protein-coding potential, functional domains, and conserved regions. Finally, the long-read RNA-seq (lrRNA-seq) based approaches for analysing co-transcriptional and post-transcriptional events, such as alternative splicing, polyadenylation, and RNA modifications, are elaborated. Conflicting recommendations, limitations, and priorities for future research for such methods reported by previous studies are also addressed. Overall, this review intends to demonstrate how integrated analyses can be achieved with lrRNA-seq in various areas of molecular biology.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111144"},"PeriodicalIF":3.0,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145321326","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 : 2025-10-16DOI: 10.1016/j.ygeno.2025.111143
Zefeng Li , Jing Lv , Zhong Wang , Feng Li , Shuaibin Wang , Xinxi He , Mingzhu Wu , Changbo Dai , Xin Xu , Xiaodong Xie , Yuhe Sun , Jun Yang , Zhaopeng Luo , Junping Gao
Quinclorac is a widely used herbicide known to inhibit tobacco growth, yet its molecular impact remains poorly understood. To elucidate tobacco's response mechanisms, we profiled long non-coding RNAs (lncRNAs) under quinclorac stress. A total of 1867 lncRNAs were identified, including 1337 novel transcripts. Differential expression analysis revealed 672 lncRNAs significantly altered by quinclorac treatment. Co-expression clustering grouped these into 20 distinct expression profiles. Target prediction indicated that 415 lncRNAs potentially regulate mRNAs via cis- and/or trans-acting interactions. Functional enrichment of their targets highlighted overrepresentation of photosynthesis and stress-response pathways. Moreover, we constructed regulatory networks linking lncRNAs to quinclorac-resistance–associated genes involved in hormone biosynthesis and signaling, molecular transport, and xenobiotic metabolism. These findings uncover a repertoire of lncRNAs responsive to quinclorac and suggest their roles in mediating herbicide tolerance in tobacco.
{"title":"Identification and analysis of long non-coding RNAs response to quinclorac stress in tobacco","authors":"Zefeng Li , Jing Lv , Zhong Wang , Feng Li , Shuaibin Wang , Xinxi He , Mingzhu Wu , Changbo Dai , Xin Xu , Xiaodong Xie , Yuhe Sun , Jun Yang , Zhaopeng Luo , Junping Gao","doi":"10.1016/j.ygeno.2025.111143","DOIUrl":"10.1016/j.ygeno.2025.111143","url":null,"abstract":"<div><div>Quinclorac is a widely used herbicide known to inhibit tobacco growth, yet its molecular impact remains poorly understood. To elucidate tobacco's response mechanisms, we profiled long non-coding RNAs (lncRNAs) under quinclorac stress. A total of 1867 lncRNAs were identified, including 1337 novel transcripts. Differential expression analysis revealed 672 lncRNAs significantly altered by quinclorac treatment. Co-expression clustering grouped these into 20 distinct expression profiles. Target prediction indicated that 415 lncRNAs potentially regulate mRNAs via <em>cis</em>- and/or <em>trans</em>-acting interactions. Functional enrichment of their targets highlighted overrepresentation of photosynthesis and stress-response pathways. Moreover, we constructed regulatory networks linking lncRNAs to quinclorac-resistance–associated genes involved in hormone biosynthesis and signaling, molecular transport, and xenobiotic metabolism. These findings uncover a repertoire of lncRNAs responsive to quinclorac and suggest their roles in mediating herbicide tolerance in tobacco.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111143"},"PeriodicalIF":3.0,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318146","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 : 2025-10-16DOI: 10.1016/j.ygeno.2025.111145
Nana Chen , Xinying Zhong , Hongwei Li , Yaxuan Wang , Linshan Tang , Guiyuan Shi , Delin Xu , Lin Li
Dendrobine is a bioactive sesquiterpene alkaloid from Dendrobium nobile with notable pharmacological properties, yet its sustainable production remains challenging. Here, we focused on an endophytic fungal isolate, Fusarium sp. DN689, from Dendrobium nobile and confirmed its capacity for consistent dendrobine production under liquid fermentation conditions. Whole genome sequencing and mining of DN689 identified 13 terpenoid biosynthetic gene clusters, including genes of the core mevalonate (MVA) pathway as well as downstream tailoring enzymes. Furthermore, quantitative PCR revealed that the expression of four candidate cyclase and oxidase genes was positively correlated with dendrobine accumulation. Among these, a sesquiterpene cyclase encoded by one candidate gene was identified as a key enzyme in the biosynthetic pathway. Collectively, this work provides the first genomic framework for fungal dendrobine biosynthesis, and lays a foundation for future metabolic engineering and sustainable production of this valuable compound.
{"title":"Genomic insights into dendrobine biosynthesis in the endophytic fungus Fusarium sp. DN689","authors":"Nana Chen , Xinying Zhong , Hongwei Li , Yaxuan Wang , Linshan Tang , Guiyuan Shi , Delin Xu , Lin Li","doi":"10.1016/j.ygeno.2025.111145","DOIUrl":"10.1016/j.ygeno.2025.111145","url":null,"abstract":"<div><div>Dendrobine is a bioactive sesquiterpene alkaloid from <em>Dendrobium nobile</em> with notable pharmacological properties, yet its sustainable production remains challenging. Here, we focused on an endophytic fungal isolate, <em>Fusarium</em> sp. DN689, from <em>Dendrobium nobile</em> and confirmed its capacity for consistent dendrobine production under liquid fermentation conditions. Whole genome sequencing and mining of DN689 identified 13 terpenoid biosynthetic gene clusters, including genes of the core mevalonate (MVA) pathway as well as downstream tailoring enzymes. Furthermore, quantitative PCR revealed that the expression of four candidate cyclase and oxidase genes was positively correlated with dendrobine accumulation. Among these, a sesquiterpene cyclase encoded by one candidate gene was identified as a key enzyme in the biosynthetic pathway. Collectively, this work provides the first genomic framework for fungal dendrobine biosynthesis, and lays a foundation for future metabolic engineering and sustainable production of this valuable compound.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111145"},"PeriodicalIF":3.0,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318018","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}
N6-adenosine RNA methylation (m6A) is a key regulator of gene expression during embryogenesis and neurogenesis in mammals and insects. However, its functional relevance remains unknown in lophotrochozoans like the Pacific oyster Crassostrea gigas, despite its association with developmental gene expression.
We treated oyster embryos with STM2457, a METTL3 methyltransferase-inhibitor. m6A-RNA reduction in treated embryos induced morphological alterations and 5-HT immunohistochemistry revealed impaired neuronal development. Transcriptome and proteome analyses indicated that m6A inhibition disturbs transcription and translation. Epitranscriptome sequencing showed that m6A inhibition increased transcript length by exon and intron retention, suggesting m6A-dependent recruitment of splicing factors at intron–exon boundaries.
Together, our results support an essential role for m6A in neural differentiation and development in the oyster by regulating alternative splicing. This study provides the first evidence of a functional role for m6A in lophotrochozoan development, providing new eco-evo-devo insights of epitranscriptomic processes.
{"title":"m6A-RNA epitranscriptomes regulate splicing and neuronal development in the Pacific oyster Crassostrea gigas","authors":"Natacha Clairet , Hélène Auger , Roberto-Carlos Arredondo-Espinoza , Hugo Koechlin , Benoît Bernay , Lukas Manoury , Didier Goux , Guillaume Rivière","doi":"10.1016/j.ygeno.2025.111142","DOIUrl":"10.1016/j.ygeno.2025.111142","url":null,"abstract":"<div><div>N6-adenosine RNA methylation (m<sup>6</sup>A) is a key regulator of gene expression during embryogenesis and neurogenesis in mammals and insects. However, its functional relevance remains unknown in lophotrochozoans like the Pacific oyster <em>Crassostrea gigas</em>, despite its association with developmental gene expression.</div><div>We treated oyster embryos with STM2457, a METTL3 methyltransferase-inhibitor. m<sup>6</sup>A-RNA reduction in treated embryos induced morphological alterations and 5-HT immunohistochemistry revealed impaired neuronal development. Transcriptome and proteome analyses indicated that m<sup>6</sup>A inhibition disturbs transcription and translation. Epitranscriptome sequencing showed that m<sup>6</sup>A inhibition increased transcript length by exon and intron retention, suggesting m<sup>6</sup>A-dependent recruitment of splicing factors at intron–exon boundaries.</div><div>Together, our results support an essential role for m<sup>6</sup>A in neural differentiation and development in the oyster by regulating alternative splicing. This study provides the first evidence of a functional role for m<sup>6</sup>A in lophotrochozoan development, providing new eco-evo-devo insights of epitranscriptomic processes.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111142"},"PeriodicalIF":3.0,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145299598","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 : 2025-10-13DOI: 10.1016/j.ygeno.2025.111141
Dongbin Zheng , Yihui Liu , Changjiu Dai , Hongyu Chen , Chao A , Pengliang Liu , Yongliang Fan , Yiren Gu , Xun Wang , Mingzhou Li , Long Jin
The Tibetan pig, as a typical highland breed, has a higher newborn-to-sow weight ratio than low-altitude breeds, which may be associated with better offspring survival in high-altitude environments. This suggests Tibetan pigs need a healthier physiological state during gestation. Understanding physiological changes during pregnancy is thus crucial for improving their reproductive performance. The ovaries secrete pregnancy-related hormones, while the spleen regulates immunity as a key immune organ. Both are vital for maintaining maternal health, yet their physiological changes during pregnancy in Tibetan pigs remain unclear. This study compared the transcriptome changes of the ovaries and spleens in non-pregnant and pregnant Tibetan pigs. The ovaries showed more pronounced transcriptional changes, with 757 differentially expressed PCGs (466 upregulated, e.g., ISM1, PRKAA2, STAR, CEBPB; 291 downregulated, e.g., BMP15, MOS) and 53 differentially expressed lncRNAs (34 upregulated, 19 downregulated). In the spleen, 229 PCGs were differentially expressed (76 upregulated, e.g., ISM1, PRKAA2, ESR1, CXCL8; 153 downregulated, e.g., NFATC4), along with 14 differentially expressed lncRNAs (5 upregulated, 9 downregulated). Functional analysis revealed enhanced ovarian hormone synthesis and suppressed oocyte activity, alongside reduced splenic inflammation during pregnancy. Notably, both organs showed increased lipid metabolism, and inflammation-related pathways were activated in the ovaries. Key candidate genes and regulatory factors potentially involved in pregnancy-related changes were also predicted. Overall, this study highlights transcriptional shifts in Tibetan pig ovaries and spleens during pregnancy, offering insights into plateau animal reproduction and strategies to improve Tibetan pig fertility.
{"title":"Transcriptional changes in Tibetan pig ovaries and spleen during gestation","authors":"Dongbin Zheng , Yihui Liu , Changjiu Dai , Hongyu Chen , Chao A , Pengliang Liu , Yongliang Fan , Yiren Gu , Xun Wang , Mingzhou Li , Long Jin","doi":"10.1016/j.ygeno.2025.111141","DOIUrl":"10.1016/j.ygeno.2025.111141","url":null,"abstract":"<div><div>The Tibetan pig, as a typical highland breed, has a higher newborn-to-sow weight ratio than low-altitude breeds, which may be associated with better offspring survival in high-altitude environments. This suggests Tibetan pigs need a healthier physiological state during gestation. Understanding physiological changes during pregnancy is thus crucial for improving their reproductive performance. The ovaries secrete pregnancy-related hormones, while the spleen regulates immunity as a key immune organ. Both are vital for maintaining maternal health, yet their physiological changes during pregnancy in Tibetan pigs remain unclear. This study compared the transcriptome changes of the ovaries and spleens in non-pregnant and pregnant Tibetan pigs. The ovaries showed more pronounced transcriptional changes, with 757 differentially expressed PCGs (466 upregulated, e.g., <em>ISM1</em>, <em>PRKAA2</em>, <em>STAR</em>, <em>CEBPB</em>; 291 downregulated, e.g., <em>BMP15</em>, <em>MOS</em>) and 53 differentially expressed lncRNAs (34 upregulated, 19 downregulated). In the spleen, 229 PCGs were differentially expressed (76 upregulated, e.g., <em>ISM1</em>, <em>PRKAA2</em>, <em>ESR1</em>, <em>CXCL8</em>; 153 downregulated, e.g., <em>NFATC4</em>), along with 14 differentially expressed lncRNAs (5 upregulated, 9 downregulated). Functional analysis revealed enhanced ovarian hormone synthesis and suppressed oocyte activity, alongside reduced splenic inflammation during pregnancy. Notably, both organs showed increased lipid metabolism, and inflammation-related pathways were activated in the ovaries. Key candidate genes and regulatory factors potentially involved in pregnancy-related changes were also predicted. Overall, this study highlights transcriptional shifts in Tibetan pig ovaries and spleens during pregnancy, offering insights into plateau animal reproduction and strategies to improve Tibetan pig fertility.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111141"},"PeriodicalIF":3.0,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145299638","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 : 2025-10-11DOI: 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":"2025-10-11","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 : 2025-10-10DOI: 10.1016/j.ygeno.2025.111134
Zhonghao Bai , Wei Chen , Zexi Cai , Goutam Sahana
Calf mortality during the rearing period is a major concern for dairy producers, impacting both profitability and animal welfare. A genome-wide association analysis of young stock survival (YSS) in Jersey cattle using whole-genome sequence variants identified a major QTL on chromosome 10 influencing survival at an early age. Within the QTL region, 27 variants were segregated in Jersey cattle but not in Holstein, suggesting a Jersey breed-specific locus associated with calf mortality. A strong colocalization signals were observed in lymph nodes between eQTL signals and five candidate variants. Gene-based association analysis identified several candidate genes. Comparison with Bos taurus assemblies revealed a 2 Mb gap region (BTA10:22499414–24,826,764), within which a 1 Mb segment remained unaligned to the Jersey-specific assembly, resulting in the absence of four lncRNA genes. Candidate genetic variants can be utilized in genetic selection to lower calf mortality to improve herd health in Jersey cattle.
{"title":"Genomic insights into young stock survival in Danish Jersey cattle: A breed-specific QTL on chromosome 10 and its regulatory potential","authors":"Zhonghao Bai , Wei Chen , Zexi Cai , Goutam Sahana","doi":"10.1016/j.ygeno.2025.111134","DOIUrl":"10.1016/j.ygeno.2025.111134","url":null,"abstract":"<div><div>Calf mortality during the rearing period is a major concern for dairy producers, impacting both profitability and animal welfare. A genome-wide association analysis of young stock survival (YSS) in Jersey cattle using whole-genome sequence variants identified a major QTL on chromosome 10 influencing survival at an early age. Within the QTL region, 27 variants were segregated in Jersey cattle but not in Holstein, suggesting a Jersey breed-specific locus associated with calf mortality. A strong colocalization signals were observed in lymph nodes between eQTL signals and five candidate variants. Gene-based association analysis identified several candidate genes. Comparison with <em>Bos taurus</em> assemblies revealed a 2 Mb gap region (BTA10:22499414–24,826,764), within which a 1 Mb segment remained unaligned to the Jersey-specific assembly, resulting in the absence of four lncRNA genes. Candidate genetic variants can be utilized in genetic selection to lower calf mortality to improve herd health in Jersey cattle.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111134"},"PeriodicalIF":3.0,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145279660","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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