Pub Date : 2026-01-15DOI: 10.1016/j.gep.2026.119407
Rui Guo, Yifeng Gu
To investigate the immunological function of TRIM13 in zebrafish (Danio rerio), we cloned the zebrafish TRIM13 homolog (DrTRIM13) and obtained its complete coding sequence (CDS) and3′-untranslated region (3′-UTR) through sequencing and sequence assembly. Reverse transcription PCR was used to examine the tissue distribution of DrTRIM13. Additionally, fluorescence microscopy was performed to visualize protein localization. Our results demonstrate that the cloned DrTRIM13 cDNA consists of a 276-bp 3′-UTR and a 1215-bp open reading frame (ORF), encoding a 404-amino acid protein. Phylogenetic analysis indicated that DrTRIM13 shares the highest homology and closest evolutionary relationship with carp (Cyprinus carpio). Subcellular localization in HeLa cells confirmed predominant cytoplasmic distribution. These findings provide a theoretical framework for mitigating viral diseases in aquaculture.
{"title":"cDNA cloning, expression analysis, and subcellular localization of TRIM13 gene in zebrafish","authors":"Rui Guo, Yifeng Gu","doi":"10.1016/j.gep.2026.119407","DOIUrl":"10.1016/j.gep.2026.119407","url":null,"abstract":"<div><div>To investigate the immunological function of TRIM13 in zebrafish (<em>Danio rerio</em>), we cloned the zebrafish TRIM13 homolog (<em>Dr</em>TRIM13) and obtained its complete coding sequence (CDS) and3′-untranslated region (3′-UTR) through sequencing and sequence assembly. Reverse transcription PCR was used to examine the tissue distribution of <em>Dr</em>TRIM13. Additionally, fluorescence microscopy was performed to visualize protein localization. Our results demonstrate that the cloned <em>Dr</em>TRIM13 cDNA consists of a 276-bp 3′-UTR and a 1215-bp open reading frame (ORF), encoding a 404-amino acid protein. Phylogenetic analysis indicated that <em>Dr</em>TRIM13 shares the highest homology and closest evolutionary relationship with carp (<em>Cyprinus carpio</em>). Subcellular localization in HeLa cells confirmed predominant cytoplasmic distribution. These findings provide a theoretical framework for mitigating viral diseases in aquaculture.</div></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"57 ","pages":"Article 119407"},"PeriodicalIF":1.1,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145994549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-09DOI: 10.1016/j.gep.2026.119406
Vaishnavi , Prekshi Garg , Prachi Srivastava
Glaucoma is a group of optic neuropathic conditions in which the progressive degeneration of retinal ganglion cells (RGC) occurs, ultimately leading to irreversible vision loss. Despite our understanding of pathophysiology, potential biomarkers and early detection are still very limited. Hence, there is an urgent need to find the potent molecular biomarker of Glaucoma so that early diagnosis and personalised glaucoma treatment can be possible. In this study, we performed comparative transcriptomic analyses to discern differentially expressed genes (DEGs) linked with Glaucoma. The aim is to find a robust candidate biomarker to facilitate early diagnosis and characterisation of Glaucoma. Advanced feature selections are performed by employing DEG identification and machine learning algorithms, enabling the selection of highly prognostic relevance genes. Furthermore, Artificial neural network (ANN) models were developed to recognise the complicated nonlinear patterns within high-dimensional data and identify the most promising genes having a potent role in glaucoma progression and risk prediction. After the analysis, NPM1P51 turned out to be the most significant contributor after performing multiple analyses, suggesting it to be a strong pseudogene biomarker. Further, CACNG7 showed moderate results in Garson and Olden plots, but better in Generalised weight plots. It encodes a subunit of the voltage-gated calcium channel complex, aligning with already established roles in the mechanisms of neurodegeneration in glaucoma, particularly in apoptosis of retinal ganglion cells through calcium dysregulation. These results provide a foundation for further experimental validations and therapeutic interventions.
{"title":"Exploring NPM1P51 as a key biomarker for glaucoma by integrating differential gene expression analysis and artificial neural network models","authors":"Vaishnavi , Prekshi Garg , Prachi Srivastava","doi":"10.1016/j.gep.2026.119406","DOIUrl":"10.1016/j.gep.2026.119406","url":null,"abstract":"<div><div>Glaucoma is a group of optic neuropathic conditions in which the progressive degeneration of retinal ganglion cells (RGC) occurs, ultimately leading to irreversible vision loss. Despite our understanding of pathophysiology, potential biomarkers and early detection are still very limited. Hence, there is an urgent need to find the potent molecular biomarker of Glaucoma so that early diagnosis and personalised glaucoma treatment can be possible. In this study, we performed comparative transcriptomic analyses to discern differentially expressed genes (DEGs) linked with Glaucoma. The aim is to find a robust candidate biomarker to facilitate early diagnosis and characterisation of Glaucoma. Advanced feature selections are performed by employing DEG identification and machine learning algorithms, enabling the selection of highly prognostic relevance genes. Furthermore, Artificial neural network (ANN) models were developed to recognise the complicated nonlinear patterns within high-dimensional data and identify the most promising genes having a potent role in glaucoma progression and risk prediction. After the analysis, NPM1P51 turned out to be the most significant contributor after performing multiple analyses, suggesting it to be a strong pseudogene biomarker. Further, CACNG7 showed moderate results in Garson and Olden plots, but better in Generalised weight plots. It encodes a subunit of the voltage-gated calcium channel complex, aligning with already established roles in the mechanisms of neurodegeneration in glaucoma, particularly in apoptosis of retinal ganglion cells through calcium dysregulation. These results provide a foundation for further experimental validations and therapeutic interventions.</div></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"57 ","pages":"Article 119406"},"PeriodicalIF":1.1,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145954117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-08-06DOI: 10.1016/j.gep.2025.119400
Li Gao, Yosuke Tona, Koichi Omori
CWC27 is a member of cyclophilin-type peptidyl-prolyl cis-trans isomerase family and takes part in the pre-mRNA splicing. The mutation of its gene, Cwc27, has been verified to be related to cancer, craniofacial and skeletal anomalies, retinal degeneration, and hearing loss. However, expression pattern of Cwc27 in the development of inner ear has not been fully understood. In this study, we studied the spatiotemporal expression of Cwc27 mRNA and CWC27 protein in the mouse inner ear from embryonic day (E) 9 to postnatal 0-day by in situ hybridization and immunohistochemistry staining, respectively. The expression level of Cwc27 was analyzed by quantitative reverse transcription polymerase chain reaction. We found that Cwc27 was expressed early in the otocyst at E9. At E13, Cwc27 was expressed in the cochlear duct, spiral ganglion area, and vestibular organ. The expression level of Cwc27 mRNA reached its maximum level at E13. From E14 onward, Cwc27 was expressed in the sensory epithelium in the cochlear duct and spiral ganglion area. From E18 onward, the distribution of CWC27 protein became more limited to the organ of Corti. Our study revealed Cwc27 might play an important part on promoting the development of developing inner ear.
{"title":"Spatiotemporal expression of CWC27 spliceosome-associated protein (CWC27) in the developing mouse inner ear.","authors":"Li Gao, Yosuke Tona, Koichi Omori","doi":"10.1016/j.gep.2025.119400","DOIUrl":"10.1016/j.gep.2025.119400","url":null,"abstract":"<p><p>CWC27 is a member of cyclophilin-type peptidyl-prolyl cis-trans isomerase family and takes part in the pre-mRNA splicing. The mutation of its gene, Cwc27, has been verified to be related to cancer, craniofacial and skeletal anomalies, retinal degeneration, and hearing loss. However, expression pattern of Cwc27 in the development of inner ear has not been fully understood. In this study, we studied the spatiotemporal expression of Cwc27 mRNA and CWC27 protein in the mouse inner ear from embryonic day (E) 9 to postnatal 0-day by in situ hybridization and immunohistochemistry staining, respectively. The expression level of Cwc27 was analyzed by quantitative reverse transcription polymerase chain reaction. We found that Cwc27 was expressed early in the otocyst at E9. At E13, Cwc27 was expressed in the cochlear duct, spiral ganglion area, and vestibular organ. The expression level of Cwc27 mRNA reached its maximum level at E13. From E14 onward, Cwc27 was expressed in the sensory epithelium in the cochlear duct and spiral ganglion area. From E18 onward, the distribution of CWC27 protein became more limited to the organ of Corti. Our study revealed Cwc27 might play an important part on promoting the development of developing inner ear.</p>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":" ","pages":"119400"},"PeriodicalIF":1.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144800997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01DOI: 10.1016/j.gep.2025.119399
Peshraw Ahmed Abdalla , Mohammed Y. Shakor , Aso Khaleel Ameen , Diyari A. Hassan
This correspondence addresses several inconsistencies identified in the article “Kurdish Handwritten Character Recognition Using Deep Learning Techniques,” published in Gene Expression Patterns. We commend the authors for their contribution to Kurdish handwriting recognition using deep learning methods. However, critical discrepancies are evident in the model architecture description, class labeling, and model summary. This letter outlines these concerns in detail and suggests revisions to enhance transparency and reproducibility.
{"title":"Critical review of the model description in ‘Kurdish handwritten character recognition using deep learning techniques’","authors":"Peshraw Ahmed Abdalla , Mohammed Y. Shakor , Aso Khaleel Ameen , Diyari A. Hassan","doi":"10.1016/j.gep.2025.119399","DOIUrl":"10.1016/j.gep.2025.119399","url":null,"abstract":"<div><div><span>This correspondence addresses several inconsistencies identified in the article “Kurdish Handwritten Character Recognition<span> Using Deep Learning Techniques,” published in </span></span><em>Gene Expression Patterns</em>. We commend the authors for their contribution to Kurdish handwriting recognition using deep learning methods. However, critical discrepancies are evident in the model architecture description, class labeling, and model summary. This letter outlines these concerns in detail and suggests revisions to enhance transparency and reproducibility.</div></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"56 ","pages":"Article 119399"},"PeriodicalIF":1.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-07DOI: 10.1016/j.gep.2025.119404
John R. Wells , Maria B. Padua , Stephanie M. Ware
The orphan G protein coupled receptor GPR101, which is implicated in X-linked acrogigantism (X-LAG), a rare pituitary disorder characterized by rapid growth a few years after birth, has received significant attention for its expression pattern in adult vertebrate tissues. However, the characterization of GPR101 expression during early embryonic development is poorly characterized. In this study, we investigated the spatiotemporal expression patterns of Gpr101 during early embryonic mouse development (E7.5-E15.5) using a global Gpr101 knock-in mouse model with an inserted LacZ reporter, Gpr101tm1b(KOMP)Mbp. Similar to previously published studies using adult tissues, we found that LacZ reporter expression was largely restricted to regions of the central nervous system. Expression was not detected until E10.5 in a region near the telencephalic vesicle. In contrast to what has been reported in adult tissues, Gpr101 expression was absent in the hypothalamus and pituitary gland during the developmental timepoints assessed. These novel observations provide a more comprehensive characterization of GPR101's expression and may offer insights into its role in growth and development across species.
{"title":"Gpr101 expression during early stages of murine development","authors":"John R. Wells , Maria B. Padua , Stephanie M. Ware","doi":"10.1016/j.gep.2025.119404","DOIUrl":"10.1016/j.gep.2025.119404","url":null,"abstract":"<div><div>The orphan G protein coupled receptor GPR101, which is implicated in X-linked acrogigantism (X-LAG), a rare pituitary disorder characterized by rapid growth a few years after birth, has received significant attention for its expression pattern in adult vertebrate tissues. However, the characterization of <em>GPR101</em> expression during early embryonic development is poorly characterized. In this study, we investigated the spatiotemporal expression patterns of <em>Gpr101</em> during early embryonic mouse development (E7.5-E15.5) using a global <em>Gpr101</em> knock-in mouse model with an inserted LacZ reporter, <em>Gpr101</em><sup><em>tm1b(KOMP)Mbp</em></sup>. Similar to previously published studies using adult tissues, we found that LacZ reporter expression was largely restricted to regions of the central nervous system. Expression was not detected until E10.5 in a region near the telencephalic vesicle. In contrast to what has been reported in adult tissues, <em>Gpr101</em> expression was absent in the hypothalamus and pituitary gland during the developmental timepoints assessed. These novel observations provide a more comprehensive characterization of GPR101's expression and may offer insights into its role in growth and development across species.</div></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"56 ","pages":"Article 119404"},"PeriodicalIF":1.1,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145477188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The regeneration of amputated body parts depends on the activation and inactivation of signaling pathways that regulate various cellular processes, such as proliferation, migration, differentiation, apoptosis, etc. In the case of annelids, gene expression of several members of the canonical Wnt pathway has been detected during regeneration of the primary body axis and it has been determined that alteration of its activity results in deficiencies in blastema and central nervous system formation, as well as in body segmentation. However, most studies have been carried out at very specific times of regeneration, in a few species and mainly in anterior regeneration. In this work, we analyzed the expression of β-catenin throughout anterior and posterior regeneration in Lumbriculus variegatus, using it as a marker for the potential activation of the pathway. We also carried out pharmacological inhibition and overactivation assays of the pathway during blastema formation and growth. We determined that the expression of β-catenin changes in anterior and posterior regeneration in a highly dynamic manner, both in its intensity and in the tissue in which it is expressed as the process progresses. We also described its potential role in chaeta regeneration. In addition, we showed that inhibition and overactivation of the pathway negatively affect blastema formation and do so differently in the anterior and posterior sections. These findings suggest that the canonical Wnt pathway participates in several cellular processes within annelid regeneration and that its activity must be finely regulated to allow the transition between one process and another.
{"title":"Wnt/β-catenin signaling pathway regulates the regeneration of the annelid Lumbriculus variegatus","authors":"Aldo Arturo Tellez-Garcia, Fausto Arellano-Carbajal","doi":"10.1016/j.gep.2025.119403","DOIUrl":"10.1016/j.gep.2025.119403","url":null,"abstract":"<div><div>The regeneration of amputated body parts depends on the activation and inactivation of signaling pathways that regulate various cellular processes, such as proliferation, migration, differentiation, apoptosis, etc. In the case of annelids, gene expression of several members of the canonical Wnt pathway has been detected during regeneration of the primary body axis and it has been determined that alteration of its activity results in deficiencies in blastema and central nervous system formation, as well as in body segmentation. However, most studies have been carried out at very specific times of regeneration, in a few species and mainly in anterior regeneration. In this work, we analyzed the expression of <em>β-catenin</em> throughout anterior and posterior regeneration in <em>Lumbriculus variegatus</em>, using it as a marker for the potential activation of the pathway. We also carried out pharmacological inhibition and overactivation assays of the pathway during blastema formation and growth. We determined that the expression of <em>β-catenin</em> changes in anterior and posterior regeneration in a highly dynamic manner, both in its intensity and in the tissue in which it is expressed as the process progresses. We also described its potential role in chaeta regeneration. In addition, we showed that inhibition and overactivation of the pathway negatively affect blastema formation and do so differently in the anterior and posterior sections. These findings suggest that the canonical Wnt pathway participates in several cellular processes within annelid regeneration and that its activity must be finely regulated to allow the transition between one process and another.</div></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"56 ","pages":"Article 119403"},"PeriodicalIF":1.1,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145356830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-14DOI: 10.1016/j.gep.2025.119402
Jennifer L. Carleton , Dewmini Dematagoda , Meg A. Schuurman , Jessica A. Willson , Bonnie Wu , Kyra Ball , Timothy F. Plageman Jr. , Darren Bridgewater , Thomas A. Drysdale
Shroom3 is an actin binding protein integral to apical constriction and apical-basal elongation during mammalian morphogenesis. Shroom3 function has been demonstrated in the development of the heart, neural tube, gut tube, eye, thyroid bud, and kidneys, with mutations linked to human congenital defects including anencephaly, spina bifida, cleft lip and palate, and ventricular septal defects. Genome-wide association studies implicate Shroom3 in human conditions such as chronic kidney disease and heterotaxy. While this suggests that Shroom3 expression continues postnatally, the extent of adult expression patterns remain unexplored.
To address this, we first harvested organs from adult mice heterozygous for a LacZ reporter inserted into the Shroom3 allele (Shroom3+/Gt). Organs were stained in wholemount with X-gal and cleared in glycerol to identify which tissues expressed Shroom3 and to localize the expression within the tissue. Wildtype organs were then harvested and fluorescently stained to localize Shroom3 protein in tissue sub-structures.
From this, we have characterized previously unknown Shroom3 expression in many adult organs including the bladder and reproductive systems, as well as established postnatal Shroom3 expression in organs thought to only have developmental expression including the eye and whisker pad. Our results also demonstrate organs which did not show Shroom3 expression, including the liver and pancreas. This data suggests that Shroom3 has roles in a wider number of tissues than previously thought and provides a foundation for future hypotheses regarding the biological and pathological significance of Shroom3.
{"title":"Mapping Shroom3 expression across the adult mouse","authors":"Jennifer L. Carleton , Dewmini Dematagoda , Meg A. Schuurman , Jessica A. Willson , Bonnie Wu , Kyra Ball , Timothy F. Plageman Jr. , Darren Bridgewater , Thomas A. Drysdale","doi":"10.1016/j.gep.2025.119402","DOIUrl":"10.1016/j.gep.2025.119402","url":null,"abstract":"<div><div>Shroom3 is an actin binding protein integral to apical constriction and apical-basal elongation during mammalian morphogenesis. Shroom3 function has been demonstrated in the development of the heart, neural tube, gut tube, eye, thyroid bud, and kidneys, with mutations linked to human congenital defects including anencephaly, spina bifida, cleft lip and palate, and ventricular septal defects. Genome-wide association studies implicate Shroom3 in human conditions such as chronic kidney disease and heterotaxy. While this suggests that Shroom3 expression continues postnatally, the extent of adult expression patterns remain unexplored.</div><div>To address this, we first harvested organs from adult mice heterozygous for a LacZ reporter inserted into the Shroom3 allele (<em>Shroom3</em><sup><em>+/Gt</em></sup>). Organs were stained in wholemount with X-gal and cleared in glycerol to identify which tissues expressed Shroom3 and to localize the expression within the tissue. Wildtype organs were then harvested and fluorescently stained to localize Shroom3 protein in tissue sub-structures.</div><div>From this, we have characterized previously unknown Shroom3 expression in many adult organs including the bladder and reproductive systems, as well as established postnatal Shroom3 expression in organs thought to only have developmental expression including the eye and whisker pad. Our results also demonstrate organs which did not show Shroom3 expression, including the liver and pancreas. This data suggests that Shroom3 has roles in a wider number of tissues than previously thought and provides a foundation for future hypotheses regarding the biological and pathological significance of Shroom3.</div></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"56 ","pages":"Article 119402"},"PeriodicalIF":1.1,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145309921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The SH2B family, which includes SH2B1, SH2B2, and SH2B3, consists of adaptor proteins that possess conserved Src homology 2 (SH2) and pleckstrin homology (PH) domains, playing essential roles as signaling mediators. However, the gene expression patterns of this family during embryonic development are still mostly unclear. In this study, we first investigated the evolutionary conservation of SH2B across multiple species using phylogenetic analysis, which revealed high sequence homology between zebrafish Sh2b and its orthologs in other vertebrates. Subsequently, we examined the expression patterns of sh2b during zebrafish embryogenesis through whole mount in situ hybridization. The findings revealed that all sh2b genes are expressed during the early developmental stages of zebrafish embryos, with a significant concentration in the brain, eyes, and spinal cord. Additionally, sh2b1 was found to be expressed in the lateral line neuromast (lln) support cells. In conclusion, our results suggest that the sh2b family is mainly localized in the brain and eyes, with sh2b1 specifically expressed in the lln support cells. This study offers important insights into the role of the sh2b family in zebrafish embryonic development.
{"title":"Expression analysis of the adaptor proteins Sh2b family during zebrafish embryonic development","authors":"Yuanyuan Peng , Qiu Jiang , liwen Zhou , Yuanqi Jia , Chang Liu","doi":"10.1016/j.gep.2025.119401","DOIUrl":"10.1016/j.gep.2025.119401","url":null,"abstract":"<div><div>The SH2B family, which includes SH2B1, SH2B2, and SH2B3, consists of adaptor proteins that possess conserved Src homology 2 (SH2) and pleckstrin homology (PH) domains, playing essential roles as signaling mediators. However, the gene expression patterns of this family during embryonic development are still mostly unclear. In this study, we first investigated the evolutionary conservation of SH2B across multiple species using phylogenetic analysis, which revealed high sequence homology between zebrafish Sh2b and its orthologs in other vertebrates. Subsequently, we examined the expression patterns of <em>sh2b</em> during zebrafish embryogenesis through whole mount <em>in situ</em> hybridization. The findings revealed that all <em>sh2b</em> genes are expressed during the early developmental stages of zebrafish embryos, with a significant concentration in the brain, eyes, and spinal cord. Additionally, <em>sh2b1</em> was found to be expressed in the lateral line neuromast (lln) support cells. In conclusion, our results suggest that the <em>sh2b</em> family is mainly localized in the brain and eyes, with <em>sh2b1</em> specifically expressed in the lln support cells. This study offers important insights into the role of the <em>sh2b</em> family in zebrafish embryonic development.</div></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"56 ","pages":"Article 119401"},"PeriodicalIF":1.1,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145014455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-26DOI: 10.1016/j.gep.2025.119398
Adrianna Matos-Nieves , Sarah C. Greskovich , Talita Z. Choudhury , Sathiyanarayanan Manivannan , Yukie Ueyama , Anupama S. Rao , Emily M. Cameron , Vidu Garg
Axon guidance signaling pathways, including the Eph/ephrin, Semaphorin, and Slit/Robo pathways, have been found to play crucial roles in cardiac development. Netrin signaling is another well-studied signaling pathway important for axon guidance, but its role in the developing heart has not been investigated. Here, we describe the novel expression pattern of Netrin-1 in the developing murine heart. Transcriptomic analysis of embryonic mouse hearts shows dynamic Netrin-1 expression from E8.5 through E14.5, where Netrin-1 expression preferentially co-localizes with developing trabecular cardiomyocytes. We further demonstrate the spatiotemporal expression pattern of Netrin-1 using a combination of RNA in situ hybridization and Netrin-1Bgeo/+ reporter mice. Netrin-1 is expressed in the developing cardiomyocytes with the highest degree of expression within the left ventricular trabecular myocardium, which has not been previously recognized. Additionally, Netrin-1 expression is observed at lower levels in the cardiomyocytes of the right ventricle and atria. This expression pattern supports a role for Netrin signaling in the developing murine myocardium requiring further functional characterization.
{"title":"Expression of Netrin-1 in the developing mouse heart","authors":"Adrianna Matos-Nieves , Sarah C. Greskovich , Talita Z. Choudhury , Sathiyanarayanan Manivannan , Yukie Ueyama , Anupama S. Rao , Emily M. Cameron , Vidu Garg","doi":"10.1016/j.gep.2025.119398","DOIUrl":"10.1016/j.gep.2025.119398","url":null,"abstract":"<div><div>Axon guidance signaling pathways, including the Eph/ephrin, Semaphorin, and Slit/Robo pathways, have been found to play crucial roles in cardiac development. Netrin signaling is another well-studied signaling pathway important for axon guidance, but its role in the developing heart has not been investigated. Here, we describe the novel expression pattern of <em>Netrin-1</em> in the developing murine heart. Transcriptomic analysis of embryonic mouse hearts shows dynamic <em>Netrin-1</em> expression from E8.5 through E14.5, where <em>Netrin-1</em> expression preferentially co-localizes with developing trabecular cardiomyocytes. We further demonstrate the spatiotemporal expression pattern of <em>Netrin-1</em> using a combination of RNA <em>in situ</em> hybridization and <em>Netrin-1</em><sup><em>Bgeo/+</em></sup> reporter mice. <em>Netrin-1</em> is expressed in the developing cardiomyocytes with the highest degree of expression within the left ventricular trabecular myocardium, which has not been previously recognized. Additionally, <em>Netrin-1</em> expression is observed at lower levels in the cardiomyocytes of the right ventricle and atria. This expression pattern supports a role for Netrin signaling in the developing murine myocardium requiring further functional characterization.</div></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"56 ","pages":"Article 119398"},"PeriodicalIF":1.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-13DOI: 10.1016/j.gep.2025.119396
Cristian Nahuel Nuñez Pedrozo , Francisco Raúl Borzone , Agustina Varela , Paola Locatelli , Daniela Fernanda Olea , Alberto José Crottogini , Gustavo Ariel Giunta , Luis Alberto Cuniberti
Background
Recently, transcriptomic analysis has been key in identifying therapeutic targets in cardiovascular regeneration. The postnatal loss of cardiomyocyte proliferative capacity has been linked to the transition from glycolysis to fatty acid oxidation in rodent models of acute myocardial infarction (AMI). However, the transcriptomic profile of these processes in large mammals more similar to humans is still unknown. The aim of this study was to examine the transcriptomic profile, from the proliferative fetal stage to the non-regenerative infarcted adult stage, in an ovine AMI model.
Methods
Samples consisted of fetal sheep hearts sequenced in our laboratory and adult sheep hearts (healthy, infarct, and infarct border) from the Gene Expression Omnibus repository (GSE164245).
Results
Fetal tissue showed changes in epigenetic regulation and a predominance of glycolytic metabolism, whereas in the adult infarct core and border zones, there was a partial activation of glycolysis and a reduction in the expression of genes associated with β-oxidation of fatty acids. Myocardial infarction in adult sheep triggers metabolic changes that partially mimic fetal regenerative processes.
Conclusions
These findings will allow for a more precise understanding of the mechanisms underlying cardiac regeneration and facilitate the translation of regenerative therapies for clinical application in humans.
{"title":"Molecular basis and key biological processes for myocardial regeneration: Transcriptomic analysis of acute myocardial infarction in a translational ovine model","authors":"Cristian Nahuel Nuñez Pedrozo , Francisco Raúl Borzone , Agustina Varela , Paola Locatelli , Daniela Fernanda Olea , Alberto José Crottogini , Gustavo Ariel Giunta , Luis Alberto Cuniberti","doi":"10.1016/j.gep.2025.119396","DOIUrl":"10.1016/j.gep.2025.119396","url":null,"abstract":"<div><h3>Background</h3><div>Recently, transcriptomic analysis has been key in identifying therapeutic targets in cardiovascular regeneration. The postnatal loss of cardiomyocyte proliferative capacity has been linked to the transition from glycolysis to fatty acid oxidation in rodent models of acute myocardial infarction (AMI). However, the transcriptomic profile of these processes in large mammals more similar to humans is still unknown. The aim of this study was to examine the transcriptomic profile, from the proliferative fetal stage to the non-regenerative infarcted adult stage, in an ovine AMI model.</div></div><div><h3>Methods</h3><div>Samples consisted of fetal sheep hearts sequenced in our laboratory and adult sheep hearts (healthy, infarct, and infarct border) from the Gene Expression Omnibus repository (GSE164245).</div></div><div><h3>Results</h3><div>Fetal tissue showed changes in epigenetic regulation and a predominance of glycolytic metabolism, whereas in the adult infarct core and border zones, there was a partial activation of glycolysis and a reduction in the expression of genes associated with β-oxidation of fatty acids. Myocardial infarction in adult sheep triggers metabolic changes that partially mimic fetal regenerative processes.</div></div><div><h3>Conclusions</h3><div>These findings will allow for a more precise understanding of the mechanisms underlying cardiac regeneration and facilitate the translation of regenerative therapies for clinical application in humans.</div></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"56 ","pages":"Article 119396"},"PeriodicalIF":1.0,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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