Pub Date : 2025-12-01Epub Date: 2025-10-13DOI: 10.1016/j.genrep.2025.102355
Hassan Ghayas , Uroosa Ejaz , Ayaz Taj , Sabiha Yousuf , Muhammad Sohail
Thermophilic microorganisms produce heat-stable metabolites with significant importance in industrial applications. In this study, we present the whole genome sequence of a thermophilic bacterium, Brevibacillus borstelensis UE10, isolated from a crocodile pond in Manghopir, Pakistan. In silico functional annotation and comparative genomic analyses provided valuable insights into the biosynthetic capabilities and metabolic potential of this strain. The draft genome of UE10 was assembled into 132 contigs with a total size of 5,322,029 bp and a GC content of 52 %. The genome contained 5080 coding sequences (CDSs), 116 tRNAs, and 4 rRNAs. Whole genome and 16S rRNA gene sequence comparisons confirmed the identification of the strain as B. borstelensis. Furthermore, seven putative biosynthetic gene clusters (BGCs) involved in the production of potentially antimicrobial and metal-chelating agents were identified. In addition to other metabolic pathways, the presence of a 13-gene xenobiotic degradation pathway, including benzoate degradation, demonstrates the strain's strong potential for bioremediation. Overall, in silico genomic evidence highlights the potential of B. borstelensis UE10 in biotechnological applications and environmental remediation.
{"title":"In silico exploration of the metabolic and biosynthetic potential of Brevibacillus borstelensis UE10 through whole genome analysis","authors":"Hassan Ghayas , Uroosa Ejaz , Ayaz Taj , Sabiha Yousuf , Muhammad Sohail","doi":"10.1016/j.genrep.2025.102355","DOIUrl":"10.1016/j.genrep.2025.102355","url":null,"abstract":"<div><div>Thermophilic microorganisms produce heat-stable metabolites with significant importance in industrial applications. In this study, we present the whole genome sequence of a thermophilic bacterium, <em>Brevibacillus borstelensis</em> UE10, isolated from a crocodile pond in Manghopir, Pakistan. In silico functional annotation and comparative genomic analyses provided valuable insights into the biosynthetic capabilities and metabolic potential of this strain. The draft genome of UE10 was assembled into 132 contigs with a total size of 5,322,029 bp and a GC content of 52 %. The genome contained 5080 coding sequences (CDSs), 116 tRNAs, and 4 rRNAs. Whole genome and 16S rRNA gene sequence comparisons confirmed the identification of the strain as <em>B. borstelensis</em>. Furthermore, seven putative biosynthetic gene clusters (BGCs) involved in the production of potentially antimicrobial and metal-chelating agents were identified. In addition to other metabolic pathways, the presence of a 13-gene xenobiotic degradation pathway, including benzoate degradation, demonstrates the strain's strong potential for bioremediation. Overall, in silico genomic evidence highlights the potential of <em>B. borstelensis</em> UE10 in biotechnological applications and environmental remediation.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102355"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145324273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-08-12DOI: 10.1016/j.genrep.2025.102320
Osama Saad Al Shaer , Eman Ramadan Abd El Gwad , Dalia Mohamed Abd E.L. Hassib , Omar Khaled Naser , Walaa Afifi Nasr Afifi , Amira Osama Abd El-Ghaffar
Background
Recurrent pregnancy loss (RPL) remains a significant clinical and emotional challenge. Despite advances in reproductive medicine, the underlying causes of RPL are sometimes elusive, with genetic factors now increasingly recognized as important contributors. Among these, the single-nucleotide polymorphism (SNP) rs1800629 in the tumor necrosis factor-alpha (TNF-α) gene has emerged as a potential factor influencing susceptibility to RPL.
Aim
This case-control study intended to examine the association of TNF-α − 308 G > A SNP with RPL in Benha University Hospital, Egypt.
Subjects & methods
A total of 190 participants (90 women with RPL and 100 healthy controls) were involved. Genotyping of the TNF-α − 308 G > A SNP was performed using the restriction fragment length polymorphism-polymerase chain reaction (PCR-RFLP) technique with the NcoI restriction endonuclease.
Results
The frequency of GA and AA genotypes were considerably higher in the RPL females compared to controls, with the AA genotype conferring the highest risk (OR = 3.75, 95 % CI: 1.17–12.05, p = 0.027). The dominant model (GA + AA) also showed a strong association with RPL (OR = 2.06, 95 % CI: 1.35–3.12, p = 0.001). The A allele was identified as a significant risk factor (OR = 2.01, 95 % CI: 1.39–2.90, p < 0.001).
Conclusion
The TNF-α − 308 G > A polymorphism appears to be linked to increased susceptibility to RPL. Larger, multi-ethnic studies are required to further confirm these outcomes and to clarify the genetic contribution to RPL.
背景：复发性妊娠丢失（RPL）仍然是一个重大的临床和情感挑战。尽管生殖医学取得了进步，但RPL的根本原因有时是难以捉摸的，遗传因素现在越来越被认为是重要的因素。其中，肿瘤坏死因子-α (TNF-α)基因的单核苷酸多态性（SNP） rs1800629被认为是影响RPL易感性的潜在因素。目的本病例对照研究旨在探讨TNF-α - 308 G >；埃及Benha大学医院的RPL SNP。科目,方法共纳入190名受试者（90名RPL女性和100名健康对照）。TNF-α - 308 G >的基因分型采用限制性片段长度多态性-聚合酶链反应（PCR-RFLP）技术与NcoI限制性内切酶进行SNP检测。结果RPL女性中GA和AA基因型的发生率明显高于对照组，其中AA基因型的风险最高（OR = 3.75, 95% CI: 1.17-12.05, p = 0.027）。优势模型（GA + AA）也与RPL有很强的相关性（OR = 2.06, 95% CI: 1.35 ~ 3.12, p = 0.001）。A等位基因被确定为显著危险因素(OR = 2.01, 95% CI: 1.39-2.90, p <；0.001)。结论TNF-α - 308 G >；多态性似乎与对RPL的易感性增加有关。需要更大的、多种族的研究来进一步证实这些结果，并澄清基因对RPL的影响。
{"title":"A study of the role of TNFα-308 (G>A) gene polymorphism in recurrent pregnancy loss in random sample from Benha University Hospital","authors":"Osama Saad Al Shaer , Eman Ramadan Abd El Gwad , Dalia Mohamed Abd E.L. Hassib , Omar Khaled Naser , Walaa Afifi Nasr Afifi , Amira Osama Abd El-Ghaffar","doi":"10.1016/j.genrep.2025.102320","DOIUrl":"10.1016/j.genrep.2025.102320","url":null,"abstract":"<div><h3>Background</h3><div>Recurrent pregnancy loss (RPL) remains a significant clinical and emotional challenge. Despite advances in reproductive medicine, the underlying causes of RPL are sometimes elusive, with genetic factors now increasingly recognized as important contributors. Among these, the single-nucleotide polymorphism (SNP) rs1800629 in the tumor necrosis factor-alpha (TNF-α) gene has emerged as a potential factor influencing susceptibility to RPL.</div></div><div><h3>Aim</h3><div>This case-control study intended to examine the association of <em>TNF-α</em> − 308 G > A SNP with RPL in Benha University Hospital, Egypt.</div></div><div><h3>Subjects & methods</h3><div>A total of 190 participants (90 women with RPL and 100 healthy controls) were involved. Genotyping of the <em>TNF-α</em> − 308 G > A SNP was performed using the restriction fragment length polymorphism-polymerase chain reaction (PCR-RFLP) technique with the <em>Nco</em>I restriction endonuclease.</div></div><div><h3>Results</h3><div>The frequency of GA and AA genotypes were considerably higher in the RPL females compared to controls, with the AA genotype conferring the highest risk (OR = 3.75, 95 % CI: 1.17–12.05, <em>p</em> = 0.027). The dominant model (GA + AA) also showed a strong association with RPL (OR = 2.06, 95 % CI: 1.35–3.12, <em>p</em> = 0.001). The A allele was identified as a significant risk factor (OR = 2.01, 95 % CI: 1.39–2.90, <em>p</em> < 0.001).</div></div><div><h3>Conclusion</h3><div>The <em>TNF-α</em> − 308 G > A polymorphism appears to be linked to increased susceptibility to RPL. Larger, multi-ethnic studies are required to further confirm these outcomes and to clarify the genetic contribution to RPL.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102320"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144841002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-09-18DOI: 10.1016/j.genrep.2025.102339
S. Hari Krishna Kumar , Ragothaman Prathiviraj , Muregesan Sobanaa , George Seghal Kiran , Joseph Selvin
Antimicrobial-resistant pathogens are poorly understood and pose emerging threats to coral reef ecosystems. Coral-associated microbial diversity is crucial for reef resilience; however, there is a limited understanding of opportunistic pathogens from Indian reefs. Here, we report the identification of Serratia marcescens CAB03, which may be associated with coral disease, isolated from Acropora cythera of Palk Bay coral reef, India. Whole genome sequencing of S. marcescens CAB03 produced 24 contigs (total G + C 59.7 %) and 4713 predicted genes. Identification of functional annotation revealed 17 antimicrobial resistance (AMR) genes, including three copies of the adeF gene, which encapsulates a resistance-nodulation-division (RND) efflux system that provides resistance to tetracyclines and fluoroquinolones. At the same time, related genes were also associated with resistance to β-lactams, aminoglycosides, macrolides, glycopeptides, and disinfectants, suggesting that this strain may have multidrug resistance potential. Further secondary metabolite prediction revealed biosynthetic gene clusters for ririwpeptide, a cyclic lipopetide with membrane-disrupting antibacterial and anticancer activity, and prodigiosin, which has gained notoriety for its antimicrobial, anticancer, and immunosuppressant activities as a red-colored pigment. Genome-based evidence clearly indicates that S. marcescens CAB03 is a contributor to coral health degradation through the proliferation of AMR bacteria and also a potential repository of bioactive compounds for pharmaceutical purposes. We used whole-genome sequencing here to address a long-standing knowledge gap regarding AMR bacteria associated with coral from Indian reefs. This study illustrates the need for genomic surveillance and conservation for AMR bacteria, ideally and more generally advances the study of microbial metabolites for drug discovery. Linking pathogen genomic profiles to reef health and advances in applied biotechnology reveal new reasons for coral reef conservation and provide new sources of data for potential drug development.
人们对耐抗生素病原体了解甚少，并对珊瑚礁生态系统构成新威胁。与珊瑚相关的微生物多样性对珊瑚礁的恢复力至关重要；然而，人们对来自印度珊瑚礁的机会性病原体的了解有限。本文报道了从印度Palk Bay珊瑚礁的Acropora cythera中分离到的可能与珊瑚病有关的粘质沙雷氏菌CAB03。S. marcescens CAB03全基因组测序得到24个contigs（总G + C 59.7%）和4713个预测基因。功能注释鉴定揭示了17个抗微生物药物耐药性（AMR）基因，其中包括3个拷贝的adeF基因，该基因封装了一个耐药-结核-分裂（RND）外排系统，提供对四环素和氟喹诺酮类药物的耐药性。同时，相关基因还与β-内酰胺类、氨基糖苷类、大环内酯类、糖肽类和消毒剂耐药有关，提示该菌株可能具有多药耐药潜力。进一步的次生代谢物预测揭示了ririwpeptide（一种具有破坏膜的抗菌和抗癌活性的环状脂肽）和prodigiosin（作为一种红色色素，因其抗菌、抗癌和免疫抑制活性而闻名）的生物合成基因簇。基于基因组的证据清楚地表明，S. marcescens CAB03是通过AMR细菌的增殖导致珊瑚健康退化的一个贡献者，也是用于制药目的的生物活性化合物的潜在储存库。我们在这里使用全基因组测序来解决长期以来关于与印度珊瑚礁珊瑚相关的AMR细菌的知识差距。这项研究说明了AMR细菌基因组监测和保护的必要性，理想地和更广泛地推进了药物发现的微生物代谢物研究。将病原体基因组图谱与珊瑚礁健康和应用生物技术的进展联系起来，揭示了保护珊瑚礁的新理由，并为潜在的药物开发提供了新的数据来源。
{"title":"Antimicrobial resistance and bioactive metabolites of Serratia marcescens CAB03 from a Palk Bay coral reef","authors":"S. Hari Krishna Kumar , Ragothaman Prathiviraj , Muregesan Sobanaa , George Seghal Kiran , Joseph Selvin","doi":"10.1016/j.genrep.2025.102339","DOIUrl":"10.1016/j.genrep.2025.102339","url":null,"abstract":"<div><div>Antimicrobial-resistant pathogens are poorly understood and pose emerging threats to coral reef ecosystems. Coral-associated microbial diversity is crucial for reef resilience; however, there is a limited understanding of opportunistic pathogens from Indian reefs. Here, we report the identification of <em>Serratia marcescens</em> CAB03, which may be associated with coral disease, isolated from <em>Acropora cythera</em> of Palk Bay coral reef, India. Whole genome sequencing of <em>S. marcescens</em> CAB03 produced 24 contigs (total G + C 59.7 %) and 4713 predicted genes. Identification of functional annotation revealed 17 antimicrobial resistance (AMR) genes, including three copies of the <em>adeF</em> gene, which encapsulates a resistance-nodulation-division (RND) efflux system that provides resistance to tetracyclines and fluoroquinolones. At the same time, related genes were also associated with resistance to β-lactams, aminoglycosides, macrolides, glycopeptides, and disinfectants, suggesting that this strain may have multidrug resistance potential. Further secondary metabolite prediction revealed biosynthetic gene clusters for ririwpeptide, a cyclic lipopetide with membrane-disrupting antibacterial and anticancer activity, and prodigiosin, which has gained notoriety for its antimicrobial, anticancer, and immunosuppressant activities as a red-colored pigment. Genome-based evidence clearly indicates that <em>S. marcescens</em> CAB03 is a contributor to coral health degradation through the proliferation of AMR bacteria and also a potential repository of bioactive compounds for pharmaceutical purposes. We used whole-genome sequencing here to address a long-standing knowledge gap regarding AMR bacteria associated with coral from Indian reefs. This study illustrates the need for genomic surveillance and conservation for AMR bacteria, ideally and more generally advances the study of microbial metabolites for drug discovery. Linking pathogen genomic profiles to reef health and advances in applied biotechnology reveal new reasons for coral reef conservation and provide new sources of data for potential drug development.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102339"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145216396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-10-14DOI: 10.1016/j.genrep.2025.102356
José Germán Serrano-Gamboa , José Tomás Tavarez-Arriaga , Mario L. Iza-Arteaga , Martín Romualdo Ide-Pérez , Irán Tapia-Vázquez , Jorge L. Folch-Mallol
A novel strain of the genus Pseudomonas was isolated from a high-altitude volcano in Toluca, Mexico. This isolate, designed as Pseudomonas marginalis BMH-2007, could grow at 4 °C, whereas other microbes usually stop growth at this temperature. The fact of its isolation from snow implies that the population was big enough to thrive at low temperature, making it a psychrotolerant bacterium.
Previous characterization of BMH-2007 revealed interesting characteristics related to plant growth promotion, including auxin production, siderophore production, and phosphate solubilization capacity. In this work, the ability of BMH-2007 to stimulate the early development of Capsicum annuum plants without signs of phytopathogenicity was proven. A thorough whole-genome analysis revealed that isolate BMH-2007 belongs to the Pseudomonas fluorescens species complex, specifically to the species P. marginalis, with a Mash distance of 0.0118927 from the closest reference genome (RefSeq: GCF_007858175.1).
The phylogenomic evidence allowed us to confirm the new strain designation. Notably, its genomic features were consistent with those of plant growth-promoting traits, and we observed coding sequences for IAA biosynthesis and iron and phosphate transport, among others. As it is a species associated with phytopathogenicity, the virulence factors encoded by the genome were analyzed, which revealed the presence of a type VI secretion system associated with both biological control and plant growth promotion.
{"title":"Phylogenomic insights into a psychrotolerant, plant growth-promoting strain of Pseudomonas marginalis isolated from Xinantécatl volcano","authors":"José Germán Serrano-Gamboa , José Tomás Tavarez-Arriaga , Mario L. Iza-Arteaga , Martín Romualdo Ide-Pérez , Irán Tapia-Vázquez , Jorge L. Folch-Mallol","doi":"10.1016/j.genrep.2025.102356","DOIUrl":"10.1016/j.genrep.2025.102356","url":null,"abstract":"<div><div>A novel strain of the genus <em>Pseudomonas</em> was isolated from a high-altitude volcano in Toluca, Mexico. This isolate, designed as <em>Pseudomonas marginalis</em> BMH-2007, could grow at 4 °C, whereas other microbes usually stop growth at this temperature. The fact of its isolation from snow implies that the population was big enough to thrive at low temperature, making it a psychrotolerant bacterium.</div><div>Previous characterization of BMH-2007 revealed interesting characteristics related to plant growth promotion, including auxin production, siderophore production, and phosphate solubilization capacity. In this work, the ability of BMH-2007 to stimulate the early development of <em>Capsicum annuum</em> plants without signs of phytopathogenicity was proven. A thorough whole-genome analysis revealed that isolate BMH-2007 belongs to the <em>Pseudomonas fluorescens</em> species complex, specifically to the species <em>P. marginalis</em>, with a Mash distance of 0.0118927 from the closest reference genome (RefSeq: GCF_007858175.1).</div><div>The phylogenomic evidence allowed us to confirm the new strain designation. Notably, its genomic features were consistent with those of plant growth-promoting traits, and we observed coding sequences for IAA biosynthesis and iron and phosphate transport, among others. As it is a species associated with phytopathogenicity, the virulence factors encoded by the genome were analyzed, which revealed the presence of a type VI secretion system associated with both biological control and plant growth promotion.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102356"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-08-05DOI: 10.1016/j.genrep.2025.102311
Murtada Alsiddig , Tarig Badri , Hind Widaa , Bojiang Li , Honglin Liu
Sperm adhesion molecule 1(SPAM1) is a vital candidate gene that plays an important role in fertilization and hatchability of geese. In this study, we investigated for the first time the genetic variation of the SPAM1 gene and its association with egg production trait in Yangzhou geese. By using the direct sequencing technique, we detected three single nucleotide polymorphisms, g206 G>C, c123 T>A, and c159 T>C, located in the promoter and exon one regions, respectively. Six alleles and nine genotypes (GG, CC, GC, TT, TA, AA, TT, TC and CC) were obtained, respectively. The results indicated that the GG (g206 G>C) genotype had a significantly higher egg production rate during the 34-week egg-laying period. In the case of the SNPs c123 T > A and c159 T > C individuals with the AA and TT genotypes produced more eggs number, respectively. The SPAM 1 gene was highly expressed in the oviduct, abdominal fat, ovary and small intestine tissues. The mRNA expression level in the oviduct and ovary indicated that the geese with GG genotype recorded significantly lower expression levels (0.72 ± 0.02; 0.93 ± 0.02) compared to the geese with CC genotype (1.27 ± 0.19, 1.11 ± 0.06), respectively. Transcriptional activity results showed that both constructed vectors (pGL3-328G and pGL3-333C) had higher and more significant luciferase activity than the pGL3-basic vector. Future studies in Yangzhou and other native breeds of geese may be required to validate the association between these polymorphisms and egg production traits.
精子粘附分子1（Sperm adhesion molecule 1, SPAM1）是鹅受精和孵化过程中重要的候选基因。本研究首次研究了扬州鹅SPAM1基因的遗传变异及其与产蛋性状的关系。通过直接测序技术，我们检测到g206 G>；C、c123 T>；A和c159 T>；C三个单核苷酸多态性，分别位于启动子区和外显子1区。共获得6个等位基因和9个基因型（GG、CC、GC、TT、TA、AA、TT、TC和CC）。结果表明，GG （g206 G>；C）基因型在34周产蛋期产蛋率显著高于其他基因型。在snp c123 T >；A和c159 T >；AA和TT基因型的C个体分别产蛋量较多。SPAM - 1基因在输卵管、腹部脂肪、卵巢和小肠组织中高度表达。输卵管和卵巢mRNA表达量表明，GG基因型鹅的mRNA表达量显著低于对照组(0.72±0.02；0.93±0.02)，而CC基因型鹅分别为（1.27±0.19）、（1.11±0.06）。转录活性结果显示，构建载体pGL3-328G和pGL3-333C的荧光素酶活性均高于pGL3-basic载体。未来的研究可能需要在扬州和其他地方鹅品种中验证这些多态性与产蛋性状之间的关系。
{"title":"Single-nucleotide polymorphisms (SNPs) in sperm adhesion molecule 1 (SPAM1) gene are associated with egg production in Yangzhou geese","authors":"Murtada Alsiddig , Tarig Badri , Hind Widaa , Bojiang Li , Honglin Liu","doi":"10.1016/j.genrep.2025.102311","DOIUrl":"10.1016/j.genrep.2025.102311","url":null,"abstract":"<div><div>Sperm adhesion molecule 1(SPAM1) is a vital candidate gene that plays an important role in fertilization and hatchability of geese. In this study, we investigated for the first time the genetic variation of the SPAM1 gene and its association with egg production trait in Yangzhou geese. By using the direct sequencing technique, we detected three single nucleotide polymorphisms, g206 G>C, c123 T>A, and c159 T>C, located in the promoter and exon one regions, respectively. Six alleles and nine genotypes (GG, CC, GC, TT, TA, AA, TT, TC and CC) were obtained, respectively. The results indicated that the GG (g206 G>C) genotype had a significantly higher egg production rate during the 34-week egg-laying period. In the case of the SNPs c123 T > A and c159 T > C individuals with the AA and TT genotypes produced more eggs number, respectively. The SPAM 1 gene was highly expressed in the oviduct, abdominal fat, ovary and small intestine tissues. The mRNA expression level in the oviduct and ovary indicated that the geese with GG genotype recorded significantly lower expression levels (0.72 ± 0.02; 0.93 ± 0.02) compared to the geese with CC genotype (1.27 ± 0.19, 1.11 ± 0.06), respectively. Transcriptional activity results showed that both constructed vectors (pGL3-328G and pGL3-333C) had higher and more significant luciferase activity than the pGL3-basic vector. Future studies in Yangzhou and other native breeds of geese may be required to validate the association between these polymorphisms and egg production traits.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102311"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144771853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Copy number variation in the SMN1 gene is the main cause of Spinal Muscular Atrophy (SMA). We assessed the carrier frequency of SMA, which is the second most common genetic disease, in the Iranian population. This paper demonstrates the largest population including unrelated subjects and also provides an evaluation with variant analysis of SMN1 in cis. To acquire inclusive molecular data about the carrier frequency of SMA and the frequency of SMN1 polymorphisms g.27134T>G (c.*3+80T>G) among Iranian population, we analyzed data from 2157 individuals referred to the Pars-Genome and Genome-Nilou laboratories for SMA carrier detection between 2018 and 2024. A total of 2003 unrelated non-consanguineous healthy individuals were selected from 2157 individuals underwent MLPA using kit P460 or P021. We also assessed available whole exome sequencing (WES) data of another cohort of patients for the presence of the c.*3+80T>G variant in the SMN1. The results indicated that 3.5 % (n = 70) were carriers of the disease, possessing only one copy of the SMN1 gene. Totally, 89 % (n = 1783) of all participants exhibited two copies of SMN1. Among 526 cases underwent assessment by P460 kit and 2211 cases underwent WES, c.*3+80T>G variant was detected in 28 (1 %) cases. This data can be used in the genetic counseling, carrier screening, and prenatal diagnosis of SMA in Iran.
{"title":"Carrier frequency of spinal muscular atrophy: a large-scale study in Iranian population","authors":"Shahram Savad , Mohammad-Hossein Modarressi , Mahnaz Seifi-Alan , Niusha Samadaian , Saloomeh Amidi , Mona Masoomy , Shima Norouzi , Sanaz Seifi-Alan , Alireza Ronagh , Shahab Nourian , Sarang Younesi , Mohammad Mahdi Taheri Amin , Maryam Eslami , Mostafa Iranpour , Asyeh Mohammadi , Bahar Parastooei , Mahdi Heydari , Amirreza Boroumand , Mahmoud Reza Ashrafi , Donya Jahedi , Soudeh Ghafouri-Fard","doi":"10.1016/j.genrep.2025.102378","DOIUrl":"10.1016/j.genrep.2025.102378","url":null,"abstract":"<div><div>Copy number variation in the <em>SMN1</em> gene is the main cause of Spinal Muscular Atrophy (SMA). We assessed the carrier frequency of SMA, which is the second most common genetic disease, in the Iranian population. This paper demonstrates the largest population including unrelated subjects and also provides an evaluation with variant analysis of <em>SMN1</em> in <em>cis</em>. To acquire inclusive molecular data about the carrier frequency of SMA and the frequency of <em>SMN1</em> polymorphisms g.27134T>G (c.*3+80T>G) among Iranian population, we analyzed data from 2157 individuals referred to the Pars-Genome and Genome-Nilou laboratories for SMA carrier detection between 2018 and 2024. A total of 2003 unrelated non-consanguineous healthy individuals were selected from 2157 individuals underwent MLPA using kit P460 or P021. We also assessed available whole exome sequencing (WES) data of another cohort of patients for the presence of the c.*3+80T>G variant in the <em>SMN1</em>. The results indicated that 3.5 % (<em>n</em> = 70) were carriers of the disease, possessing only one copy of the <em>SMN1</em> gene. Totally, 89 % (<em>n</em> = 1783) of all participants exhibited two copies of <em>SMN1</em>. Among 526 cases underwent assessment by P460 kit and 2211 cases underwent WES, c.*3+80T>G variant was detected in 28 (1 %) cases. This data can be used in the genetic counseling, carrier screening, and prenatal diagnosis of SMA in Iran.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102378"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145462419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-08-02DOI: 10.1016/j.genrep.2025.102313
Duaa K. Mohammed , Layla O. Farhan
Beta-thalassemia (β-TH) is a hereditary hemoglobinopathy that presents in various clinical forms, including major and intermedia. Emerging evidence suggests that neurotrophin-3 (NT-3), which is a key neurotrophic factor, may play a role in hematological and systemic responses to chronic anemia. This study quantified serum neurotrophin-3 (NT-3) levels in 120 subjects: 55 with (β-TH) major, 25 with β-TH intermedia, and 40 healthy control, using enzyme-linked immunosorbent assay (ELISA). NT-3 levels were significantly decreased in β-TH patients compared to controls (p < 0.001), with a progressive decline from controls to intermedia and major groups. The lower NT-3 levels in the intermedia group are attributed to irregular blood transfusions and inconsistent treatment adherence. Multivariate regression revealed no significant correlation between NT-3 and hemoglobin A2 or fetal hemoglobin. The receiver operating characteristic (ROC) curve analysis demonstrated a high diagnostic accuracy for NT-3 in distinguishing β-TH patients from controls (AUC = 0.998) with a cut-off value ≤1921.84 pg/mL. These findings highlight the potential role of NT-3 as a novel, non-invasive biomarker reflecting disease severity and hypoxia-related oxidative stress in β-TH.
{"title":"Investigation of NT-3 as a diagnostic indicator in beta thalassemia with emphasis on relationship with hemoglobin electrophoresis patterns","authors":"Duaa K. Mohammed , Layla O. Farhan","doi":"10.1016/j.genrep.2025.102313","DOIUrl":"10.1016/j.genrep.2025.102313","url":null,"abstract":"<div><div>Beta-thalassemia (β-TH) is a hereditary hemoglobinopathy that presents in various clinical forms, including major and intermedia. Emerging evidence suggests that neurotrophin-3 (NT-3), which is a key neurotrophic factor, may play a role in hematological and systemic responses to chronic anemia. This study quantified serum neurotrophin-3 (NT-3) levels in 120 subjects: 55 with (β-TH) major, 25 with β-TH intermedia, and 40 healthy control, using enzyme-linked immunosorbent assay (ELISA). NT-3 levels were significantly decreased in β-TH patients compared to controls (p < 0.001), with a progressive decline from controls to intermedia and major groups. The lower NT-3 levels in the intermedia group are attributed to irregular blood transfusions and inconsistent treatment adherence. Multivariate regression revealed no significant correlation between NT-3 and hemoglobin A2 or fetal hemoglobin. The receiver operating characteristic (ROC) curve analysis demonstrated a high diagnostic accuracy for NT-3 in distinguishing β-TH patients from controls (AUC = 0.998) with a cut-off value ≤1921.84 pg/mL. These findings highlight the potential role of NT-3 as a novel, non-invasive biomarker reflecting disease severity and hypoxia-related oxidative stress in β-TH.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102313"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144757412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-08-19DOI: 10.1016/j.genrep.2025.102325
Jiaqi Mu , Aquib Nazar , Muhammad Asim Ali , Athar Hussain
Breast cancer is one of the most common cancers that significantly affects a large population of women, emphasizing its importance in early detection for effective treatments. The advancement in technologies, especially in machine learning and its integration with multi-omics data, such as genomics, transcriptomics, proteomics, metabolomics, and imaging, is not only revolutionizing the diagnosis and prognosis of breast cancer at its early stages but also providing a door for personalized treatment plans to improve patient outcomes. However, achieving truly personalized treatment requires integration of causal inference methods into machine learning frameworks, as correlational models alone may not ensure effective or safe decision-making. The current study revisits the progress made in this research area, providing a comprehensive insight into the challenges of breast cancer early detection, machine learning (ML) in cancer detection, ML-Omics integration, clinical applications, case studies, and future directions and innovations.
{"title":"Integrating machine learning with OMICs data for early detection in breast cancer","authors":"Jiaqi Mu , Aquib Nazar , Muhammad Asim Ali , Athar Hussain","doi":"10.1016/j.genrep.2025.102325","DOIUrl":"10.1016/j.genrep.2025.102325","url":null,"abstract":"<div><div>Breast cancer is one of the most common cancers that significantly affects a large population of women, emphasizing its importance in early detection for effective treatments. The advancement in technologies, especially in machine learning and its integration with multi-omics data, such as genomics, transcriptomics, proteomics, metabolomics, and imaging, is not only revolutionizing the diagnosis and prognosis of breast cancer at its early stages but also providing a door for personalized treatment plans to improve patient outcomes. However, achieving truly personalized treatment requires integration of causal inference methods into machine learning frameworks, as correlational models alone may not ensure effective or safe decision-making. The current study revisits the progress made in this research area, providing a comprehensive insight into the challenges of breast cancer early detection, machine learning (ML) in cancer detection, ML-Omics integration, clinical applications, case studies, and future directions and innovations.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102325"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144886620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Transposable elements (TEs) are mobile genetic elements that can disrupt genomic integrity, influencing gene regulation and contributing to various diseases, including cancer. The accurate identification and characterization of TEs in high-throughput sequencing data is essential for understanding their role in genomic instability and tumorigenesis. To streamline this process, we developed MeX_Docker, a pipeline that utilizes Docker containerization to overcome software dependency issues and ensure reproducibility across different computing environments. Docker provides a standardized, portable solution that allows researchers to deploy and run the pipeline seamlessly, eliminating common obstacles in bioinformatics workflows. MeX_Docker integrates widely-used tools such as FastQC, Fastp, SAMtools, TEfinder, and Ensembl Variant Effect Predictor (VEP) for efficient data preprocessing, alignment, TE calling, and annotation. The pipeline was applied to human paired end whole-genome sequencing cancer datasets (breast, lung, and colorectal cancers), successfully identifying reference and non-reference Alu and L1 elements. In a lung cancer sample, an in-frame insertion in the CATSPERD gene was detected, which was classified as benign polymorphism. These findings highlight the use of MeX_Docker as an efficient tool for studying the impact of transposable elements on genomic instability and their potential role in cancer biology.
{"title":"MeX_Docker: An integrated application for transposon identification and annotation based on the Docker platform","authors":"P. Preeti , Mihir Nakul , Chhavi Dudeja , Abhishek Singh , Arushi Gupta , Yuktika Malhotra , Deepika Yadav , Kamal Rawal","doi":"10.1016/j.genrep.2025.102364","DOIUrl":"10.1016/j.genrep.2025.102364","url":null,"abstract":"<div><div>Transposable elements (TEs) are mobile genetic elements that can disrupt genomic integrity, influencing gene regulation and contributing to various diseases, including cancer. The accurate identification and characterization of TEs in high-throughput sequencing data is essential for understanding their role in genomic instability and tumorigenesis. To streamline this process, we developed MeX_Docker, a pipeline that utilizes Docker containerization to overcome software dependency issues and ensure reproducibility across different computing environments. Docker provides a standardized, portable solution that allows researchers to deploy and run the pipeline seamlessly, eliminating common obstacles in bioinformatics workflows. MeX_Docker integrates widely-used tools such as FastQC, Fastp, SAMtools, TEfinder, and Ensembl Variant Effect Predictor (VEP) for efficient data preprocessing, alignment, TE calling, and annotation. The pipeline was applied to human paired end whole-genome sequencing cancer datasets (breast, lung, and colorectal cancers), successfully identifying reference and non-reference Alu and L1 elements. In a lung cancer sample, an in-frame insertion in the CATSPERD gene was detected, which was classified as benign polymorphism. These findings highlight the use of MeX_Docker as an efficient tool for studying the impact of transposable elements on genomic instability and their potential role in cancer biology.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102364"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145412788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Recent researches have highlighted the promising potential of long non-coding RNA (lncRNAs) as an important regulator in endometriosis. Accumulating shreds of evidence has shown an important role of HOTTIP (HOXA transcript at the distal tip) in cell proliferation, differentiation, and migration. The function of HOTTIP in relation to endometriosis is still not well understood.
Materials and methods
The goal of this research was to examine the expression profile of HOTTIP and HOXA genes in 70 matched eutopic endometrium (EU) and ectopic endometrium (EC) samples from women with endometriosis, with 85 normal endometrium control samples (C) from healthy women. Quantitative real-time PCR (qRT-PCR) assay was performed to measure the level of gene expression. Cell viability was assessed using the CCK-8 assay. Two endometriotic cell lines were transfected with siRNA against HOTTIP (si-HOTTIP) and then used to monitor the effect of HOTTIP on the expression of HOXA13. Bioinformatic tools and the Cytoscape platform were utilized to perform network analysis and gene enrichment analysis.
Results
Results indicated that the expression of HOXA13 and HOTTIP was elevated in EC and EU samples in comparison to the C group (p < 0.05). However, HOXA9, HOXA10, and HOXA11 showed decreased expression in EC samples compared to their levels in the C and EU samples. The expression levels of HOTTIP RNA showed a positive correlation with HOXA13 in patients with endometriosis. qRT-PCR data exhibited that si-HOTTIP triggered the reduction of both HOTTIP and HOXA13 expression levels and cell viability, and bioinformatics analysis in the Cytoscape platform helped us to make our laboratory results more reliable. In conclusion, the dysregulation of HOXA genes by HOTTIP lncRNA, characterized by the upregulation of HOXA13 and the downregulation of HOXA9, HOXA10 and HOXA11, suggests its significant role in the development of endometriosis and its potential as a therapeutic target.
{"title":"The Survey of long non-coding RNA HOTTIP expression level in endometriosis","authors":"Parisa Vesal , Amirhossein Rezvani Rezvandeh , Namdar Razmavar , Zivar Salehi , Farhad Mashayekhi , Kiana Sojoudi , Ziba Zahiri , Zakieh Siahpoosh","doi":"10.1016/j.genrep.2025.102338","DOIUrl":"10.1016/j.genrep.2025.102338","url":null,"abstract":"<div><h3>Background</h3><div>Recent researches have highlighted the promising potential of long non-coding RNA (lncRNAs) as an important regulator in endometriosis. Accumulating shreds of evidence has shown an important role of HOTTIP (HOXA transcript at the distal tip) in cell proliferation, differentiation, and migration. The function of HOTTIP in relation to endometriosis is still not well understood.</div></div><div><h3>Materials and methods</h3><div>The goal of this research was to examine the expression profile of HOTTIP and HOXA genes in 70 matched eutopic endometrium (EU) and ectopic endometrium (EC) samples from women with endometriosis, with 85 normal endometrium control samples (C) from healthy women. Quantitative real-time PCR (qRT-PCR) assay was performed to measure the level of gene expression. Cell viability was assessed using the CCK-8 assay. Two endometriotic cell lines were transfected with siRNA against HOTTIP (si-HOTTIP) and then used to monitor the effect of HOTTIP on the expression of HOXA13. Bioinformatic tools and the Cytoscape platform were utilized to perform network analysis and gene enrichment analysis.</div></div><div><h3>Results</h3><div>Results indicated that the expression of HOXA13 and HOTTIP was elevated in EC and EU samples in comparison to the C group (<em>p</em> < 0.05). However, HOXA9, HOXA10, and HOXA11 showed decreased expression in EC samples compared to their levels in the C and EU samples. The expression levels of HOTTIP RNA showed a positive correlation with HOXA13 in patients with endometriosis. qRT-PCR data exhibited that si-HOTTIP triggered the reduction of both HOTTIP and HOXA13 expression levels and cell viability, and bioinformatics analysis in the Cytoscape platform helped us to make our laboratory results more reliable. In conclusion, the dysregulation of <em>HOXA</em> genes by HOTTIP lncRNA, characterized by the upregulation of <em>HOXA13</em> and the downregulation of <em>HOXA9</em>, <em>HOXA10</em> and <em>HOXA11</em>, suggests its significant role in the development of endometriosis and its potential as a therapeutic target.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102338"},"PeriodicalIF":0.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145060422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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