Pub Date : 2026-02-10Epub Date: 2025-11-25DOI: 10.1016/j.gene.2025.149919
Carlotta Frascolla , Riccardo Mastroianni , Giuseppe Simone , Giovanni Blandino
Bladder cancer (BCa) remains one of the most challenging malignancies in oncology, driven by deep molecular heterogeneity, dynamic tumor evolution and complex tumor–microenvironment interactions. Despite advances in molecular characterization and the introduction of new treatments, translating biological knowledge into meaningful clinical benefits remains a major bottleneck. In recent years, next-generation 3D preclinical models have emerged as essential tools to recapitulate BCa complexity, offering new opportunities to investigate tumor biology and support the development of personalized treatment strategies. This review provides an overview of available 3D models for BCa, discusses their application and highlights their growing integration into clinical trials to guide real-time therapeutic decisions.
{"title":"The role of 3D preclinical models in the Era of precision medicine: A bladder cancer perspective","authors":"Carlotta Frascolla , Riccardo Mastroianni , Giuseppe Simone , Giovanni Blandino","doi":"10.1016/j.gene.2025.149919","DOIUrl":"10.1016/j.gene.2025.149919","url":null,"abstract":"<div><div>Bladder cancer (BCa) remains one of the most challenging malignancies in oncology, driven by deep molecular heterogeneity, dynamic tumor evolution and complex tumor–microenvironment interactions. Despite advances in molecular characterization and the introduction of new treatments, translating biological knowledge into meaningful clinical benefits remains a major bottleneck. In recent years, next-generation 3D preclinical models have emerged as essential tools to recapitulate BCa complexity, offering new opportunities to investigate tumor biology and support the development of personalized treatment strategies. This review provides an overview of available 3D models for BCa, discusses their application and highlights their growing integration into clinical trials to guide real-time therapeutic decisions.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149919"},"PeriodicalIF":2.4,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-10Epub Date: 2025-12-06DOI: 10.1016/j.gene.2025.149934
Xin Lin , Zi-yan Xu , Li-jun Xie , Juan Zhu , Hong-ping Yu , Ruo-li Wang , Yi-jia Luo , Jing Zou , Jian-hui Zhang , Qian Chen , Peng-fei Wang , Dan-dan Ruan , Yan-feng Zhou , Li Chen , Fang-meng Huang , Mei-zhu Gao , Li Zhang , Yun-fei Li , Zhu-ting Fang , Jue Wang , Jie-wei Luo
Type A insulin resistance syndrome (TAIRS) is a rare autosomal dominant disorder associated with variants in the Insulin Receptor (INSR) gene. It is characterized by insulin resistance, hyperandrogenism, and acanthosis nigricans. The severity of the condition may be influenced by homozygosity or heterozygosity, with some female patients being misdiagnosed with polycystic ovary syndrome (PCOS). A 13-year-old female proband from a family was identified with hyperinsulinemia, hyperandrogenism, acanthosis nigricans, hirsutism, acne, oligomenorrhea, and masculinization. Exome sequencing and Sanger sequencing confirmed that the proband was a carrier of the INSR (NM_000208.2): c.3734 T > A(p.V1245E) variant. This variant is not listed in the Human Gene Mutation Database (HGMD) or ClinVar. The novel variant was predicted to be deleterious by the bioinformatic tools SIFT, MutationTaster, and Condel. According to the American College of Medical Genetics and Genomics (ACMG) criteria, it was evaluated as PM6, PM2_Supporting, and PP3, and classified as uncertain significance. The variant was not detected in the proband’s parents or other family members, all of whom lacked the associated clinical phenotypes. The p.V1245E variant was found to be a de novo variant. SWISS-MODEL analysis suggested that the p.V1245E variant induces structural changes in the three-dimensional configuration of the INSR protein, potentially impairing its normal function. RT-qPCR revealed a significant reduction in INSR mRNA expression in the proband. In a 293 T cell model transfected with lentivirus carrying the p.V1245E variant, both Western blotting and RT-qPCR demonstrated decreased INSR mRNA and protein expression, while immunofluorescence showed reduced INSR protein levels with altered localization. Therefore, the ACMG evaluation (PS2, PS3, PM2_Supporting, PP3) was further upgraded to pathogenic. In conclusion, this de novo variant represents the pathogenic variant responsible for TAIRS in this family, expanding the variant spectrum of the INSR gene.
A型胰岛素抵抗综合征(TAIRS)是一种罕见的常染色体显性遗传病,与胰岛素受体(INSR)基因变异有关。它的特点是胰岛素抵抗、雄激素过多和黑棘皮病。多囊卵巢综合征的严重程度可能受纯合性或杂合性的影响,一些女性患者被误诊为多囊卵巢综合征(PCOS)。来自一个家庭的13岁女性先证被鉴定为高胰岛素血症、高雄激素症、黑棘皮病、多毛症、痤疮、少月经和男性化。外显子组测序和Sanger测序证实先证者为INSR (NM_000208.2)的携带者:c.3734 T > a (p。V1245E)变异。这种变异没有在人类基因突变数据库(HGMD)或ClinVar中列出。通过生物信息学工具SIFT、MutationTaster和Condel预测该新变异是有害的。根据美国医学遗传学和基因组学学会(ACMG)的标准,评估为PM6、pm2_support和PP3,并归类为不确定意义。该变异未在先证者的父母或其他家庭成员中检测到,他们都缺乏相关的临床表型。p.V1245E改型被发现是一个全新的改型。SWISS-MODEL分析表明,p.V1245E变异诱导了INSR蛋白三维构型的结构变化,潜在地损害了其正常功能。RT-qPCR显示先证者中INSR mRNA表达显著降低。在携带p.V1245E变异体的慢病毒转染293 T细胞模型中,Western blotting和RT-qPCR均显示INSR mRNA和蛋白表达降低,而免疫荧光显示INSR蛋白水平降低,定位改变。因此,ACMG评价(PS2、PS3、pm2_support、PP3)进一步升级为致病性。总之,这一新生变异代表了该家族中导致TAIRS的致病变异,扩大了INSR基因的变异谱。
{"title":"A de novo INSR variant in Type A insulin resistance syndrome: familial investigation and genetic implications","authors":"Xin Lin , Zi-yan Xu , Li-jun Xie , Juan Zhu , Hong-ping Yu , Ruo-li Wang , Yi-jia Luo , Jing Zou , Jian-hui Zhang , Qian Chen , Peng-fei Wang , Dan-dan Ruan , Yan-feng Zhou , Li Chen , Fang-meng Huang , Mei-zhu Gao , Li Zhang , Yun-fei Li , Zhu-ting Fang , Jue Wang , Jie-wei Luo","doi":"10.1016/j.gene.2025.149934","DOIUrl":"10.1016/j.gene.2025.149934","url":null,"abstract":"<div><div>Type A insulin resistance syndrome (TAIRS) is a rare autosomal dominant disorder associated with variants in the Insulin Receptor (<em>INSR</em>) gene. It is characterized by insulin resistance, hyperandrogenism, and acanthosis nigricans. The severity of the condition may be influenced by homozygosity or heterozygosity, with some female patients being misdiagnosed with polycystic ovary syndrome (PCOS). A 13-year-old female proband from a family was identified with hyperinsulinemia, hyperandrogenism, acanthosis nigricans, hirsutism, acne, oligomenorrhea, and masculinization. Exome sequencing and Sanger sequencing confirmed that the proband was a carrier of the <em>INSR</em> (NM_000208.2): c.3734 T > A(p.V1245E) variant. This variant is not listed in the Human Gene Mutation Database (HGMD) or ClinVar. The novel variant was predicted to be deleterious by the bioinformatic tools SIFT, MutationTaster, and Condel. According to the American College of Medical Genetics and Genomics (ACMG) criteria, it was evaluated as PM6, PM2_Supporting, and PP3, and classified as uncertain significance. The variant was not detected in the proband’s parents or other family members, all of whom lacked the associated clinical phenotypes. The p.V1245E variant was found to be a <em>de novo</em> variant. SWISS-MODEL analysis suggested that the p.V1245E variant induces structural changes in the three-dimensional configuration of the <em>INSR</em> protein, potentially impairing its normal function. RT-qPCR revealed a significant reduction in <em>INSR</em> mRNA expression in the proband. In a 293 T cell model transfected with lentivirus carrying the p.V1245E variant, both Western blotting and RT-qPCR demonstrated decreased <em>INSR</em> mRNA and protein expression, while immunofluorescence showed reduced <em>INSR</em> protein levels with altered localization. Therefore, the ACMG evaluation (PS2, PS3, PM2_Supporting, PP3) was further upgraded to pathogenic. In conclusion, this de novo variant represents the pathogenic variant responsible for TAIRS in this family, expanding the variant spectrum of the <em>INSR</em> gene.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149934"},"PeriodicalIF":2.4,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145707930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-10Epub Date: 2025-12-03DOI: 10.1016/j.gene.2025.149932
Chun Feng , Teng Zhang , Yuan Li , Yuyun Long , Qian Meng , Shi-Wen Jiang
Syncytin-2 is an endogenous retroviral envelope protein constitutively expressed in human placental trophoblasts. As a membrane glycoprotein, Syncytin-2 together with Syncytin-1 mediates the fusion of mononucleated cytotrophoblasts to form multinucleated syncytiotrophoblasts. Syncytiotrophoblasts constitute the fetal-maternal interface important for fetal-maternal exchange, barrier and endocrine functions of the placenta. Besides the fusogenic function, Syncytin-2 also possesses an immunosuppressive activity. In this study, the results of quantitative PCR indicated that Syncytin-2 expression was downregulated in third-trimester preeclamptic placentas, which is consistent with the result of previous studies. Importantly, the results of Combined Bisulfite Restriction Assay (COBRA) suggested hypermethylation of the downstream CpG-rich region, but not the promoter/exon1/intron1 and exon2 CpG- rich regions of SYN-2 gene in third-trimester preeclamptic placentas. Subsequent bisulfite conversion and PCR amplification, cloning and sequencing of the downstream CpG- rich region confirmed hypermethylation of the 4 CpGs in this region in preeclamptic placentas. Moreover, treatment of human choriocarcinoma BeWo cells with DNMT inhibitor ADC (5-aza-deoxycytidine) resulted in a dose-responsive demethylation of the downstream CpG-rich region and an increased SYN-2 mRNA level. Thus, the hypermethylation of the downstream CpG-rich region closely correlated with the downregulation of Syncytin-2 expression in preeclamptic placentas. These new findings underscore the significance of epigenetic alterations in preeclamptic placentas, and facilitate a better understanding on the pathological mechanism of preeclampsia.
{"title":"Downregulation of Syncytin-2 expression in preeclamptic placentas is associated with DNA hypermethylation of the downstream CpG-rich region","authors":"Chun Feng , Teng Zhang , Yuan Li , Yuyun Long , Qian Meng , Shi-Wen Jiang","doi":"10.1016/j.gene.2025.149932","DOIUrl":"10.1016/j.gene.2025.149932","url":null,"abstract":"<div><div>Syncytin-2 is an endogenous retroviral envelope protein constitutively expressed in human placental trophoblasts. As a membrane glycoprotein, Syncytin-2 together with Syncytin-1 mediates the fusion of mononucleated cytotrophoblasts to form multinucleated syncytiotrophoblasts. Syncytiotrophoblasts constitute the fetal-maternal interface important for fetal-maternal exchange, barrier and endocrine functions of the placenta. Besides the fusogenic function, Syncytin-2 also possesses an immunosuppressive activity. In this study, the results of quantitative PCR indicated that Syncytin-2 expression was downregulated in third-trimester preeclamptic placentas, which is consistent with the result of previous studies. Importantly, the results of Combined Bisulfite Restriction Assay (COBRA) suggested hypermethylation of the downstream CpG-rich region, but not the promoter/exon1/intron1 and exon2 CpG- rich regions of <em>SYN-2</em> gene in third-trimester preeclamptic placentas. Subsequent bisulfite conversion and PCR amplification, cloning and sequencing of the downstream CpG- rich region confirmed hypermethylation of the 4 CpGs in this region in preeclamptic placentas. Moreover, treatment of human choriocarcinoma BeWo cells with DNMT inhibitor ADC (5-aza-deoxycytidine) resulted in a dose-responsive demethylation of the downstream CpG-rich region and an increased <em>SYN-2</em> mRNA level. Thus, the hypermethylation of the downstream CpG-rich region closely correlated with the downregulation of Syncytin-2 expression in preeclamptic placentas. These new findings underscore the significance of epigenetic alterations in preeclamptic placentas, and facilitate a better understanding on the pathological mechanism of preeclampsia.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149932"},"PeriodicalIF":2.4,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145687167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-10Epub Date: 2025-11-13DOI: 10.1016/j.gene.2025.149893
Rosyely da Silva Oliveira , Nilson César Oliveira Alves Filho , Walter de Barros Gomes Netto , Denis de Castro Silva , Mônica Silva de Oliveira , Ana Carolina Favacho Miranda de Oliveira , Rafael Azevedo Baraúna , Diego Assis das Graças , Artur Silva , Adonney Allan de Oliveira Veras
To determine the gene content of an organism, the reads generated by the sequencing process must be assembled using an assembly strategy, either by reference or de novo. However, this process often results in multiple sequences called contigs, which, after the sorting steps, are grouped into scaffolds. The completion stage aims to obtain a single genomic sequence, called a complete genome, which is not a trivial task. Various analytical strategies have been developed to help in this process, many of which have been implemented in computer tools to obtain complete genomes or as close to this as possible, the so-called drafts. The manuscript presents ContigPolishing, a computational tool with a simple and intuitive graphical interface, developed to improve the assembly of prokaryotic genomes, such as bacteria and metagenomes. Despite existing software, there is a gap for solutions that combine simplicity and robustness. ContigPolishing addresses this need, featuring an integrated database that allows processing to be resumed at any time. The tool was validated with 90 NCBI datasets from genera such as Escherichia coli, Corynebacterium, and Nocardia, as well as raw reads from the SRA database to simulate real-world situations. The results showed improvement in the contiguity of the assemblies, with an increase in N50 and improvement in L50, and a reduction in the number of contigs, by extending the contigs using the similarity between their flanks. In some cases, the software was able to elevate the status of genomes from draft to complete, proving its efficiency. ContigPolishing is available at: https://github.com/allanverasce/contigpolishing.
{"title":"ContigPolishing: A User-Friendly Java GUI for contig extension and refinement in prokaryotic genomes","authors":"Rosyely da Silva Oliveira , Nilson César Oliveira Alves Filho , Walter de Barros Gomes Netto , Denis de Castro Silva , Mônica Silva de Oliveira , Ana Carolina Favacho Miranda de Oliveira , Rafael Azevedo Baraúna , Diego Assis das Graças , Artur Silva , Adonney Allan de Oliveira Veras","doi":"10.1016/j.gene.2025.149893","DOIUrl":"10.1016/j.gene.2025.149893","url":null,"abstract":"<div><div>To determine the gene content of an organism, the reads generated by the sequencing process must be assembled using an assembly strategy, either by reference or de novo. However, this process often results in multiple sequences called contigs, which, after the sorting steps, are grouped into scaffolds. The completion stage aims to obtain a single genomic sequence, called a complete genome, which is not a trivial task. Various analytical strategies have been developed to help in this process, many of which have been implemented in computer tools to obtain complete genomes or as close to this as possible, the so-called drafts. The manuscript presents ContigPolishing, a computational tool with a simple and intuitive graphical interface, developed to improve the assembly of prokaryotic genomes, such as bacteria and metagenomes. Despite existing software, there is a gap for solutions that combine simplicity and robustness. ContigPolishing addresses this need, featuring an integrated database that allows processing to be resumed at any time. The tool was validated with 90 NCBI datasets from genera such as Escherichia coli, Corynebacterium, and Nocardia, as well as raw reads from the SRA database to simulate real-world situations. The results showed improvement in the contiguity of the assemblies, with an increase in N50 and improvement in L50, and a reduction in the number of contigs, by extending the contigs using the similarity between their flanks. In some cases, the software was able to elevate the status of genomes from draft to complete, proving its efficiency. ContigPolishing is available at: <span><span>https://github.com/allanverasce/contigpolishing</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149893"},"PeriodicalIF":2.4,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145523192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-10Epub Date: 2025-11-29DOI: 10.1016/j.gene.2025.149929
Si-han Liu , Xiao-yan Kong , Miao Li , Shu-mei Wang
Background
Pediatric brain tumors (PBTs) are the leading type of solid tumors in children, profoundly affecting both survival rates and quality of life. Methotrexate (MTX) is an essential chemotherapy drug for treating these tumors; however, its efficacy and toxicity vary among patients due to genetic factors.
Objective
This study examined the impact of the intronic rs3780130 polymorphism in the gamma-glutamyl hydrolase (GGH) gene on MTX concentrations and related toxicities in patients with PBTs.
Methods
The GGH rs3780130 T > A polymorphism was genotyped using the Sequenom MassARRAY iPLEX platform in a cohort of 73 PBT patients.
Results
We found that children with the AA genotype had significantly higher MTX concentrations compared to those with TT and TA genotypes (P < 0.05). Additionally, the AA genotype was significantly associated with a higher incidence of hepatotoxicity relative to the TT genotype (P < 0.05). It showed a significantly lower occurrence of gastrointestinal toxicities when compared to the TA genotype (P < 0.05). Bioinformatics analysis revealed that the rs3780130 polymorphism had a significant effect on GGH expression across various tissues, suggesting a potential mechanism by which this variant modulated MTX metabolism.
Conclusion
Our findings highlight the importance of GGH polymorphisms in personalizing MTX therapy for PBT patients and emphasize the necessity for further research to explore the clinical implications of GGH genotypes in larger cohorts, ultimately aiming for more precise therapeutic strategies.
背景:儿童脑肿瘤(PBTs)是儿童实体肿瘤的主要类型,深刻影响着儿童的生存率和生活质量。甲氨蝶呤(MTX)是治疗这些肿瘤的重要化疗药物;然而,由于遗传因素,其疗效和毒性因患者而异。目的:研究γ -谷氨酰水解酶(GGH)基因rs3780130内含子多态性对pbt患者MTX浓度及相关毒性的影响。方法:使用Sequenom MassARRAY iPLEX平台对73例PBT患者的GGH rs3780130 T > A多态性进行基因分型。结果:我们发现AA基因型儿童的MTX浓度明显高于TT和TA基因型儿童(P )。结论:我们的研究结果强调了GGH多态性对PBT患者个性化MTX治疗的重要性,并强调了进一步研究的必要性,以在更大的队列中探索GGH基因型的临床意义,最终旨在制定更精确的治疗策略。
{"title":"GGH intronic variant rs3780130 is associated with methotrexate levels in children with brain tumors","authors":"Si-han Liu , Xiao-yan Kong , Miao Li , Shu-mei Wang","doi":"10.1016/j.gene.2025.149929","DOIUrl":"10.1016/j.gene.2025.149929","url":null,"abstract":"<div><h3>Background</h3><div>Pediatric brain tumors (PBTs) are the leading type of solid tumors in children, profoundly affecting both survival rates and quality of life. Methotrexate (MTX) is an essential chemotherapy drug for treating these tumors; however, its efficacy and toxicity vary among patients due to genetic factors.</div></div><div><h3>Objective</h3><div>This study examined the impact of the intronic rs3780130 polymorphism in the gamma-glutamyl hydrolase (<em>GGH</em>) gene on MTX concentrations and related toxicities in patients with PBTs.</div></div><div><h3>Methods</h3><div>The <em>GGH</em> rs3780130 T > A polymorphism was genotyped using the Sequenom MassARRAY iPLEX platform in a cohort of 73 PBT patients.</div></div><div><h3>Results</h3><div>We found that children with the AA genotype had significantly higher MTX concentrations compared to those with TT and TA genotypes (<em>P</em> < 0.05). Additionally, the AA genotype was significantly associated with a higher incidence of hepatotoxicity relative to the TT genotype (<em>P</em> < 0.05). It showed a significantly lower occurrence of gastrointestinal toxicities when compared to the TA genotype (<em>P</em> < 0.05). Bioinformatics analysis revealed that the rs3780130 polymorphism had a significant effect on <em>GGH</em> expression across various tissues, suggesting a potential mechanism by which this variant modulated MTX metabolism.</div></div><div><h3>Conclusion</h3><div>Our findings highlight the importance of <em>GGH</em> polymorphisms in personalizing MTX therapy for PBT patients and emphasize the necessity for further research to explore the clinical implications of <em>GGH</em> genotypes in larger cohorts, ultimately aiming for more precise therapeutic strategies.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149929"},"PeriodicalIF":2.4,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145653732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-10Epub Date: 2025-11-23DOI: 10.1016/j.gene.2025.149916
Marcelo Arancibia , Jefferson Rojas , M. Leonor Bustamante
Advances in genetics and genomics have transformed our understanding of personality. The observation that personality traits run in families has prompted extensive study into their heritability and underlying genetic architecture. However, there is a significant discrepancy between psychiatric classifications of personality disorders and genomic findings, suggesting a need to reorient these classifications toward a more dimensional, biologically informed perspective. This article reviews key genetic and genomic findings in personality, focusing on the “Big Five” model, which has proven consistency with genomic research. Twin studies estimate heritability accounts for about 40–50 % of personality traits, while the rest of phenotypic variation is explained by the non-shared environment, which influence personality through epigenetic changes. Genome-wide association studies (GWAS) have identified numerous genetic variants on nearly all chromosomes that influence personality traits, particularly neuroticism. These variants are involved in biological pathways such as neurogenesis and neuronal differentiation. GWAS have also revealed significant genetic correlations between personality traits and major psychiatric disorders, supporting a biological continuum between them. This supports the hypothesis which states that a typical behavioral trait is associated with many genetic variants, each contributing a very small effect. Future research should incorporate epigenetic evidence, study genetic interactions, and expand the diversity of study populations beyond European ancestry to improve the generalizability of findings.
{"title":"Heredity and personality: A review of concepts, methods, and evidence","authors":"Marcelo Arancibia , Jefferson Rojas , M. Leonor Bustamante","doi":"10.1016/j.gene.2025.149916","DOIUrl":"10.1016/j.gene.2025.149916","url":null,"abstract":"<div><div>Advances in genetics and genomics have transformed our understanding of personality. The observation that personality traits run in families has prompted extensive study into their heritability and underlying genetic architecture. However, there is a significant discrepancy between psychiatric classifications of personality disorders and genomic findings, suggesting a need to reorient these classifications toward a more dimensional, biologically informed perspective. This article reviews key genetic and genomic findings in personality, focusing on the “Big Five” model, which has proven consistency with genomic research. Twin studies estimate heritability accounts for about 40–50 % of personality traits, while the rest of phenotypic variation is explained by the non-shared environment, which influence personality through epigenetic changes. Genome-wide association studies (GWAS) have identified numerous genetic variants on nearly all chromosomes that influence personality traits, particularly neuroticism. These variants are involved in biological pathways such as neurogenesis and neuronal differentiation. GWAS have also revealed significant genetic correlations between personality traits and major psychiatric disorders, supporting a biological continuum between them. This supports the hypothesis which states that a typical behavioral trait is associated with many genetic variants, each contributing a very small effect. Future research should incorporate epigenetic evidence, study genetic interactions, and expand the diversity of study populations beyond European ancestry to improve the generalizability of findings.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149916"},"PeriodicalIF":2.4,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145603455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-05Epub Date: 2025-11-19DOI: 10.1016/j.gene.2025.149913
Mahamane T. Diakité , Shan Sun , Anou M. Somboro , Brehima Diakité , Amadou Koné , Yaya Kassogué , Djeneba Fofana , Saidou Balam , Cheick B Traoré , Aminata Maiga , Bakarou Kamaté , Djibril Ba , Modibo Diarra , Soungou Boré , Almoustapha I. Maiga , Qi Dai , Drew Robert Nannini , Jane Holl , Robert Murphy , Lifang Hou , Mamoudou Maiga
Aim
To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.
Methods
Shotgun sequencing was performed to characterize participants’ fecal microbiota using Illumina’s HiSeq platform. This case-control study involved newly diagnosed CRC patients (n = 23) prior to any treatment initiation, and unrelated healthy controls (n = 24) to elucidate their microbial diversity and relative abundance.
Results
The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R2 = 0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy.
Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY: aerobactin biosynthesis.
Conclusion
Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.
{"title":"Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study","authors":"Mahamane T. Diakité , Shan Sun , Anou M. Somboro , Brehima Diakité , Amadou Koné , Yaya Kassogué , Djeneba Fofana , Saidou Balam , Cheick B Traoré , Aminata Maiga , Bakarou Kamaté , Djibril Ba , Modibo Diarra , Soungou Boré , Almoustapha I. Maiga , Qi Dai , Drew Robert Nannini , Jane Holl , Robert Murphy , Lifang Hou , Mamoudou Maiga","doi":"10.1016/j.gene.2025.149913","DOIUrl":"10.1016/j.gene.2025.149913","url":null,"abstract":"<div><h3>Aim</h3><div>To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.</div></div><div><h3>Methods</h3><div>Shotgun sequencing was performed to characterize participants’ fecal microbiota using Illumina’s HiSeq platform. This case-control study involved newly diagnosed CRC patients (n = 23) prior to any treatment initiation, and unrelated healthy controls (n = 24) to elucidate their microbial diversity and relative abundance.</div></div><div><h3>Results</h3><div>The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R<sup>2</sup> = 0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy.</div><div>Levels of <em>Pseudomonadota</em>, <em>Escherichia</em>, <em>Citrobacter freundii</em>, <em>Klebsiella</em> sp. <em>LTGPAF-6F</em>, <em>Escherichia albertii, Escherichia coli, Caudovirales</em>, <em>Apicomplexa,</em> and <em>Verrucomicrobiota</em> populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to <em>HEMESYN2-PWY: heme biosynthesis II (anaerobic)</em>, <em>PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline)</em>, <em>FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation</em>, <em>ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis,</em> and <em>AEROBACTINSYN-PWY: aerobactin biosynthesis.</em></div></div><div><h3>Conclusion</h3><div>Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"978 ","pages":"Article 149913"},"PeriodicalIF":2.4,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145573420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ecDNA is a circular DNA extensively present in human cancers, particularly advanced tumors, but rarely detected in healthy cells. Previously, they were named “minute chromatin bodies,” which eventually changed into “Double minutes (DMs)” as they exist in pairs. Due to their structural and epigenetic modifications, they confer specific advantages, helping them to survive and persist within cells. Rapid amplification of drug-resistant genes or oncogenes, increased chromatin accessibility, and non-Mendelian inheritance all contribute significantly to tumor adaptability, aggressiveness, and resistance to drug or chemotherapy treatment. Thus, this review paper aims to discuss DMs’ formation, mechanism, and maintenance, examining the tools used to detect them and investigating the commonly observed oncogenes in different cancer types. Lastly, the therapeutic approaches applied over the years have been to reduce or eliminate DMs in tumor cells.
{"title":"Double minutes: exploring the formation and oncogenic roles in cancer progression","authors":"Mahjabin Sanam, Chowdhury Fatema Tuz Zohra Hossain, Jahin Fairuj Oishi, Reasat Tarannum, Nusrat Zahan Rouf","doi":"10.1016/j.gene.2025.149879","DOIUrl":"10.1016/j.gene.2025.149879","url":null,"abstract":"<div><div>ecDNA is a circular DNA extensively present in human cancers, particularly advanced tumors, but rarely detected in healthy cells. Previously, they were named “minute chromatin bodies,” which eventually changed into “Double minutes (DMs)” as they exist in pairs. Due to their structural and epigenetic modifications, they confer specific advantages, helping them to survive and persist within cells. Rapid amplification of drug-resistant genes or oncogenes, increased chromatin accessibility, and non-Mendelian inheritance all contribute significantly to tumor adaptability, aggressiveness, and resistance to drug or chemotherapy treatment. Thus, this review paper aims to discuss DMs’ formation, mechanism, and maintenance, examining the tools used to detect them and investigating the commonly observed oncogenes in different cancer types. Lastly, the therapeutic approaches applied over the years have been to reduce or eliminate DMs in tumor cells.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"978 ","pages":"Article 149879"},"PeriodicalIF":2.4,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145487869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-05Epub Date: 2025-11-20DOI: 10.1016/j.gene.2025.149910
Lilian de Sá Garcia Landeiro , Pedro Augusto Silva dos Santos Rodrigues , Almirane Lima de Oliveira , Katarina Mattos Brandão , Laryssa Cardoso Calmon , João Victor Andrade Cruz , Mailane dos Anjos Silva , Bruna Ramos Tosta , Ingrid de Marins de Almeida , João Locke Ferreira de Araújo , Thamara Miranda Barbosa dos Santos , Milca de Jesus Silva , Gabriela Pimentel Pinheiro das Chagas , Álvaro Augusto Souza da Cruz Filho , Camila Alexandrina Viana de Figueirêdo , Pablo de Moura Santos , Ryan dos Santos Costa
Objective
Rheumatoid arthritis (RA) is a chronic inflammatory disease that can lead to progressive disability. TNF inhibitors (TNFi) have shown promise in improving disease progression and prognosis; however, only 60% to 70% of patients respond well. Genetic variations have been linked to this therapeutic failure. Genetic variants in the IL17 gene are associated with TNFi therapy responses and RA susceptibility, but few studies have explored this in the Brazilian population. This study assesses variants in the IL-17 pathway (rs763780, rs2275913, rs3819024) in RA patients undergoing TNFi treatment in Salvador, BA. Methods: A total of 497 individuals (294 RA patients, 203 healthy controls) were included. Plasma levels of IL-17, IL-1β, TNF, and other cytokines were measured in a subpopulation. Meta-analysis of published studies was conducted to consolidate associations between IL and 17 variants and RA susceptibility. Results: No significant associations were found between SNVs and RA susceptibility in the cohort, while the meta-analysis revealed protective and risk associations. The rs3819024-G allele was associated with improved TNFi response, particularly in infliximab users, whereas rs2275913-AA carriers had higher risk of treatment.
{"title":"IL17 genetic variants impact the response and safety of TNFi treatment in rheumatoid arthritis patients from Bahia, Brazil","authors":"Lilian de Sá Garcia Landeiro , Pedro Augusto Silva dos Santos Rodrigues , Almirane Lima de Oliveira , Katarina Mattos Brandão , Laryssa Cardoso Calmon , João Victor Andrade Cruz , Mailane dos Anjos Silva , Bruna Ramos Tosta , Ingrid de Marins de Almeida , João Locke Ferreira de Araújo , Thamara Miranda Barbosa dos Santos , Milca de Jesus Silva , Gabriela Pimentel Pinheiro das Chagas , Álvaro Augusto Souza da Cruz Filho , Camila Alexandrina Viana de Figueirêdo , Pablo de Moura Santos , Ryan dos Santos Costa","doi":"10.1016/j.gene.2025.149910","DOIUrl":"10.1016/j.gene.2025.149910","url":null,"abstract":"<div><h3>Objective</h3><div>Rheumatoid arthritis (RA) is a chronic inflammatory disease that can lead to progressive disability. TNF inhibitors (TNFi) have shown promise in improving disease progression and prognosis; however, only 60% to 70% of patients respond well. Genetic variations have been linked to this therapeutic failure. Genetic variants in the IL17 gene are associated with TNFi therapy responses and RA susceptibility, but few studies have explored this in the Brazilian population. This study assesses variants in the IL-17 pathway (rs763780, rs2275913, rs3819024) in RA patients undergoing TNFi treatment in Salvador, BA. Methods: A total of 497 individuals (294 RA patients, 203 healthy controls) were included. Plasma levels of IL-17, IL-1β, TNF, and other cytokines were measured in a subpopulation. Meta-analysis of published studies was conducted to consolidate associations between IL and 17 variants and RA susceptibility. Results: No significant associations were found between SNVs and RA susceptibility in the cohort, while the <em>meta</em>-analysis revealed protective and risk associations. The rs3819024-G allele was associated with improved TNFi response, particularly in infliximab users, whereas rs2275913-AA carriers had higher risk of treatment.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"978 ","pages":"Article 149910"},"PeriodicalIF":2.4,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145577705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}