Prostate cancer poses a significant public health challenge worldwide, and its hereditary forms are increasingly recognized in clinical practice. Pathogenic variants in the BRCA1 and BRCA2 genes contribute to the risk of hereditary prostate cancer, but data from North African populations are still limited. This study examined germline variants in the BRCA1/2 genes in 30 Moroccan patients diagnosed with prostate cancer. Next-generation sequencing was used to analyze the full coding regions and intron-exon boundaries of both genes.
Two deleterious frameshift insertions were identified: BRCA1 c.3514_3515insT and BRCA2 c.4240_4241insA, each detected in two unrelated patients. These gene carriers had high-risk disease (tumor stage ≥ 2 and Gleason score ≥ 7). A BRCA2 variant of uncertain significance (c.681 + 56C > T) was present in almost half of the cohort, alongside several intronic variants and benign polymorphisms. Importantly, almost half of the identified variants were absent from existing North African genomic databases.
These findings provide new insights into the spectrum of BRCA1/2 germline variants in prostate cancer and highlight the need for reference genomic data on ancestry. Broader inclusion of underrepresented populations will be essential to improve variant interpretation and guide precision medicine in hereditary prostate cancer worldwide.
{"title":"Identification of BRCA1/BRCA2 pathogenic variants implicated in prostate cancer by next-generation sequencing","authors":"Khaoula Elghazali , Youssef Ennaji , Abdelilah Laraqui , Ahmed Ameur , Moulay Mustapha Ennaji","doi":"10.1016/j.genrep.2025.102397","DOIUrl":"10.1016/j.genrep.2025.102397","url":null,"abstract":"<div><div>Prostate cancer poses a significant public health challenge worldwide, and its hereditary forms are increasingly recognized in clinical practice. Pathogenic variants in the BRCA1 and BRCA2 genes contribute to the risk of hereditary prostate cancer, but data from North African populations are still limited. This study examined germline variants in the BRCA1/2 genes in 30 Moroccan patients diagnosed with prostate cancer. Next-generation sequencing was used to analyze the full coding regions and intron-exon boundaries of both genes.</div><div>Two deleterious frameshift insertions were identified: BRCA1 c.3514_3515insT and BRCA2 c.4240_4241insA, each detected in two unrelated patients. These gene carriers had high-risk disease (tumor stage ≥ 2 and Gleason score ≥ 7). A BRCA2 variant of uncertain significance (c.681 + 56C > T) was present in almost half of the cohort, alongside several intronic variants and benign polymorphisms. Importantly, almost half of the identified variants were absent from existing North African genomic databases.</div><div>These findings provide new insights into the spectrum of BRCA1/2 germline variants in prostate cancer and highlight the need for reference genomic data on ancestry. Broader inclusion of underrepresented populations will be essential to improve variant interpretation and guide precision medicine in hereditary prostate cancer worldwide.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102397"},"PeriodicalIF":0.9,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733249","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 : 2025-11-26DOI: 10.1016/j.genrep.2025.102393
Surajit Malakar , Tathagata Das , Tamali Halder , Vikrant Yadav , Anurag Sahu , Parimal Das
Background
Alexander disease (AxD) is a rare, progressive and fatal neurological disorder characterized by degeneration of the white matter of the brain accompanied by the formation of Rosenthal fibers, distinct cytoplasmic inclusion within astrocytes (non-neuronal cells) in the brain. The disease phenotype is commonly identified to be associated with heterozygous de novo variation in the Glial Fibrillary Acidic Protein (GFAP) gene. Rare instances of familial AxD have also been reported with genetic anticipation.
Methods and result
The study aimed to determine the genetic cause of a clinically diagnosed case of juvenile AxD from India with macrocephaly and psychomotor delay, followed by regression, spastic paraparesis, and feeding difficulties. DNA was extracted from peripheral blood sample and was taken for whole-exome-sequencing. Two pathogenic heterozygous missense variations were identified in GFAP, the potential candidate for AxD (c.626G > A leading to p.R209Q and c.983 T > C leading to p.L328P), notably, p.L328P is being reported here first time. The karyotype of the proband revealed no chromosomal anomalies. Following confirmation by Sanger sequencing, variants including their cumulative effect in Double Mutant were characterized in silico for prediction of pathogenicity, protein stability, physiochemical analysis, molecular simulation, principal component analysis and molecular docking. Collectively, these findings reveal both compensatory and synergistic effects that may influence intermediate filament dynamics and related signaling pathways.
Conclusion
This altered GFAP protein gets accumulated in the cytoplasm of the astrocyte cells, leading to the formation of Rosenthal fibers, which impairs cell function. While in silico analysis supports the pathogenic nature of the studied variants, which is consistent with the observed AxD pathophysiology in the current study.
{"title":"Computational exploration of novel (p.L328P) and reported (p.R209Q) variants identified in Glial Fibrillary Acidic Protein (GFAP) gene in a patient with Alexander disease from India","authors":"Surajit Malakar , Tathagata Das , Tamali Halder , Vikrant Yadav , Anurag Sahu , Parimal Das","doi":"10.1016/j.genrep.2025.102393","DOIUrl":"10.1016/j.genrep.2025.102393","url":null,"abstract":"<div><h3>Background</h3><div>Alexander disease (AxD) is a rare, progressive and fatal neurological disorder characterized by degeneration of the white matter of the brain accompanied by the formation of Rosenthal fibers, distinct cytoplasmic inclusion within astrocytes (non-neuronal cells) in the brain. The disease phenotype is commonly identified to be associated with heterozygous <em>de novo</em> variation in the Glial Fibrillary Acidic Protein (<em>GFAP</em>) gene. Rare instances of familial AxD have also been reported with genetic anticipation.</div></div><div><h3>Methods and result</h3><div>The study aimed to determine the genetic cause of a clinically diagnosed case of juvenile AxD from India with macrocephaly and psychomotor delay, followed by regression, spastic paraparesis, and feeding difficulties. DNA was extracted from peripheral blood sample and was taken for whole-exome-sequencing. Two pathogenic heterozygous missense variations were identified in <em>GFAP,</em> the potential candidate for AxD (c.626G > A leading to p.R209Q and c.983 T > C leading to p.L328P), notably, p.L328P is being reported here first time. The karyotype of the proband revealed no chromosomal anomalies. Following confirmation by Sanger sequencing, variants including their cumulative effect in Double Mutant were characterized <em>in silico</em> for prediction of pathogenicity, protein stability, physiochemical analysis, molecular simulation, principal component analysis and molecular docking. Collectively, these findings reveal both compensatory and synergistic effects that may influence intermediate filament dynamics and related signaling pathways.</div></div><div><h3>Conclusion</h3><div>This altered GFAP protein gets accumulated in the cytoplasm of the astrocyte cells, leading to the formation of Rosenthal fibers, which impairs cell function. While <em>in silico</em> analysis supports the pathogenic nature of the studied variants, which is consistent with the observed AxD pathophysiology in the current study.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102393"},"PeriodicalIF":0.9,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145621827","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 : 2025-11-26DOI: 10.1016/j.genrep.2025.102391
İpek Kuşcu Özücer , Alper Alnak , Hilal Akköprü , Zeynep Nur Karadoğan , Ahmet Okay Çağlayan , Saliha B. Selman , Murat Coskun
Background
Trimethyllysine Hydroxylase, Epsilon (TMLHE) gene mutations have been clinically associated with an increased risk of autism spectrum disorder (ASD). This study aimed to evaluate the peripheral expression profile of the TMLHE gene and its association with ASD phenotype in a clinical sample of youth diagnosed with ASD.
Methods
The study sample included 205 participants (ASD: n = 100; controls: n = 105, Mage = 9.25 years, SD = 3.74). The Childhood Autism Rating Scale and the Aberrant Behavior Checklist were administered to assess the severity of ASD and associated symptoms. Peripheral blood samples were collected from all participants, and TMLHE gene expression levels were analyzed using quantitative reverse transcription PCR (RT-qPCR).
Results
TMLHE gene expression was significantly downregulated in the ASD group compared to controls (p < .001). Notably, significant correlations were identified between TMLHE expression levels and the CARS subscales for object use (p = .043) and listening response (p = .038).
Conclusion
This study represents the first case-control investigation of peripheral TMLHE gene expression in ASD, revealing that TMLHE expression is reduced in children with ASD compared to typically developing peers. These findings contribute to a deeper understanding of the potential implications of TMLHE gene mutations in the etiology of ASD.
{"title":"Reduction in peripheral expression of the TMLHE gene in Turkish youth with autism spectrum disorder","authors":"İpek Kuşcu Özücer , Alper Alnak , Hilal Akköprü , Zeynep Nur Karadoğan , Ahmet Okay Çağlayan , Saliha B. Selman , Murat Coskun","doi":"10.1016/j.genrep.2025.102391","DOIUrl":"10.1016/j.genrep.2025.102391","url":null,"abstract":"<div><h3>Background</h3><div>Trimethyllysine Hydroxylase, Epsilon (<em>TMLHE</em>) gene mutations have been clinically associated with an increased risk of autism spectrum disorder (ASD). This study aimed to evaluate the peripheral expression profile of the <em>TMLHE</em> gene and its association with ASD phenotype in a clinical sample of youth diagnosed with ASD.</div></div><div><h3>Methods</h3><div>The study sample included 205 participants (ASD: <em>n</em> = 100; controls: <em>n</em> = 105, <em>M</em><sub><em>age</em></sub> = 9.25 years, <em>SD</em> = 3.74). The Childhood Autism Rating Scale and the Aberrant Behavior Checklist were administered to assess the severity of ASD and associated symptoms. Peripheral blood samples were collected from all participants, and <em>TMLHE</em> gene expression levels were analyzed using quantitative reverse transcription PCR (RT-qPCR).</div></div><div><h3>Results</h3><div><em>TMLHE</em> gene expression was significantly downregulated in the ASD group compared to controls (<em>p</em> < .001). Notably, significant correlations were identified between <em>TMLHE</em> expression levels and the CARS subscales for object use (<em>p</em> = .043) and listening response (<em>p</em> = .038).</div></div><div><h3>Conclusion</h3><div>This study represents the first case-control investigation of peripheral <em>TMLHE</em> gene expression in ASD, revealing that <em>TMLHE</em> expression is reduced in children with ASD compared to typically developing peers. These findings contribute to a deeper understanding of the potential implications of <em>TMLHE</em> gene mutations in the etiology of ASD.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102391"},"PeriodicalIF":0.9,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681586","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}
Epigenetic modifications, such as DNA methylation, histone modifications, and non-coding RNA regulation, have attracted attention as potential cancer therapy targets. Breast cancer is heavily influenced by epigenetic dysregulation (e.g., BRCA1/2 tumor suppressor genes deactivation) alongside genetic and environmental factors. Dietary flavonoids in fruits and vegetables, such as genistein, epigallocatechin gallate, luteolin, and hesperidin, have been shown to regulate epigenetic pathways by reversing these aberrations. The motive of this systematic review is to evaluate studies reporting flavonoid-induced epigenetic changes in breast cancer and their potential to overcome therapy resistance. A systematic search was conducted across PubMed, Scopus, Web of Science, and Cochrane from inception to February 2025, identifying 550 studies. Studies were selected based on their focus on selected flavonoids, use of in vivo or in vitro experiments, and breast cancer models. Ultimately, 48 eligible studies were included for qualitative synthesis, in which genistein (24 studies) and EGCG (19 studies) were the most extensively investigated; these compounds demonstrated consistent demethylation effects and regulation of histone and microRNA expression, whereas luteolin (7 studies) and hesperidin (2 studies) showed preliminary yet promising outcomes. Most of the studies show robust preclinical data with low bias (45/48 studies) across diverse models; however, there are bioavailability challenges and limited studies on epigenetic effects of hesperidin and luteolin. The chemopreventive role and synergistic potentials with conventional agents support flavonoids as potential complementary therapies for breast cancer, though further clinical validation and strategies for bioavailability optimization are merited.
表观遗传修饰，如DNA甲基化、组蛋白修饰和非编码RNA调控，作为潜在的癌症治疗靶点引起了人们的关注。乳腺癌在很大程度上受表观遗传失调（如BRCA1/2肿瘤抑制基因失活）以及遗传和环境因素的影响。饮食中的类黄酮水果和蔬菜，如染料木素、表没食子儿茶素没食子酸酯、木犀草素和橙皮苷，已被证明通过逆转这些畸变来调节表观遗传途径。本系统综述的目的是评估报道类黄酮诱导的乳腺癌表观遗传变化及其克服治疗耐药的潜力的研究。系统检索了PubMed、Scopus、Web of Science和Cochrane从成立到2025年2月的550项研究。研究的选择是基于它们对选定的类黄酮的关注，体内或体外实验的使用以及乳腺癌模型。最终，48项符合条件的研究被纳入定性合成，其中染料木素（24项研究）和EGCG（19项研究）被研究得最广泛；这些化合物显示出一致的去甲基化作用和组蛋白和microRNA表达的调节，而木犀草素（7项研究）和橙皮苷（2项研究）显示了初步但有希望的结果。大多数研究在不同模型中显示了低偏倚的可靠临床前数据（45/48项研究）；然而，橙皮苷和木犀草素的表观遗传效应存在生物利用度方面的挑战和有限的研究。化学预防作用和与传统药物的协同作用支持黄酮类化合物作为乳腺癌的潜在补充疗法，尽管需要进一步的临床验证和生物利用度优化策略。
{"title":"The role of epigenetic alterations induced by genistein, EGCG, luteolin, and hesperidin in breast cancer: A systematic review","authors":"Amirhossein Rajabalinejad , Mahsa Jalili , Rasool Rajabi , Maryam Nazari","doi":"10.1016/j.genrep.2025.102394","DOIUrl":"10.1016/j.genrep.2025.102394","url":null,"abstract":"<div><div>Epigenetic modifications, such as DNA methylation, histone modifications, and non-coding RNA regulation, have attracted attention as potential cancer therapy targets. Breast cancer is heavily influenced by epigenetic dysregulation (<em>e.g.</em>, BRCA1/2 tumor suppressor genes deactivation) alongside genetic and environmental factors. Dietary flavonoids in fruits and vegetables, such as genistein, epigallocatechin gallate, luteolin, and hesperidin, have been shown to regulate epigenetic pathways by reversing these aberrations. The motive of this systematic review is to evaluate studies reporting flavonoid-induced epigenetic changes in breast cancer and their potential to overcome therapy resistance. A systematic search was conducted across PubMed, Scopus, Web of Science, and Cochrane from inception to February 2025, identifying 550 studies. Studies were selected based on their focus on selected flavonoids, use of <em>in vivo</em> or <em>in vitro</em> experiments, and breast cancer models. Ultimately, 48 eligible studies were included for qualitative synthesis, in which genistein (24 studies) and EGCG (19 studies) were the most extensively investigated; these compounds demonstrated consistent demethylation effects and regulation of histone and microRNA expression, whereas luteolin (7 studies) and hesperidin (2 studies) showed preliminary yet promising outcomes. Most of the studies show robust preclinical data with low bias (45/48 studies) across diverse models; however, there are bioavailability challenges and limited studies on epigenetic effects of hesperidin and luteolin. The chemopreventive role and synergistic potentials with conventional agents support flavonoids as potential complementary therapies for breast cancer, though further clinical validation and strategies for bioavailability optimization are merited.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102394"},"PeriodicalIF":0.9,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145621825","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 : 2025-11-25DOI: 10.1016/j.genrep.2025.102386
Md Abu Hanif, Yusin Cho, Shaharior Hossen, Kang Hee Kho
The proteins of the 14-3-3 family participate in diverse biological events by regulating diverse cell signaling pathways and the formation of protein-protein interactions. To understand the potential growth regulatory role of the 14-3-3 gene, the cDNA encoding Lv14-3-3ζ was isolated and characterized, and its tissue and growth-specific expression was analyzed in the Pacific white shrimp, Litopenaeus vannamei. The Lv14-3-3ζ cDNA was 2260 bp in length, containing a 741 bp open reading frame (ORF) encoding 246 putative amino acid residues flanked by a 75 bp 5′ untranslated region (UTR) and a 1443 bp 3′ UTR. Structurally, Lv14-3-3ζ is intronless and binds C-RAF phosphopeptide and fusicoccin ligands. Although this protein is predicted to have protein-succinylysine desuccinylase activity and protein-specific binding activity based on gene ontology, Lv14-3-3ζ is a multifunctional protein that interacts with diverse known and unknown proteins. Lv14-3-3ζ showed differential expression in tissue samples of the Pacific white shrimp, with the highest abundance in the digestive gland (p < 0.001), followed by lower expression in the ovary, intestine, and muscle, and low levels in the heart, nerve cord, and gill. A decreasing expression pattern of Lv14-3-3ζ was exhibited by slow to rapid-growth individuals, whereas myosin heavy chain (MHC) showed an increasing expression trend. The results of the present study provide comprehensive information on Lv14-3-3ζ gene, its structure and highlight its potential as a growth regulator in the Pacific white shrimp.
{"title":"Molecular insights and growth type-specific expression of Lv14-3-3ζ in the Pacific white shrimp, Litopenaeus vannamei","authors":"Md Abu Hanif, Yusin Cho, Shaharior Hossen, Kang Hee Kho","doi":"10.1016/j.genrep.2025.102386","DOIUrl":"10.1016/j.genrep.2025.102386","url":null,"abstract":"<div><div>The proteins of the 14-3-3 family participate in diverse biological events by regulating diverse cell signaling pathways and the formation of protein-protein interactions. To understand the potential growth regulatory role of the 14-3-3 gene, the cDNA encoding <em>Lv</em>14-3-3ζ was isolated and characterized, and its tissue and growth-specific expression was analyzed in the Pacific white shrimp, <em>Litopenaeus vannamei</em>. The <em>Lv</em>14-3-3ζ cDNA was 2260 bp in length, containing a 741 bp open reading frame (ORF) encoding 246 putative amino acid residues flanked by a 75 bp 5′ untranslated region (UTR) and a 1443 bp 3′ UTR. Structurally, <em>Lv</em>14-3-3ζ is intronless and binds C-RAF phosphopeptide and fusicoccin ligands. Although this protein is predicted to have protein-succinylysine desuccinylase activity and protein-specific binding activity based on gene ontology, <em>Lv</em>14-3-3ζ is a multifunctional protein that interacts with diverse known and unknown proteins. <em>Lv</em>14-3-3ζ showed differential expression in tissue samples of the Pacific white shrimp, with the highest abundance in the digestive gland (<em>p</em> < 0.001), followed by lower expression in the ovary, intestine, and muscle, and low levels in the heart, nerve cord, and gill. A decreasing expression pattern of <em>Lv</em>14-3-3ζ was exhibited by slow to rapid-growth individuals, whereas myosin heavy chain (MHC) showed an increasing expression trend. The results of the present study provide comprehensive information on <em>Lv</em>14-3-3ζ gene, its structure and highlight its potential as a growth regulator in the Pacific white shrimp.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102386"},"PeriodicalIF":0.9,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145621831","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 : 2025-11-24DOI: 10.1016/j.genrep.2025.102392
Hadis Nazeri , Amin Talebi Bezmin Abadi , Abbas Ali Imani Fooladi , Farid Rahimi
Acinetobacter baumannii is a leading cause of hospital-acquired infections and characterized by multidrug resistance and different virulence mechanisms. We aimed to characterize the antibiotic susceptibility profiles of A. baumannii in clinical isolates collected between 2022 and 2024. We confirmed A. baumannii by polymerase chain reaction (PCR) targeting 16S rRNA in fifty samples which included tracheal aspirates, urine, blood, wound, sputum, bronchoalveolar lavage, and ascitic fluid. We tested antibiotic susceptibility according to the 2022 guidelines of the Clinical and Laboratory Standards Institute and screened for resistance genes blaOXA-23-like, blaOXA-24-like, and blaOXA-58-like by PCR. We used reverse transcription quantitative PCR of 20 representative samples in duplicates to profile pilA and csuD expression, normalized to 16S rRNA. csuD expression was higher in the target group than in controls, while pilA was only slightly increased; however, neither difference was statistically significant (P = 0.123 and P = 0.554, respectively), showing no meaningful differences among groups. Our findings highlight the importance of pili and chaperone–usher genes (PilA and CsuD) as they function in biofilm formation and adherence. Continually surveying for resistance and virulence factors is essential for guiding treatment strategies against carbapenem-resistant A. baumannii.
{"title":"Investigating the expression of virulence genes pilA and csuD of Acinetobacter baumannii in patients' samples in Tehran, Iran","authors":"Hadis Nazeri , Amin Talebi Bezmin Abadi , Abbas Ali Imani Fooladi , Farid Rahimi","doi":"10.1016/j.genrep.2025.102392","DOIUrl":"10.1016/j.genrep.2025.102392","url":null,"abstract":"<div><div><em>Acinetobacter baumannii</em> is a leading cause of hospital-acquired infections and characterized by multidrug resistance and different virulence mechanisms. We aimed to characterize the antibiotic susceptibility profiles <em>of A. baumannii</em> in clinical isolates collected between 2022 and 2024. We confirmed <em>A. baumannii</em> by polymerase chain reaction (PCR) targeting <em>16S rRNA</em> in fifty samples which included tracheal aspirates, urine, blood, wound, sputum, bronchoalveolar lavage, and ascitic fluid. We tested antibiotic susceptibility according to the 2022 guidelines of the Clinical and Laboratory Standards Institute and screened for resistance genes <em>bla</em><sub><em>OXA-23-like</em></sub><em>, bla</em><sub><em>OXA-24-like</em></sub><em>, and bla</em><sub><em>OXA-58-like</em></sub> by PCR. We used reverse transcription quantitative PCR of 20 representative samples in duplicates to profile <em>pilA</em> and <em>csuD</em> expression, normalized to <em>16S rRNA</em>. <em>csuD</em> expression was higher in the target group than in controls, while <em>pilA</em> was only slightly increased; however, neither difference was statistically significant (<em>P</em> = 0.123 and <em>P</em> = 0.554, respectively), showing no meaningful differences among groups. Our findings highlight the importance of pili and chaperone–usher genes (<em>PilA and CsuD</em>) as they function in biofilm formation and adherence. Continually surveying for resistance and virulence factors is essential for guiding treatment strategies against carbapenem-resistant <em>A. baumannii</em>.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102392"},"PeriodicalIF":0.9,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681582","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 : 2025-11-20DOI: 10.1016/j.genrep.2025.102390
Lucas Miguel de Carvalho , Bárbara Regina Bazzo , Camila Carlos-Shanley , Carlos Augusto Colombo , Gonçalo Amarante Guimarães Pereira , Marcelo Falsarella Carazzolle
The macauba palm (Acrocomia aculeata) is an emerging oilseed species with promising applications in biodiesel production, as well as in food and cosmetic industries. Native to the Neotropics, it is in the early stages of domestication and distributed across diverse environments and edaphoclimatic conditions. However, genomic studies of macauba are limited due to the scarcity of publicly available sequence data, as it is considered a non-model plant. In this study, we present an exploratory analysis of a transcriptome dataset comprising seven different organs (roots, bulbs, male and female flowers, leaves, leaf sheath, and fruits). A total of 22,703 transcripts were assembled into a single reference dataset. Of these, 9729 transcripts (42.85 %) were annotated using KEGG orthology. Gene expression profiling revealed 306, 32, 41, 67, 92, 158 and 916 organ-specific transcripts in leaves, leaf sheaths, bulbs, female flower, male flower, fruit and root, respectively. Comparative analysis with oil palm (Elaeis guineensis) and date palm (Phoenix dactylifera) revealed 55 gene families exclusive to macauba palm. In addition, 221 transcripts related to drought stress were identified through functional annotation and grouped into 112 gene families. Root libraries revealed 7091 fungal transcripts - approximately 3.9 % of all reads – mainly derived from arbuscular mycorrhizal fungi (AMF) Rhizophagus spp. These findings highlight the central role of signal transduction pathways in response to environmental stresses in macauba palm. The transcriptome dataset generated in this study provides a valuable genomic resource for future genotype-phenotype investigations in macauba palm. Furthermore, the presence of AMF-associated transcripts suggests a potentially important role for these symbiotic fungi in macauba palm growth and development.
{"title":"A transcriptomic atlas of macauba palm reveals organ-specific gene expression and stress-related pathways","authors":"Lucas Miguel de Carvalho , Bárbara Regina Bazzo , Camila Carlos-Shanley , Carlos Augusto Colombo , Gonçalo Amarante Guimarães Pereira , Marcelo Falsarella Carazzolle","doi":"10.1016/j.genrep.2025.102390","DOIUrl":"10.1016/j.genrep.2025.102390","url":null,"abstract":"<div><div>The macauba palm (<em>Acrocomia aculeata</em>) is an emerging oilseed species with promising applications in biodiesel production, as well as in food and cosmetic industries. Native to the Neotropics, it is in the early stages of domestication and distributed across diverse environments and edaphoclimatic conditions. However, genomic studies of macauba are limited due to the scarcity of publicly available sequence data, as it is considered a non-model plant. In this study, we present an exploratory analysis of a transcriptome dataset comprising seven different organs (roots, bulbs, male and female flowers, leaves, leaf sheath, and fruits). A total of 22,703 transcripts were assembled into a single reference dataset. Of these, 9729 transcripts (42.85 %) were annotated using KEGG orthology. Gene expression profiling revealed 306, 32, 41, 67, 92, 158 and 916 organ-specific transcripts in leaves, leaf sheaths, bulbs, female flower, male flower, fruit and root, respectively. Comparative analysis with oil palm (<em>Elaeis guineensis</em>) and date palm (<em>Phoenix dactylifera</em>) revealed 55 gene families exclusive to macauba palm. In addition, 221 transcripts related to drought stress were identified through functional annotation and grouped into 112 gene families. Root libraries revealed 7091 fungal transcripts - approximately 3.9 % of all reads – mainly derived from arbuscular mycorrhizal fungi (AMF) Rhizophagus spp. These findings highlight the central role of signal transduction pathways in response to environmental stresses in macauba palm. The transcriptome dataset generated in this study provides a valuable genomic resource for future genotype-phenotype investigations in macauba palm. Furthermore, the presence of AMF-associated transcripts suggests a potentially important role for these symbiotic fungi in macauba palm growth and development.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102390"},"PeriodicalIF":0.9,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145621828","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}
TBC1D32 gene has a role in ciliary function and Sonic Hedgehog signaling. Pathogenic variants within this gene have been associated with hypopituitarism, ciliopathy and a range of dysmorphic features. Here, we used whole exome sequencing to find the molecular basis of dysmorphic features in a patient who presented with craniofacial phenotypes, intellectual disability, and growth hormone deficiency. Our results show that the patient carried a novel variant in the intron 27 of TBC1D32 gene (c.3054-2A > T). Based on the ACMG criteria, it is likely pathogenic. Thus, the current study broadens the spectrum of TBC1D32-related phenotypes.
{"title":"Whole-exome sequencing identifies a novel splicing variant within TBC1D32 causing dysmorphic features and growth hormone deficiency","authors":"Milad Gholami , Mahshid Fattahi , Dorsa Rostampour , Saeedeh Sadat Mir-Abdolhagh , Maryam Maktabi , Soudeh Ghafouri-Fard","doi":"10.1016/j.genrep.2025.102389","DOIUrl":"10.1016/j.genrep.2025.102389","url":null,"abstract":"<div><div><em>TBC1D32</em> gene has a role in ciliary function and Sonic Hedgehog signaling. Pathogenic variants within this gene have been associated with hypopituitarism, ciliopathy and a range of dysmorphic features. Here, we used whole exome sequencing to find the molecular basis of dysmorphic features in a patient who presented with craniofacial phenotypes, intellectual disability, and growth hormone deficiency. Our results show that the patient carried a novel variant in the intron 27 of <em>TBC1D32</em> gene (c.3054-2A > T). Based on the ACMG criteria, it is likely pathogenic. Thus, the current study broadens the spectrum of <em>TBC1D32</em>-related phenotypes.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102389"},"PeriodicalIF":0.9,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145621829","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}
The etiology of malocclusion is multifactorial. The genetic basis of the development of malocclusion is well established in the literature. Therefore, this systematic review aims to evaluate the genetic basis underlying the development of malocclusion.
Material and methods
Several renowned electronic databases were searched with predefined eligibility criteria. Two independent reviewers performed the study selection and data extraction process. The JBI critical appraisal tool was used to evaluate the quality of the included studies.
Results
After a rigorous selection process, a total of 19 studies met all criteria and were included in the systematic review. We observed that the notable genes, such as MYO1H, ADAMTS1, DLX6, and VDR, have shown consistent associations with specific malocclusion subtypes.
Conclusion
The results of the present study pave the way for incorporating genetic insights into clinical orthodontics, particularly for conditions like primary failure of eruption and syndromic malocclusions.
{"title":"Genes to jaws: A systematic review uncovering the role of genetics in malocclusion","authors":"T.P. Chaturvedi , Riddhi Mishra , Vipul Kumar Sharma , A.V. Aparna , Sakshee Nagvanshi","doi":"10.1016/j.genrep.2025.102388","DOIUrl":"10.1016/j.genrep.2025.102388","url":null,"abstract":"<div><h3>Background</h3><div>The etiology of malocclusion is multifactorial. The genetic basis of the development of malocclusion is well established in the literature. Therefore, this systematic review aims to evaluate the genetic basis underlying the development of malocclusion.</div></div><div><h3>Material and methods</h3><div>Several renowned electronic databases were searched with predefined eligibility criteria. Two independent reviewers performed the study selection and data extraction process. The JBI critical appraisal tool was used to evaluate the quality of the included studies.</div></div><div><h3>Results</h3><div>After a rigorous selection process, a total of 19 studies met all criteria and were included in the systematic review. We observed that the notable genes, such as MYO1H, ADAMTS1, DLX6, and VDR, have shown consistent associations with specific malocclusion subtypes.</div></div><div><h3>Conclusion</h3><div>The results of the present study pave the way for incorporating genetic insights into clinical orthodontics, particularly for conditions like primary failure of eruption and syndromic malocclusions.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102388"},"PeriodicalIF":0.9,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145621832","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}
Pattern recognition receptors (PRRs) of the innate immune system potentially detect pathogen-associated molecular patterns (PAMPs) following viral invasion. While some Toll-like receptors (TLRs) offer protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, various studies suggest that Toll-like Receptor 2 (TLR2) activity is linked to heightened inflammatory responses and severe disease outcomes.
Methods
This study investigated two TLR2 single-nucleotide polymorphisms (SNPs), rs5743708 and rs3804099, using polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) in patients with mild and severe COVID-19.
Results
Genotypic and allelic analyses revealed no statistically significant differences between severity groups. However, rs3804099 showed a significant association with creatinine and sodium levels in severe COVID-19 patients—creatinine differed between CT and TT genotypes, and sodium between CT and CC genotypes. Previous evidence associates this polymorphism with proteinuria after kidney transplantation, suggesting a role in renal homeostasis.
Conclusion
Our findings raise the possibility that rs3804099 may serve as a genetic marker for susceptibility to renal dysfunction and electrolyte imbalance during COVID-19, extending the clinical relevance of TLR2 polymorphisms beyond inflammatory signaling.
{"title":"Impact of genetic variants TLR2 rs5743708 and rs3804099 on the susceptibility of individuals to severe coronavirus disease 2019","authors":"Maryam Noroozi , Kamran Heidarnejad , Reza Shafiei , Reza Shahbazi , Kurosh Kalantar , Mona Fani","doi":"10.1016/j.genrep.2025.102384","DOIUrl":"10.1016/j.genrep.2025.102384","url":null,"abstract":"<div><h3>Background</h3><div>Pattern recognition receptors (PRRs) of the innate immune system potentially detect pathogen-associated molecular patterns (PAMPs) following viral invasion. While some Toll-like receptors (TLRs) offer protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, various studies suggest that Toll-like Receptor 2 (TLR2) activity is linked to heightened inflammatory responses and severe disease outcomes.</div></div><div><h3>Methods</h3><div>This study investigated two TLR2 single-nucleotide polymorphisms (SNPs), rs5743708 and rs3804099, using polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) in patients with mild and severe COVID-19.</div></div><div><h3>Results</h3><div>Genotypic and allelic analyses revealed no statistically significant differences between severity groups. However, rs3804099 showed a significant association with creatinine and sodium levels in severe COVID-19 patients—creatinine differed between CT and TT genotypes, and sodium between CT and CC genotypes. Previous evidence associates this polymorphism with proteinuria after kidney transplantation, suggesting a role in renal homeostasis.</div></div><div><h3>Conclusion</h3><div>Our findings raise the possibility that rs3804099 may serve as a genetic marker for susceptibility to renal dysfunction and electrolyte imbalance during COVID-19, extending the clinical relevance of TLR2 polymorphisms beyond inflammatory signaling.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"42 ","pages":"Article 102384"},"PeriodicalIF":0.9,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145621338","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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