Genes最新文献

{"title":"Fossil or Non-Fossil: A Case Study in the Archaeological Wheat <i>Triticum parvicoccum</i> (Poaceae: Triticeae).","authors":"Diego Rivera, P Pablo Ferrer-Gallego, Concepción Obón, Francisco Alcaraz, Emilio Laguna, Nikolay P Goncharov, Mordechai Kislev","doi":"10.3390/genes16030274","DOIUrl":"10.3390/genes16030274","url":null,"abstract":"<p><strong>Background/objectives: </strong>The archaeobotanical taxon \"<i>Triticum parvicoccum</i>\" was first described in 1980 as a small-grained, naked, free-threshing, and dense ear tetraploid wheat species (2<i>n</i> = 4<i>x</i> = 28) identified from archaeological remains. This primitive tetraploid, cultivated in the Levant approximately 9000 years ago and subsequently dispersed throughout the Fertile Crescent, represents a potential contributor of the BBAA genomes to <i>T. aestivum</i>. This study aims to resolve the complex nomenclatural status of this taxon, which has remained ambiguous due to competing interpretations under fossil and non-fossil taxonomic regulations.</p><p><strong>Methods: </strong>We conducted a comprehensive nomenclatural review to evaluate the taxonomic validity of <i>T. parvicoccum</i>, analyzing previous research on the classification of archaeobotanical materials in relation to fossil status.</p><p><strong>Results: </strong>Our analysis demonstrated that archaeobotanical materials do not qualify as fossils and led to the validation of the taxon at a subspecific rank as a non-fossil entity: <i>T. turgidum</i> subsp. <i>parvicoccum</i> Kislev. subsp. nov. The holotype was established using a charred rachis fragment from Timnah (Tel Batash), an archaeological site on the inner Coastal Plain (Shfela) adjacent to the western piedmont of the Judean Mountains, Israel.</p><p><strong>Conclusions: </strong>This study resolves the longstanding nomenclatural uncertainty surrounding this archaeologically significant wheat taxon, providing a valid taxonomic designation that reflects its biological and historical importance while adhering to current botanical nomenclature standards.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Exploratory Genomic and Transcriptomic Analysis Between <i>Choloepus didactylus</i> and <i>Homo sapiens</i>.","authors":"Ariella Baran, Antony Ibrahim, Yuka Nakano, Hideyuki Aoshima, Takeshi Ozeki, Iri Sato-Baran, David D Ordinario","doi":"10.3390/genes16030272","DOIUrl":"10.3390/genes16030272","url":null,"abstract":"<p><p><i>Background/Objectives:</i> Sloths, a group of xenarthran mammals currently comprising six recognized distinct species, have been the focus of much physiological animal research due to their extremely slow metabolisms, deliberate movements, and their status as a species relatively unchanged for over 26 million years. However, despite all the effort aimed at understanding these unique characteristics, the sloth genome remains largely unexplored. Due to the link between genetics and observed traits, such an investigation could potentially lead to insights regarding the genetic basis of unique sloth behaviors and characteristics, such as slow movement, low metabolism, and longevity. <i>Methods:</i> In this exploratory investigation, we performed whole genomic and transcriptomic analysis of a female <i>Choloepus didactylus</i> (Linnaeus's Two-Toed Sloth). Through whole genome sequencing (WGS), the genetic overlap between female two-toed sloths and female humans was estimated in line with evolutionary biology. <i>Results:</i> Transcriptome analysis of peripheral blood mononuclear cells (PBMCs) showed significant differences between gene expression levels in two-toed sloths and humans related to metabolism, body temperature control, cell cycle regulation, telomere maintenance, circadian rhythm regulation, and cancer prevention. <i>Conclusions:</i> The discovered differences imply a relationship to the low metabolisms, slow movements, and longevity displayed by sloths. Future exploratory research will include additional testing to determine if these findings are universal among all recognized sloth species, as well as to address the relationship between specific gene and protein functions and observed traits.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the Role of <i>IRF6</i> in Perinatal Arterial Ischemic Stroke: A Case of a Newborn with Craniofacial Malformations.","authors":"Lorenzo Perilli, Simona Negro, Samanta Carbone, Michele Minerva, Maria Rosaria Curcio, Federica Lotti, Maria Antonietta Mencarelli, Francesca Ariani, Alessandra Renieri, Barbara Tomasini, Salvatore Grosso","doi":"10.3390/genes16030271","DOIUrl":"10.3390/genes16030271","url":null,"abstract":"<p><p><b>Background/Objectives:</b> Ischemic arterial stroke (AIS) is a cerebrovascular event that can occur acutely within the first hours or days of life, presenting as a neurological emergency. To date, clearly defined genetic risk factors for AIS have not been established, although certain genes involved in cerebrovascular regulation mechanisms are suspected to play a role. The Interferon Regulatory Factor 6 (<i>IRF6</i>) gene is a transcription factor involved in craniofacial and epidermal development. Recently, pathogenic variants of <i>IRF6</i> have been implicated in the cytoprotective pathway of ischemic cerebrovascular disease. The aim of this manuscript is to further support the already-reported association between <i>IRF6</i> and AIS. <b>Materials and Methods</b>: Genetic counseling and exome sequencing analysis were conducted for diagnostic purposes. <b>Results</b>: We report the case of a female newborn with palatoschisis, cleft palate, sensorineural deafness, facial dysmorphisms, and cutaneous defects who suffered an ischemic stroke in the territory of the left middle cerebral artery on day 1 of life. Family and pregnancy histories revealed no identifiable risk factors, and coagulation studies were normal. Exome sequencing identified a de novo c.1124T>C (p.Phe375Ser) variant in the <i>IRF6</i> gene. The child developed right spastic hemiplegia and began motor rehabilitation therapy. Recently, a genome-wide association study (GWAS) using m6A-SNPs identified a statistical association between AIS and a single nucleotide polymorphism (SNP) that influences the expression of the <i>IRF6</i> gene as an expression quantitative trait locus (eQTL). <b>Conclusions</b>: To our knowledge, this is the first report of neonatal ischemic stroke in a child carrying a de novo <i>IRF6</i> pathogenic variant, further supporting its potential role as a genetic factor influencing cerebrovascular events. Further studies are needed to elucidate the precise relationship between IRF6 and AIS.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941822/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical Implications of Cell-Free DNA in Managing <i>BRAF</i> V600E Mutation-Positive Colorectal Cancer.","authors":"Takuma Iwai, Takeshi Yamada, Kay Uehara, Seiichi Shinji, Akihisa Matsuda, Yasuyuki Yokoyama, Goro Takahashi, Toshimitsu Miyasaka, Hiroshi Yoshida","doi":"10.3390/genes16030275","DOIUrl":"10.3390/genes16030275","url":null,"abstract":"<p><p><b>Background/Objectives:</b><i>BRAF</i>^V600E-mutant colorectal cancer (CRC) is associated with poor prognosis, and despite the introduction of BEACON therapy, significant treatment challenges remain. This study investigates the clinical utility of <i>BRAF</i>^V600E in cell-free DNA (cfDNA <i>BRAF</i>^V600E) as a biomarker for real-time treatment monitoring in metastatic cases and for evaluating minimal residual disease (MRD) after curative resection. <b>Methods</b>: This single-center, prospective observational study included 37 patients with <i>BRAF</i>^V600E-mutant CRC treated at Nippon Medical School Hospital between April 2017 and June 2024. Patients were divided into two cohorts: Cohort 1 (Stage IV cases): Evaluated cfDNA <i>BRAF</i>^V600E for treatment monitoring. Cohort 2 (Stage I-III curatively resected cases): Assessed cfDNA <i>BRAF</i>^V600E for recurrence risk prediction. Blood samples were collected before and during treatment and analyzed using droplet digital PCR (ddPCR) to measure cfDNA <i>BRAF</i>^V600E levels. <b>Results</b>: Cohort 1 (Stage IV, <i>n</i> = 14): Pre-treatment cfDNA <i>BRAF</i>^V600E was detected in 93% of cases. Patients with a decrease in cfDNA <i>BRAF</i>^V600E variant allele frequency (VAF) after chemotherapy had significantly longer overall survival (511 vs. 189 days, <i>p</i> = 0.03) than those without a decrease. Cohort 2 (curatively resected, <i>n</i> = 23): cfDNA <i>BRAF</i>^V600E was detected in 4/23 patients (17.4%) at 1 month post-surgery. cfDNA <i>BRAF</i>^V600E showed better recurrence prediction compared to CEA (100% vs. 18.8%, <i>p</i> = 0.004). Among the seven patients who experienced recurrence, those with postoperative cfDNA <i>BRAF</i>^V600E positivity had significantly shorter disease-free survival compared to cfDNA <i>BRAF</i>^V600E-negative patients (179 vs. 840 days, <i>p</i> = 0.04). <b>Conclusions</b>: These findings support cfDNA <i>BRAF</i>^V600E as a promising biomarker for monitoring treatment response and MRD detection in <i>BRAF</i>^V600E-mutant CRC, reinforcing its role in guiding personalized treatment strategies and postoperative surveillance.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogeny and Specific Determination of <i>Gloydius halys-intermedius</i> Complex Based on Complete Mitochondrial Genes.","authors":"Lijie Jin, Zuyao Xia, Ning Liu, Shengyue Hou, Chuandong Lv, Lianyou Tang, Shuguang Feng, Jingsong Shi, Ming Bai","doi":"10.3390/genes16030276","DOIUrl":"10.3390/genes16030276","url":null,"abstract":"<p><p><b>Background</b>: The phylogenetic resolution within the <i>Gloydius halys-intermedius</i> Complex remains debatable due to the following reasons: loci selection in previous studies varied between authors; limited dataset (1-5 mitochondrial or nuclear gene fragments); lack of sampling density; and nodal supports at specific nodes remain weak, specifically within <i>Gloydius cognatus</i>, <i>G. halys</i>, and <i>G. stejnegeri</i>. <b>Objectives</b>: To revise the taxonomic and phylogenetic relationships within the <i>G. halys-intermedius</i> Complex, we reconstructed the molecular phylogeny and performed species delimitation based on the complete mitochondrial genomes. <b>Methods</b>: In this study, twelve nomenclatural groups of <i>Gloydius</i> species were involved in the computation of Bayesian phylogenomic inference, five of the twelve nomenclature groups were newly sequenced, while the rest were acquired from the National Center for Biotechnology Information (NCBI). The Bayesian phylogenomic inference was constructed based on 13 mitochondrial protein-coding genes. Species delimitation was performed by two distance-based methods (ABGD and ASAP) and two tree-based methods (GMYC and bPTP). <b>Results</b>: This research resolved the systematic relationship within the <i>G. intermedius</i> Complex with the support of mitogenome-based phylogenomics, while indicating cryptic diversity within the <i>Gloydius halys-intermedius</i> Complex: <i>G. intermedius</i> samples from South Korea show as paraphyletic to the cluster of the samples from northeastern China. Species delimitation results based on four models resemble each other, supporting <i>Gloydius caucasicus</i>, <i>G. cognatus</i>, <i>G. halys</i>, and <i>G. stejnegeri</i>, each representing full species. The species delimitation results of this research also resemble the nomenclatural species based on previous morphometrical results. This research indicates that species delimitation efforts based on the phylogenomic approach would likely resolve complex evolutionary relationships.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Abnormalities and Carcinogenesis in Barrett's Esophagus: Implications for Cancer Treatment and Prevention.","authors":"Thaís Cabral de Melo Viana, Eric Toshiyuki Nakamura, Amanda Park, Kaique Flávio Xavier Cardoso Filardi, Rodrigo Moisés de Almeida Leite, Luiz Fernando Sposito Ribeiro Baltazar, Pedro Luiz Serrano Usón Junior, Francisco Tustumi","doi":"10.3390/genes16030270","DOIUrl":"10.3390/genes16030270","url":null,"abstract":"<p><strong>Background: </strong>Barrett's esophagus (BE) is described by the transformation of the normal squamous epithelium into metaplastic columnar epithelium, driven by chronic gastroesophageal reflux disease (GERD). BE is a recognized premalignant condition and the main precursor to esophageal adenocarcinoma (EAC). Understanding the molecular mechanisms underlying BE carcinogenesis is crucial for improving prevention, surveillance, and treatment strategies.</p><p><strong>Methods: </strong>This narrative review examines the molecular abnormalities associated with the progression of BE to EAC.</p><p><strong>Results: </strong>This study highlights inflammatory, genetic, epigenetic, and chromosomal alterations, emphasizing key pathways and biomarkers. BE progression follows a multistep process involving dysplasia and genetic alterations such as TP53 and CDKN2A (p16) mutations, chromosomal instability, and dysregulation of pathways like PI3K/AKT/mTOR. Epigenetic alterations, including aberrant microRNA expression or DNA methylation, further contribute to this progression. These molecular changes are stage-specific, with some alterations occurring early in BE during the transition to high-grade dysplasia or EAC. Innovations in chemoprevention, such as combining proton pump inhibitors and aspirin, and the potential of antireflux surgery to halt disease progression are promising. Incorporating molecular biomarkers into surveillance strategies and advancing precision medicine may enable earlier detection and personalized treatments.</p><p><strong>Conclusions: </strong>BE is the primary preneoplastic condition for EAC. A deeper understanding of its molecular transformation can enhance surveillance protocols, optimize the management of gastroesophageal reflux inflammation, and refine prevention and therapeutic strategies, ultimately contributing to a reduction in the global burden of EAC.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Forensic Approach to Complex Identification Cases: The Collapse of an Italian Cemetery into the Sea.","authors":"Camilla Tettamanti, Francesca Frigiolini, Lorenzo Franceschetti, Rosario Barranco, Sara Lo Pinto, Lucia Casarino, Simonetta Verdiani, Mattia Porcu, Cristina Cattaneo, Danilo De Angelis, Marco Cummaudo, Francesco De Stefano, Francesco Ventura","doi":"10.3390/genes16030277","DOIUrl":"10.3390/genes16030277","url":null,"abstract":"<p><strong>Background/objectives: </strong>On 22 February 2021, a coastal landslide in Italy caused the collapse of an old cemetery, displacing approximately 370 coffins, with over 200 plunging into the sea. This disaster necessitated the recovery and identification of human remains under challenging conditions to provide closure to families and uphold the dignity of the deceased.</p><p><strong>Methods: </strong>Recovery operations involved firefighters and scuba divers, followed by forensic analysis conducted by the Medical Staff of Legal and Forensic Medicine. A post-mortem team utilized forms adapted from Interpol's Disaster Victim Identification (DVI) standards to document remains, which included 140 decomposed bodies and 193 bags of commingled skeletal remains. DNA samples were collected from 147 bone fragments, primarily long bones and teeth, and compared with ante-mortem data gathered from relatives.</p><p><strong>Results: </strong>Of the 77 eligible relatives, 66 consented to DNA sample collection for genetic profiling, and 28 bodies were identified. Personal effects, clothing, medical devices, and a strong match between non-genetic AM and PM data led to an attribution of identity of other 19 individuals. Advanced post-mortem phenomena were observed in remains spanning from the late 19th century to 2017. An identification area at the cemetery facilitated streamlined operations, emphasizing environmental preservation and forensic accuracy.</p><p><strong>Conclusions: </strong>The cemetery collapse highlights the necessity for tailored forensic approaches in disaster scenarios. Accurate identification methods, combining genetic analysis and secondary means, are crucial for ensuring dignified burials and providing closure to affected families.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A New Function of the DRD1 Gene: GnRH Secretion Regulation in Sheep Hypothalamic Neurons.","authors":"Manjun Zhai, Shaoqi Cao, Huihui Liang, Yifan Xie, Zongsheng Zhao","doi":"10.3390/genes16030273","DOIUrl":"10.3390/genes16030273","url":null,"abstract":"<p><strong>Background: </strong>Dopamine (DA) is an important neurotransmitter that is widely present in the central nervous system. DA plays a crucial regulatory role in mammalian emotion, endocrine function, and reproduction through the activation of dopamine receptors. We compared the transcriptomes of hypothalamic tissues from Kazakh sheep during the nonbreeding season of anoestrus and during the nutrient-induced nonbreeding season of oestrus. Our research findings suggest that the dopamine receptor D1 (<i>DRD1</i>) gene may be a candidate gene for the regulation of sheep oestrus. However, the underlying mechanism through which <i>DRD1</i> regulates sheep oestrus is still poorly understood.</p><p><strong>Methods: </strong>In the present study, the expression of <i>DRD1</i> mRNA in the hypothalamus of oestrous Kazakh sheep was significantly greater than that in the anoestrous phase. Immunohistochemical staining revealed that <i>DRD1</i> was more widely expressed in hypothalamic tissue and was more highly expressed during oestrus than during anoestrus. Hypothalamic neuron experiments further indicated that <i>DRD1</i> affects the expression of GnRH through dopamine synapses and calcium signalling pathways.</p><p><strong>Results: </strong>moreover, the overexpression of the <i>DRD1</i> gene promoted the secretion of GnRH, while knocking down the <i>DRD1</i> gene reduced the secretion of GnRH.</p><p><strong>Conclusions: </strong>The present study revealed that the <i>DRD1</i> gene plays a crucial regulatory role in the secretion of the hormone GnRH in the hypothalamus of Kazakh sheep.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sustained Epigenetic Reactivation in Fragile X Neurons with an RNA-Binding Small Molecule.","authors":"Christina W Kam, Jason G Dumelie, Gabriele Ciceri, Wang-Yong Yang, Matthew D Disney, Lorenz Studer, Samie R Jaffrey","doi":"10.3390/genes16030278","DOIUrl":"10.3390/genes16030278","url":null,"abstract":"<p><strong>Background/objectives: </strong>Fragile X syndrome (FXS) is a disease of pathologic epigenetic silencing induced by RNA. In FXS, an expanded CGG repeat tract in the <i>FMR1</i> gene induces epigenetic silencing during embryogenesis. <i>FMR1</i> silencing can be reversed with 5-aza-deoxyctidine (5-aza-dC), a nonspecific epigenetic reactivator; however, continuous administration of 5-aza-dC is problematic due to its toxicity. We describe an approach to restore <i>FMR1</i> expression in FXS neurons by transient treatment with 5-aza-dC, followed by treatment with 2HE-5NMe, which binds the CGG repeat expansion in the <i>FMR1</i> mRNA and could block the resilencing of the <i>FMR1</i> gene after withdrawal of 5-aza-dC.</p><p><strong>Methods: </strong>This study uses immunofluorescence and fluorescent in situ hybridization (FISH) to measure whether <i>FMR1</i> expression is maintained in FXS post-mitotic neurons treated with 2HE-5NMe. Genome-wide profiling of histone marks was used to monitor epigenetic changes and drug selectivity in response to 5-aza-dC followed by 2HE-5NMe treatment. Changes to dendritic morphology were visualized using confocal microscopy.</p><p><strong>Results: </strong>In this study, we find that 2HE-5Nme maintains <i>FMR1</i> in a reactivated state after reactivation using 5-aza-dC in post-mitotic neurons. <i>FMR1</i> reactivation in neurons results in the re-expression of FMRP and reversal of FXS-associated dendritic spine defects.</p><p><strong>Conclusions: </strong>These results demonstrate that an RNA-binding small molecule can achieve gene-specific epigenetic control and provide an approach for the restoration of FMRP in FXS neurons.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942054/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying Cancer Stage-Related Biomarkers for Lung Adenocarcinoma by Integrating Both Node and Edge Features.","authors":"Zige Wang, Hamza Benhammouda, Bolin Chen","doi":"10.3390/genes16030261","DOIUrl":"10.3390/genes16030261","url":null,"abstract":"<p><p><b>Background</b>: In order to characterize phenotypes and diseases, genetic factors and their interactions in biological systems must be considered. Although genes or node features are the core units of genetic information, their connections, also known as edge features, are composed of a network of gene interactions. These components are crucial for understanding the molecular basis of disease and phenotype development. Existing research typically utilizes node biomarkers composed of individual genes or proteins for the binary classification of cancer. However, due to significant heterogeneity among patients, these methods cannot adapt to the subtle changes required for precise cancer staging, and relying solely on node biomarkers often leads to poor accuracy in classifying cancer staging. <b>Methods</b>: In this study, a computational framework was developed to diagnose lung adenocarcinoma, integrating node and edge features such as correlation, covariance, and residuals. The proposed method allows for precise diagnosis in the case of a single sample, which can identify the minimum feature set that effectively distinguishes cancer staging. <b>Results</b>: The advantages of the proposed method are: (i) it can diagnose each individual test sample, promoting personalized treatment; (ii) integrating node and edge features can improve diagnostic accuracy, indicating that each type of feature can capture unique aspects of the disease; (iii) it significantly reduces the number of features required to accurately classify the four stages of cancer, thereby achieving optimal cross-validation accuracy. <b>Conclusions</b>: This streamlined and effective feature set highlights the potential of our approach in advancing personalized medicine and improving clinical outcomes for cancer patients.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}