Front Genet [JOURNAL]
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200 papers
Rhizospheric soil alter extracellular vesicles in the roots of and their carried miRNA.
Li N, Zhou L, Li J
Front Genet · 2026 · PMID 42205177 · Full text
INTRODUCTION: As a valuable traditional medicinal plant, it is unclear whether the roots of produce extracellular vesicles (EVs), or whether the addition of rhizospheric soil influences the characterization of EVs and t...
INTRODUCTION: As a valuable traditional medicinal plant, it is unclear whether the roots of produce extracellular vesicles (EVs), or whether the addition of rhizospheric soil influences the characterization of EVs and the microRNAs (miRNAs) involved. METHODS: In this study, we compared EVs from the roots of grown in rhizospheric soil and sterilized peat moss and sequenced the miRNAs within these EVs. RESULTS AND DISCUSSION: EVs from the treated roots of grown in field rhizospheric soil had a significantly smaller size and higher density compared to those from blank roots grown on sterilized peat moss. The results suggested that the physio-chemical properties or soil microbial communities induced by the addition of rhizospheric soil may play an important role in producing of EVs in the roots of . Among the 242 known miRNAs, the miR166 family had the most observed miRNAs (27 members), followed by the miR156 (26 members), miR159 (24 members), and miR319 (17 members) families. Principal component analysis revealed a clear separation between the treated and blank samples. A total of 20 differentially expressed miRNAs (DE-miRNAs) were filtered, with 10 up-regulated and 10 downregulated. For 12 DE-miRNAs, 183 target genes were predicted. All miRNAs targeted more than four genes, suggesting that these miRNAs had diverse roles. The predicted target genes included numerous transcription factors and genes with different functions. Furthermore, the function of the predicted target genes was annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. A total of 295 GO terms were enriched, with 157 related to biological processes, 89 to molecular functions, and 49 to cellular components. KEGG analysis showed that the target genes of DE-miRNAs were involved in diverse biological and biochemical processes. Twenty-six target genes were associated with 26 KEGG pathways, and the top five enriched pathways were "Nitrogen metabolism", "Lipoic acid metabolism", "Linoleic acid metabolism", "Propanoate metabolism", "alpha-Linolenic acid metabolism". Our results could provide a foundation for the development and application of EVs from the roots of .
Comprehensive genomic profiling of neuroendocrine neoplasms of the colorectum.
Xu H, Jin X, Chen M … +6 more , Yang S, He G, Ou L, Li T, Liang Q, Cai D
Front Genet · 2026 · PMID 42200202 · Full text
Neuroendocrine tumors (NETs) are classified into G1, G2, and G3, corresponding to low-grade, intermediate-grade, and high-grade tumors, higher grades show greater aggressiveness and poorer outcomes, with molecular mechan...
Neuroendocrine tumors (NETs) are classified into G1, G2, and G3, corresponding to low-grade, intermediate-grade, and high-grade tumors, higher grades show greater aggressiveness and poorer outcomes, with molecular mechanisms remaining unclear. This study aimed to investigate gene mutations across G1, G2, and G3 in 24 colorectal neuroendocrine tumors (CRNETs) using whole-exome sequencing to identify somatic single nucleotide polymorphisms (SNPs). The results showed a prominent T>C single nucleotide variant (SNV) in G1 samples, while C>T was prevalent in G2 and G3. The analysis of significant mutated genes revealed that (100%) was present in all grades, though mutation sites and frequencies differed. Particularly, tumor-associated HYDIN mutations were exclusive to G3, suggesting it may serve as a candidate biomarker for distinguishing high-grade from lower grades. Important copy number variations (CNVs) were identified in genes such as (G1), PPARG, , and (G2), as well as and (G3). The gene, associated with potential clinical drug responses, exhibited specific mutation sites across all samples. The study identified seven primary mutation signatures, with signature 6 predominant in G3, and highlighted a link to carcinogenic pathways like RTK-RAS, Notch, WNT, and Hippo, thus providing valuable insights into the pathogenesis of CRNETs.
Extracellular vesicle-associated and non-vesicle-associated microRNAs for early breast cancer detection: a systematic review.
Romero Urrego JD, Parra-López CA, Isaza-Ruget MA … +1 more , Pacheco Y
Front Genet · 2026 · PMID 42200201 · Full text
Breast cancer remains a leading cause of morbidity and mortality worldwide, with survival outcomes strongly dependent on early detection. Conventional mammography, while widely adopted, faces limitations in sensitivity-p...
Breast cancer remains a leading cause of morbidity and mortality worldwide, with survival outcomes strongly dependent on early detection. Conventional mammography, while widely adopted, faces limitations in sensitivity-particularly in dense breast tissue-and is not without invasiveness. Circulating microRNAs (miRNAs), both exosomal and non-exosomal, have emerged as promising non-invasive biomarkers due to their stability in biofluids and cancer-associated dysregulation. This systematic review evaluated studies published between 2016 and 2025 assessing the diagnostic performance of blood-derived miRNAs for early breast cancer detection. Several individual miRNAs, including miR-21-5p and miR-200c, as well as panels such as those comprising miR-106a-3p, miR-106a-5p, miR-20b-5p, and miR-92a-2-5p, demonstrated high diagnostic accuracy (Area Under the Curve (AUC) > 0.9) in distinguishing breast cancer patients from healthy controls. Despite challenges related to tumor heterogeneity and pre-analytical standardization, integrating circulating miRNA biomarkers with current imaging modalities holds significant potential to enhance early detection and support personalized management strategies.
Comparative genomic and evolutionary analysis of stress-associated proteins in and distinct plant species under abiotic stress.
Zhang W, Zainal Z, Md Isa N
Front Genet · 2026 · PMID 42200200 · Full text
Stress-Associated Proteins (SAPs) are important zinc-finger proteins containing A20 and/or AN1 domains and are widely involved in plant stress responses and hormone signaling. However, the SAP gene family in peach () has...
Stress-Associated Proteins (SAPs) are important zinc-finger proteins containing A20 and/or AN1 domains and are widely involved in plant stress responses and hormone signaling. However, the SAP gene family in peach () has not yet been systematically characterized. In this study, we performed a genome-wide identification and comparative analysis of the family to investigate its evolutionary relationships, structural features, promoter characteristics, and stress-responsive expression patterns. A total of nine () were identified and classified into four phylogenetic clades, providing a framework for understanding SAP family diversification in peach and other representative plant species. Comparative analysis showed that the SAP gene family is relatively conserved within species but exhibits greater divergence in more distantly related species, such as and , suggesting lineage-specific evolutionary differentiation. Promoter analysis revealed that contain abundant cis-regulatory elements associated with stress responses and hormone signaling, including ABA, GA, MYB, and anaerobic-responsive elements. RNA-seq expression profiling further demonstrated that exhibit diverse transcriptional responses under drought, salinity, ethylene, and cold stress conditions. In particular, different members displayed distinct temporal expression patterns during cold treatment, indicating potential functional divergence within the family. Overall, this study provides the first comprehensive genomic and evolutionary characterization of the gene family in peach and identifies several stress-responsive candidate genes for future functional validation and peach stress-resilience improvement.
Perfluorooctanesulfonic acid contributes to primary open-angle glaucoma in a FABP4-Dependent manner: a novel mechanism for environmental risk of glaucoma.
Lin J, Zhang Y, Li Y … +3 more , He N, Liu Y, Zheng H
Front Genet · 2026 · PMID 42200199 · Full text
BACKGROUND: Primary open-angle glaucoma (POAG) is the most prevalent form of glaucoma globally, with environmental factors increasingly recognized as critical determinants of its onset and progression. However, the poten...
BACKGROUND: Primary open-angle glaucoma (POAG) is the most prevalent form of glaucoma globally, with environmental factors increasingly recognized as critical determinants of its onset and progression. However, the potential association between perfluorooctanesulfonic acid (PFOS) exposure and POAG remains poorly understood, and its underlying molecular mechanisms have yet to be elucidated. METHODS AND RESULTS: Utilizing cross-sectional data from the NHANES database, we identified a significant positive correlation between serum PFOS levels and glaucoma prevalence. The robustness of our study population selection and the focus on POAG were further validated through the Global Burden of Disease (GBD) database and systematic literature review. Network toxicology analysis identified 20 PFOS-exposure-related genes in POAG, with functional enrichment highlighting the biosynthesis of unsaturated fatty acids as a key pathway. Integrated machine learning and bioinformatic analysis pinpointed FABP4 as a pivotal candidate gene. Molecular docking and dynamics simulations confirmed stable binding affinity between PFOS and the FABP4 protein. experiments using human trabecular meshwork cells (HTMCs) demonstrated that PFOS exposure induced cellular senescence, as evidenced by SA-β-gal staining. Western blot analysis revealed that PFOS significantly upregulated the expression of FABP4 and the senescence marker P21. Crucially, targeted functional inhibition of the FABP4 protein successfully rescued PFOS-induced senescence and downregulated P21 expression. CONCLUSION: These findings provide novel insights into the toxicological profile of PFOS, suggesting that it contributes to POAG pathogenesis by modulating FABP4-mediated cellular senescence. This study offers a theoretical basis for environmental risk assessment and the development of preventive strategies for POAG.
Benchmarking major somatic structural variant callers on the HG008 genome.
Cui X, Liu Y, Qian L … +1 more , Wang Y
Front Genet · 2026 · PMID 42200198 · Full text
Somatic structural variants (SVs) are the predominant source of cancer driver mutations and play a critical role in oncogenesis. Comprehensive characterization of somatic SVs is critical for elucidating the mechanisms un...
Somatic structural variants (SVs) are the predominant source of cancer driver mutations and play a critical role in oncogenesis. Comprehensive characterization of somatic SVs is critical for elucidating the mechanisms underlying tumorigenesis and for identifying biomarkers with diagnostic and therapeutic potential. However, their accurate detection remains challenging, primarily because most existing SV detection algorithms were originally developed for germline variants and are not well-suited to addressing the high heterogeneity of somatic mutations. In recent years, although several tools specifically designed for somatic SVs have emerged, their detection performance has not yet been rigorously validated. To bridge this gap, we conducted a comprehensive benchmarking of four leading somatic SV detection tools, namely, Sniffles2, Nanomonsv, Savana, and Severus, on the HG008 genome from Genome in a Bottle Consortium (GIAB). Their outputs were evaluated against the HG008 clonal somatic SV draft benchmark to assess overall performance. We further integrated the somatic SV callsets from multiple tools and compared them with the benchmark set, thereby establishing a multi-tool ensemble strategy for SV detection to achieve more accurate and comprehensive identification of somatic SVs.
High prevalence of Hb Q-Thailand not in cis with the -α deletion: genotypes, phenotypes, and implications in the cenxi population of southern China.
Li Y, Wu M, Zheng L … +2 more , Liang L, Li Y
Front Genet · 2026 · PMID 42186461 · Full text
OBJECTIVES: Hb Q-Thailand, a common hemoglobin variation in Southeast Asia, has historically been associated with the -α deletion. However, in the Cenxi population of southern China, this variant is frequently detected w...
OBJECTIVES: Hb Q-Thailand, a common hemoglobin variation in Southeast Asia, has historically been associated with the -α deletion. However, in the Cenxi population of southern China, this variant is frequently detected without the -α deletion. This study aimed to investigate the carrier rate, genotype distribution, and phenotypic characteristics of Hb Q-Thailand not associated with the -α deletion in this population. METHODS: A total of 23,546 individuals who underwent capillary electrophoresis screening at our hospital between January 2024 and December 2025 were enrolled in this study. Deletional α-thalassemia mutations were detected using Gap-PCR, while common α-globin chain mutations were identified by PCR-reverse dot blot hybridization (PCR-RDB). Additionally, 17 common β-thalassemia point mutations were analyzed using PCR-RDB. Sanger sequencing was performed to characterize α-globin variants. RESULTS: Thirty-seven positive cases were identified among the 23,546 screened individuals, yielding a positive screening rate of 0.16% (37/23,546) in the Cenxi population. Genetic confirmation was performed in 22 cases, of which 21 were confirmed to carry Hb Q-Thailand, while the remaining case was identified as a rare variant, Hb Zhaoqing. Notably, 10 samples exhibited Hb Q-Thailand without linkage to the -α deletion, accounting for a substantial proportion of 47.6% (10/21) among confirmed cases. In the group with Hb Q-Thailand not linked to the -α deletion, hematological phenotypes were largely within normal ranges. The Hb Q-Thailand level in simple heterozygotes was 16.6% ± 0.4%, which increased to 22.4% ± 0.4% when co-inherited with the -α deletion. In contrast, the majority of individuals in the group with Hb Q-Thailand linked to the -α deletion exhibited abnormal hematological parameters. The Hb Q-Thailand level in this group was 28.2% ± 0.8%, rising to 42.0% when the -α deletion was co-inherited. Additionally, one case in this group was found to co-inherit β-thalassemia trait, presenting with hematological and electrophoretic features consistent with β-thalassemia trait, characterized by elevated Hb A and reduced MCV/MCH. CONCLUSION: The Cenxi population presents a high proportion of Hb Q-Thailand cases in which the variant is not linked to the -α deletion. Hematological phenotypes differ significantly depending on the presence or absence of linkage to the -α deletion.
Identification and validation of a seven-gene metastasis-associated prognostic model in breast cancer.
Yao Y, Zheng Y, Xie J … +4 more , Liu H, Chen C, Cao J, Yin TT
Front Genet · 2026 · PMID 42186460 · Full text
INTRODUCTION: Metastasis is the primary cause of mortality in patients with breast cancer. This study aimed to develop a prognostic signature based on metastasis- and cancer-associated differentially expressed genes (M-C...
INTRODUCTION: Metastasis is the primary cause of mortality in patients with breast cancer. This study aimed to develop a prognostic signature based on metastasis- and cancer-associated differentially expressed genes (M-CA-DEGs) and to identify potential novel therapeutic genes. MATERIALS AND METHODS: Data were acquired from the TCGA-BRCA, AURORA US Network, SCAN-B, and GEO databases. M-CA-DEGs were identified, and a prognostic risk model was constructed via univariate Cox and LASSO regression analyses. The prognostic value was verified using calibration curves and decision curve analysis (DCA). Independent prognostic factors were subsequently validated. Functional enrichment was assessed through GSEA and ssGSEA. Immune infiltration and mutation profiles were compared between risk groups. A TF-mRNA regulatory network was constructed. Single-cell analysis was performed to characterize gene expression patterns. The mRNA levels of prognostic genes were examined in MCF-10A mammary epithelial cells and breast cancer cell lines. RESULTS: We developed and validated a novel seven-gene, metastasis-associated prognostic signature (, , , , , , ) for breast cancer. The risk score emerged as a powerful independent prognostic factor. The low-risk group exhibited superior survival, an immunologically "hot" phenotype with enriched activated CD8 T cells, and higher immune activity, whereas the high-risk group showed T-cell exclusion and enrichment in kinase signaling and metabolism. Somatic mutation landscapes differed significantly between groups. Crucially, we identified two previously under-characterized genes ( and ) as potential novel drivers of tumor progression. Single-cell transcriptomics unveiled their cell type-specific expression patterns, and assays confirmed differential expression in cancer cell lines. CONCLUSION: This study establishes a robust, biologically grounded, metastasis-related seven-gene prognostic model for breast cancer. Beyond prediction, our work identifies two novel therapeutic targets and reveals distinct immune and metabolic phenotypes across risk groups, thereby providing novel mechanistic insights into tumor heterogeneity and actionable targets for future therapies.
Evaluation of the contribution of trio-exome sequencing in selected prenatal indications.
Chretien M, Osouf J, Abel C … +47 more , Afenjar A, Attie-Bitach T, Brischoux-Boucher E, Burglen L, Calmels N, Chassaing N, Courtin T, Delanne J, Doco-Fenzy M, Dubourg C, Durand B, Chehadeh SE, Faivre L, Garde A, Ginglinger E, Haushalter V, Haye D, Heide S, Heidet L, Heron D, Jacquin C, Lambert L, Lamouche JB, Laugel V, Bechec AL, Lehalle D, Michel-Calemard L, Ramirez EM, Muller J, Odent S, Patat O, Piard J, Poirsier C, Putoux A, Quelin C, Racine C, Sananes N, Schalk A, Scheidecker S, Thauvin-Robinet C, Valence S, Weingertner AS, Wourms J, Dollfus H, Gerard B, Schluth-Bolard C, Schaefer E
Front Genet · 2026 · PMID 42186459 · Full text
OBJECTIVE: This study is an example of the contribution of exome sequencing (ES) in selected prenatal indications, while illustrating the complexity of interpreting prenatal genetic testing. Therefore, one of the aims of...
OBJECTIVE: This study is an example of the contribution of exome sequencing (ES) in selected prenatal indications, while illustrating the complexity of interpreting prenatal genetic testing. Therefore, one of the aims of this study was to better describe antenatal phenotypes. METHODS: This was a multicenter, comparative, prospective study assessing high-throughput sequencing performance (targeted gene panel exome sequencing) in selected prenatal indications. RESULTS: Trio-ES was performed on 86 fetuses, allowed making a definite etiological diagnosis in 28% of cases (24/86). One-third of diagnoses were obtained only after exome analysis (8/24, 33%). The diagnostic yield varied according to the indication and was the highest for vermian hypoplasia (5/12, 42%) and polymalformative syndromes (30%, 8/27) indications. The variants identified were mainly missense variants in ciliopathy (18%, 6/33) and cytoskeleton (15%, 5/33) genes. Among the etiological diagnoses, one fetus carried a postzygotic mosaic variant in . CONCLUSION: In selected indications, the diagnostic yield of ES was close to 30% and varied according to the indications, showing the importance of clearly define the malformations justifying this approach. An etiological diagnosis was made in 23 families, within a timeframe compatible with pregnancy, thus improving the management of the pregnancy and/or the unborn child.
Enhancing glaucoma prediction across ancestries: integrating functional annotation into multi-trait polygenic risk scores.
Gao XR
Front Genet · 2026 · PMID 42180521 · Full text
INTRODUCTION: Primary open-angle glaucoma (POAG) remains a leading cause of irreversible blindness worldwide, with early detection crucial for preventing vision loss. Current polygenic risk scores (PRS) for POAG, however...
INTRODUCTION: Primary open-angle glaucoma (POAG) remains a leading cause of irreversible blindness worldwide, with early detection crucial for preventing vision loss. Current polygenic risk scores (PRS) for POAG, however, demonstrate limited predictive power. METHODS: Here, we present a multi-trait polygenic probability risk score (PPRS) approach that integrates PRSs of multiple glaucoma-related traits, including POAG, intraocular pressure (IOP), vertical cup-to-disc ratio (VCDR), and retinal nerve fiber layer thickness, while leveraging functional genomic annotations and extensive genomic coverage (>7 million variants) to enhance POAG prediction across diverse ancestries. We evaluated the PPRS in the UK Biobank (n = 324,713, European ancestry) and the Mexican American Glaucoma Genetic Study (MAGGS, n = 4,549, Latino ancestry). RESULTS: The PPRS improved prediction compared with conventional approaches, achieving area under the receiver operating characteristic curve (AUC) values of 0.814 in Europeans and 0.802 in Latinos, versus 0.721 and 0.753 for baseline models with age and sex alone. Genetic contributions varied by ancestry: IOP PRS showed the strongest association in Europeans (OR = 1.63, P = 5.37 × 10), whereas VCDR PRS predominated in Latinos (OR = 1.64, P = 2.04 × 10). Risk stratification was substantial, with the highest PPRS decile showing 74.4-fold and 49.3-fold greater POAG risk compared with the lowest decile in Europeans and Latinos, respectively. DISCUSSION: These findings show that integrating multiple disease-relevant PRSs and functional annotations significantly improves genetic prediction of POAG across diverse populations, supporting applications in targeted screening and early intervention.
Case Report: Ochronotic arthropathy mimicking spondyloarthritis: a case-based review of diagnostic pitfalls and a novel likely pathogenic HGD variant.
Liu Z, Xu X, Yang Y … +7 more , Li S, Bai R, Zhang Z, Guo Y, Cui R, Xu J, Liu S
Front Genet · 2026 · PMID 42180520 · Full text
BACKGROUND: Alkaptonuria (AKU) is a rare autosomal recessive metabolic disorder caused by homogentisate 1,2-dioxygenase (HGD) deficiency, leading to pigment deposition and progressive ochronotic arthropathy (OchA), which...
BACKGROUND: Alkaptonuria (AKU) is a rare autosomal recessive metabolic disorder caused by homogentisate 1,2-dioxygenase (HGD) deficiency, leading to pigment deposition and progressive ochronotic arthropathy (OchA), which may mimic chronic inflammatory or degenerative joint diseases and delay diagnosis. CASE DESCRIPTION: A 48-year-old man with chronic low back pain and right knee arthritis was initially diagnosed with spondyloarthritis (SpA). Arthroscopy revealed black-brown synovial pigmentation initially overlooked. Subsequent clinical reassessment identified auricular cartilage pigmentation and progressive urine darkening, while imaging showed multilayered intervertebral disc calcification and degenerative changes, raising suspicion for AKU. RESULTS: Genetic analysis detected a novel homozygous HGD missense variant (c.424A > G; p.Met142Val, exon 6), affecting a conserved residue and predicted to be deleterious. Classified as likely pathogenic according to ACMG criteria, it supported the diagnosis of OchA in conjunction with clinical, radiological and histopathological findings. CONCLUSION: This case highlights the diagnostic challenges of OchA mimicking SpA or osteoarthritis. Recognition of progressive urine darkening, cartilage pigmentation, and multilayered disc calcification may facilitate earlier diagnosis. The novel HGD variant expands the mutational spectrum of AKU and underscores the importance of molecular testing within a multidisciplinary framework in atypical joint degeneration. Although primarily metabolic, awareness of potential inflammatory involvement may guide symptomatic management when metabolic therapy is delayed.
Editorial: Epigenetic alterations in tumors and therapeutic resistance.
Peng Z, Huang C, Huang J … +2 more , Chen Y, Huang S
Front Genet · 2026 · PMID 42180519 · Full text
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Adaptive radiation and structural tailoring of the Vietnamese immunogenetic reservoir.
Luu AH, Budi T, Singchat W … +14 more , Nguyen CTP, Panthum T, Tanglertpaibul N, Vangnai K, Chaiyes A, Yokthongwattana C, Sinthuvanich C, Sawatdichaikul O, Han K, Muangmai N, Griffin DK, Duengkae P, Nguyen NT, Srikulnath K
Front Genet · 2026 · PMID 42180518 · Full text
BACKGROUND: The global poultry industry faces a critical sustainability crisis driven by climate change and escalating disease threats, necessitating the identification of novel genetic reservoirs for resilience. The Maj...
BACKGROUND: The global poultry industry faces a critical sustainability crisis driven by climate change and escalating disease threats, necessitating the identification of novel genetic reservoirs for resilience. The Major Histocompatibility Complex ()-linked gene, a member of the Killer Cell Lectin-like Receptor (KLR) family, serves as a molecular sentinel regulating Natural Killer (NK) cell-mediated immunity; however, its diversity remains poorly characterized in Southeast Asian avian populations. METHODS: This study utilized Illumina short-read sequencing and AlphaFold 3 modeling to investigate polymorphism across 15 Vietnamese populations that comprised 13 indigenous breeds and two ancestral Red Junglefowl () lineages. RESULTS: We identified 11 unique alleles, including the novel variant , that establish the Vietnamese gene pool as a distinct reservoir of immune diversity. Notably, eight alleles were restricted to indigenous breeds, which exhibited a higher nucleotide diversity ( = 0.012) than their wild progenitors ( = 0.009), suggesting that localized diversification has been driven by breed-specific selective pressures. Evolutionary analysis revealed a dual mechanism: (1) intense global purifying selection ( ≤ 0.035) preserving the receptor's structural scaffold and (2) localized positive selection at codons 11 and 18 that is predicted to influence the receptor's binding affinity for the Class I (BF2) ligand. The hypothesized functional relevance of this diversity is highlighted by the identification of alleles homologous to haplotypes previously associated with high resistance, such as (linked to H5N1 and Marek's disease resistance in prior studies) and (associated with respiratory virus resilience). CONCLUSION: By integrating population genomics with structural biology, this study provides the foundational data proposing as a candidate locus for future Marker-Assisted Selection (MAS) research. While experimental functional validation remains necessary, our findings establish a hypothesis-driven framework for investigating how genetic reservoirs might be leveraged to enhance avian immunocompetence and secure sustainable poultry production against emerging viral threats.
Diverse roles of YTHDC1 in chromatin and blood cancers.
Pernon B, Benchikh Y, Fournier C … +10 more , Delforge M, Dumétier B, Delva L, Durand A, Rossi C, Martin L, Guidez F, Verdel A, Aucagne R, Callanan MB
Front Genet · 2026 · PMID 42180517 · Full text
Epitranscriptomics, the study of RNA modifications, together with their functional characterization, is emerging as an important area of investigation in RNA biology. Of the over 170 RNA modifications that have been iden...
Epitranscriptomics, the study of RNA modifications, together with their functional characterization, is emerging as an important area of investigation in RNA biology. Of the over 170 RNA modifications that have been identified on mRNA and non-coding RNAs, N6-methyladenosine (mA) modification to mRNA is recognized as a key regulator of gene expression, splicing and protein translation. Functional readout of mA is mediated by mA readers mostly in the cytoplasm except for the nuclear-localized YTHDC1. mA-YTHDC1 function has recently been extended to include short and long-range fine-tuning of genome activity via chromatin-associated mechanisms. This review summarizes YTHDC1-mA nuclear functions in normal and cancer cells with special focus on its chromatin-associated roles and the ability of YTHDC1 to assemble into higher order nuclear structures called condensates. These processes are disturbed in cancer.
Genetic determinants of age-related macular degeneration in Middle Eastern populations: a systematic review.
Sannan NS
Front Genet · 2026 · PMID 42180516 · Full text
BACKGROUND: Age-related macular degeneration (AMD) is a leading cause of vision loss, with genetic factors playing a key role in disease susceptibility and progression. While extensive genetic research is being conducted...
BACKGROUND: Age-related macular degeneration (AMD) is a leading cause of vision loss, with genetic factors playing a key role in disease susceptibility and progression. While extensive genetic research is being conducted, the genetic architecture of AMD in Middle Eastern populations remains understudied. This systematic review summarizes current evidence on genetic variants associated with AMD in Middle Eastern populations. METHODS: A comprehensive literature search was conducted in PubMed, Web of Science Core Collection, and Medline databases. Studies were included if they: (1) examined cohorts from Middle Eastern participants; (2) with clinically diagnosed AMD; (3) explored genetic variants or other genomic markers; (4) no restrictions on year of publication; and (5) were published in English. RESULTS: The search yielded 449 articles (PubMed: 164, Web of Science: 99, Medline: 186). After removal of 221 duplicates, 228 unique articles were screened. Of these, 28 studies met the inclusion criteria, covering a total of 4,247 AMD cases and 3,447 controls from five countries: Turkey (n = 11), Iran (n = 11), Israel (n = 4), Jordan (n = 1), and Egypt (n = 1). Most analyses were targeted, with 25 studies targeting one to four genetic loci, two studies examining 12 variants, and one genome-wide association study. The most frequently studied genes were CFH, ARMS2, and HTRA1. The CFH Y402H variant (rs1061170) showed overall positive but heterogeneous associations with AMD risk across studied Middle Eastern populations, with reported odds ratios ranging from 0.36 to 17.34 and statistically significant p values ranging from <0.001 to 0.02 (total AMD cases and controls = 2,079). The ARMS2 A69 S variant (rs10490924) and HTRA1 promoter variant (rs11200638) demonstrated strong associations with neovascular AMD. CONCLUSION: Few studies have examined genotype-phenotype correlations across this region, and many Middle Eastern countries lack published AMD genetic data. Consequently, the genetic landscape of AMD in the Middle East remains incompletely characterized. Available evidence suggests that variants in CFH, ARMS2, and HTRA1 are important AMD-associated loci in studied Middle Eastern populations, consistent with findings in other population groups.
The NR2F1-Related 5q14.3-q21.1 deletion causing periventricular heterotopia with cerebral visual impairment: a longitudinal case report and genotype-phenotype analysis.
St Clair Tracy H, Dutton GN, Hall HN … +1 more , Blaikie A
Front Genet · 2026 · PMID 42180515 · Full text
Large interstitial deletions spanning chromosome 5q14.3 to q21.1 and encompassing are rare. Existing descriptions have largely focused on structural features and presenting manifestations, with fewer reports examining f...
Large interstitial deletions spanning chromosome 5q14.3 to q21.1 and encompassing are rare. Existing descriptions have largely focused on structural features and presenting manifestations, with fewer reports examining functional neurodevelopmental outcomes over time, particularly in individuals with large interstitial deletions. Here, we present a 16-year longitudinal analysis of an individual with a 13.58 Mb interstitial deletion of 5q14.3 to q21.1 encompassing (ClinVar accession SCV007328941), consistent with NR2F1-related neurodevelopmental disorder, historically described under OMIM:615722 (Bosch-Boonstra-Schaaf optic atrophy syndrome). We integrate longitudinal clinical, visual, neurological, and developmental data to examine relationships between optic nerve findings, periventricular heterotopia (PH; OMIM:612881, chromosome 5q14.3 deletion syndrome), cerebral visual impairment (CVI), epilepsy, hypotonia, and long-term functional outcomes. The index case manifested PH and severe CVI from infancy, with profound hypotonia associated oromotor and airway dysfunction. Epilepsy first manifested during adolescence. Longitudinal in-depth analysis suggests that CVI may represent a key mediating factor underlying cognitive, behavioral, and communicative difficulties. Substantial latent cognitive capacity was revealed once visual complexity was reduced and environments appropriately adapted. Analysis of published cases indicates that PH is an uncommon but recurrent feature of haploinsufficiency and suggests that optic atrophy can be secondary to cerebral visual pathway dysfunction. This case highlights that longitudinal functional assessment can enhance genotype-phenotype interpretation in rare genomic disorders and provide clinically actionable insights for diagnosis, management, and outcome prediction.
Unveiling the genomic secrets of through a comprehensive comparative genomics approach.
Kabiraj A, Khan D, Shaw R … +2 more , Ghorui M, Bandopadhyay R
Front Genet · 2026 · PMID 42170010 · Full text
The central motivation of this study was to analyze the unknown genomic facts of the ubiquitously distributed bacterium using comparative genomic analysis. A total of 100 contamination-free genomes were retrieved from...
The central motivation of this study was to analyze the unknown genomic facts of the ubiquitously distributed bacterium using comparative genomic analysis. A total of 100 contamination-free genomes were retrieved from the National Center for Biotechnology Information (NCBI). Among them, 12 strains from six different isolation sources were selected based on their ANI (average nucleotide identity) values to explore their niche-specific adaptation. Prokka annotation revealed that their total genome size ranged from 2.4 to 2.8 Mb, with plant-growth-promoting and heavy-metal resistance genes prevalent across the strains. There were tryptophan (precursor of indole acetic acid) biosynthesizing genes and family proteins, indicating its plant-growth promoting traits. Rapid annotation subsystem technology-based functional annotation also detected arsenic resistance ( and ), mercury resistance (, , and ), and copper homeostasis ( and ) genes. In-depth accessory genomic analysis revealed attributes such as genomic islands, prophage genomes, metal resistance, hypothetical proteins, insertion sequences (insertion sequence elements), and transposase. IslandViewer 4 identified 21-37 GIs which occupied up to 17% of the total genome. The presence of multiple IS elements was an intrinsic factor of this genome. The number ranged from 28 to 76 under 13 different families, with IS256 the most frequent element. PHASTER analysis identified PHAGE_Paenib_Tripp_NC_028930 as the most dominant prophage among strains with similar GC adaptation. Functional annotation identified 15,444 KEGG orthologs and 6,022 Pfam domains. Comprehensive Antibiotic Resistance Database suggested the antibiotic sensitivity of the species. Finally, despite the prevalent occurrence of , it is still not multi-drug-resistant and can be applied in heavy-metal-contaminated agricultural field for plant growth promotion.
Identification and exploration of potential N6-methylation related mRNAs in endometriosis.
He Y, Ren C, Lei L … +2 more , Li J, Zhang G
Front Genet · 2026 · PMID 42170009 · Full text
BACKGROUND: N6-methyladenosine (m6A) modification regulates the processes of RNA splicing, subcellular localization, translation and stability by changing the RNA structure and the interaction between RNA and RNA-binding...
BACKGROUND: N6-methyladenosine (m6A) modification regulates the processes of RNA splicing, subcellular localization, translation and stability by changing the RNA structure and the interaction between RNA and RNA-binding proteins to ensure the timely and accurate expression of genes. In this study, we investigated m6A-related mRNAs and for the first time explored effective prevention and treatment targets in endometriosis (EM). METHODS: By arraystar m6A-mRNA epitranscriptomic microarray, biological information analysis technologies, and validation of other databases, aberrant m6A-related mRNAs were uncovered, as well as efficient therapeutic drugs. RESULTS: and might be vital m6A-related mRNAs, and and may be the most important two. A few crucial small-molecule agents supply new views for the treatment of EM. CONCLUSION: These results demonstrated novel insights into m6A modification of EM and revealed potential biomarkers and precision medicine strategies for EM.
Editorial: The role of neurogenesis in cognitive decline during aging.
Liu YZ, Nielson KA, Levenson CW
Front Genet · 2026 · PMID 42170008 · Full text
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Editorial: Insights in livestock genomics.
Wu XL, Chen SY, Sölkner J … +1 more , Cassandro M
Front Genet · 2026 · PMID 42146267 · Full text
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