Frontiers in Genetics最新文献

Familial Mediterranean Fever (FMF) is a hereditary autoinflammatory disorder, particularly present in the Mediterranean populations, and associated with pathogenic variants in the MEFV gene. This study aims to investigate the distribution of MEFV variants in a large cohort of Lebanese patients, and to explore the genotype-phenotype correlation among affected individuals. A retrospective analysis was conducted on 3,167 patients referred for MEFV sequencing at the Medical Genetics and Genomics Center(CGGM) at Saint-Joseph University of Beirut-Lebanon, from 2006 to 2023. Sanger sequencing was used to detect MEFV variants, focusing initially on hot-spot exons. Among the 3,167 patients, 46.73% (N = 1,480) carried at least one MEFV variant. The most common variants detected were M694V and V726A, both found in 28.98% of cases, followed by E148Q(27.83%) and M694I(13.98%). Moreover, Shiites and Sunni Muslims, and individuals from South and North Lebanon exhibited the highest frequency of variants. Interestingly, family history was found to be significantly higher in patients having two MEFV variants than those with one variant (p = 0.0026). The most commonly reported symptoms were fever(78%), abdominal pain(88%), joint pain(65%), and thoracic pain(46%). The genotype-phenotype correlation analysis revealed a more severe phenotype in patients carrying the M694V or V726A mutations compared to those with the homozygous E148Q genotype. This study, the largest in Lebanon, highlights the high prevalence of MEFV variants, particularly M694V and V726A, in FMF patients. Our data provide valuable insights into the genetic landscape of FMF in Lebanon and emphasize the importance of early genetic screening for a better disease management and genetic counselling.

The RORB (Retinoic Acid Receptor-related orphan receptor β) gene plays a crucial role in neurodevelopment and is strongly associated with bipolar disorder, cognitive function, and Alzheimer's disease. Recently, RORB has also emerged as a novel potential gene involved in generalized epilepsy and absence seizures. However, due to the complexity of RORB gene function, reports on pathogenic variations of RORB genes are still lacking. In this study, we present a case of a 5-year-old epilepsy patient. Through trio whole-exome sequencing, a heterozygous variant was identified at the splice site of 3' end of exon 3 in the RORB gene (chr9:77249546, NM_006914.3: c.94-1G>A). This c.94-1G>A variant disrupts normal mRNA splicing, leading to the premature termination of the RORB protein. According to ACMG guidelines, this variant is classified as "likely pathogenic". Additionally, we provide a comprehensive summary of previously reported pathogenic or likely pathogenic variants in RORB, contributing to the growing body of evidence linking this gene to epilepsy. Our findings offer valuable insights into the role of RORB in epilepsy pathogenesis, and the splice site variant identified in this study further expands the mutational spectrum of the RORB gene.

Background: Hepatocellular carcinoma (HCC) accounts for over 80% of primary liver cancers and is the third leading cause of cancer-related deaths worldwide. Hepatitis B virus (HBV) infection is the primary etiological factor. Disulfidptosis is a newly discovered form of regulated cell death. This study aims to develop a novel HBV-HCC prognostic signature related to disulfidptosis and explore potential therapeutic approaches through risk stratification based on disulfidptosis.

Methods: Transcriptomic data from HBV-HCC patients were analyzed to identify BHDRGs. A prognostic model was established and validated using machine learning, with internal datasets and external datasets for verification. We then performed immune cell infiltration analysis, tumor microenvironment (TME) analysis, and immunotherapy-related analysis based on the prognostic signature. Besides, RT-qPCR and immunohistochemistry were conducted.

Results: A prognostic model was constructed using five genes (DLAT, STC2, POF1B, S100A9, and CPS1). A corresponding prognostic nomogram was developed based on riskScores, age, stage. Stratification by median risk score revealed a significant correlation between the prognostic signature and TME, tumor immune cell infiltration, immunotherapy efficacy, and drug sensitivity. The results of the experiments indicate that DLAT expression is higher in tumor tissues compared to adjacent tissues. DLAT expression is higher in HBV-HCC tumor tissues compared to normal tissues.

Conclusion: This study stratifies HBV-HCC patients into distinct subgroups based on BHDRGs, establishing a prognostic model with significant implications for prognosis assessment, TME remodeling, and personalized therapy in HBV-HCC patients.

Macrophages are known to support cardiac development and homeostasis, contributing to tissue remodeling and repair in the adult heart. However, it remains unclear whether embryonic macrophages also respond to abnormalities in the developing heart. Previously, we reported that the structural protein Sorbs2 promotes the development of the second heart field, with its deficiency resulting in atrial septal defects (ASD). In analyzing RNA-seq data, we noted an upregulation of macrophage-related genes in Sorbs2 ^-/- hearts. Immunostaining and lineage-tracing confirmed an increase in macrophage numbers, underscoring a macrophage response to myocardial abnormalities. Partial depletion of macrophages led to downregulation of genes involved in lipid metabolism, muscle development and organ regeneration, alongside upregulation of genes associated with DNA damage-induced senescence and cardiomyopathy. Additionally, a non-significant increase in septal defects in macrophage-depleted Sorbs2 ^-/- hearts suggests a potential reparative function for macrophages in maintaining structural integrity. Valve formation, however, remained unaffected. Our findings suggest that embryonic macrophages might sense abnormalities in embryonic cardiomyocytes and could adaptively support cardiac structure and function development in response to myocardial abnormalities.

Case presentation: A girl aged 2 years and 5 months presented to the hospital with chief complaints of intermittent fever and weakness of the left limb for more than 1 month. The child had transient urticaria appearing on her face for 5 days. The inflammatory biomarkers were significantly increased. Brain MRI showed multiple ischemic lesions in the brain's small vessels. The patient exhibited significant systemic inflammation and multiple vasculitis. Whole-exome sequencing showed c.1358A>G p. (Tyr453Cys) and c.1082-7T>A compound heterozygous variants in the adenosine deaminase 2 (ADA2) gene, of which the c.1082-7T>A variant has not been reported yet in previous literature. Peripheral blood mRNA reverse transcription-Sanger sequencing confirmed that this variant affected mRNA splicing, resulting in a frameshift with premature stop codon c.1083_1103del p. (Leu362Glnfs*45). Peripheral blood test suggested a significant decrease in ADA2 activity. Eventually, the patient was diagnosed with deficiency of adenosine deaminase 2 (DADA2). Her condition improved after treatment with etanercept. She had no more fevers, and no hemiplegia attacks were observed during the 3 years of follow-up.

Conclusion: Fever and hemiplegia were the main manifestations in this patient, without typical rashes. DADA2 was finally confirmed by enzymology and genetic testing, and we believe this is the first reported case of the c.1082-7T>A intronic variant in DADA2, and the RNA studies conducted in this case have been pivotal in assessing its pathogenicity.

Introduction: Due to its favorable traits-such as lower lignin content, higher oil concentration, and increased protein levels-the genetic improvement of yellow-seeded rapeseed has attracted more attention than other rapeseed color variations. Traditionally, yellow-seeded rapeseed has been identified visually, but the complex variability in the seed coat color of Brassica napus has made manual identification challenging and often inaccurate. Another method, using the RGB color system, is frequently employed but is sensitive to photographic conditions, including lighting and camera settings.

Methods: We present four data-driven models to identify yellow-seeded B. napus using hyperspectral features combined with simple yet intelligent techniques. One model employs partial least squares regression (PLSR) to predict the R, G, and B color channels, effectively distinguishing yellow-seeded varieties from others according to globally accepted yellow-seed classification protocols. Another model uses logistic regression (Logit-R) to produce a probability-based assessment of yellow-seeded status. Additionally, we implement two intelligent models, random forest and support vector classifier to evaluate features selected through lasso-penalized logistic regression.

Results and discussion: Our findings indicate significant recognition accuracies of 96.55% and 98% for the PLSR and Logit-R models, respectively, aligning closely with the accuracy of previous methods. This approach represents a meaningful advancement in identifying yellow-seeded rapeseed, with high recognition accuracy demonstrating the practical applicability of these models.

Objectives: This study aimed to investigate the impact of low-intensity pulsed ultrasound (LIPUS) treatment on the miRNA and mRNA profiles of stem cell-derived extracellular vesicles (EVs). Specifically, it sought to identify key miRNAs and their target mRNAs associated with enhanced therapeutic efficacy in LIPUS-treated stem cell-derived EVs.

Methods: Utilizing miRNA deep-sequencing data from the Gene Expression Omnibus database, differential gene analysis was performed. MiRNA-mRNA target analysis, functional and pathway enrichment analysis, protein-protein interaction network construction, and hub gene identification were conducted. Validation of differentially expressed miRNAs was performed via RT-qPCR in human umbilical cord mesenchymal stem cells (hUC-MSCs) treated with LIPUS.

Results: Ten differentially expressed miRNAs were identified, with six upregulated and four downregulated miRNAs in LIPUS-treated stem cell-derived EVs. Functional enrichment analysis revealed involvement in biological processes such as regulation of metabolic processes, cellular component organization, and response to stress, as well as signaling pathways like cell cycle, MAPK signaling, and Hippo signaling. Protein-protein interaction network analysis identified key hub genes including MYC, GAPDH, HSP90AA1, EP300, JUN, PTEN, DAC1, STAT3, HSPA8, and HIF1A associated with LIPUS treatment. RT-qPCR validation confirmed differential expression of selected miRNAs (hsa-miR-933, hsa-miR-3943, hsa-miR-4633-5p, hsa-miR-592, hsa-miR-659-5p, hsa-miR-4766-3p) in LIPUS-treated hUC-MSCs.

Conclusion: This study sheds light on the potential therapeutic mechanisms underlying LIPUS-treated stem cell-derived EVs. The identified differentially expressed miRNAs and their potential target mRNAs offer valuable insights into the biological processes influenced by LIPUS treatment. While further investigation is necessary to validate their roles as therapeutic targets, this study lays the groundwork for future research on optimizing SC-EV therapy with LIPUS preconditioning.

Background: Neoadjuvant, endocrine, and targeted therapies have significantly improved the prognosis of breast cancer (BC). However, due to the high heterogeneity of cancer, some patients cannot benefit from existing treatments. Increasing evidence suggests that amino acids and their metabolites can alter the tumor malignant behavior through reshaping tumor microenvironment and regulation of immune cell function. Breast cancer cell lines have been identified as methionine-dependent, and methionine restriction has been proposed as a potential cancer treatment strategy.

Methods: We integrated transcriptomic and single-cell RNA sequencing (ScRNA-seq) analyses based on The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) datasets. Then we applied weighted gene co-expression network analysis (WGCNA) and Cox regression to evaluate methionine metabolism-related genes (MRGs) in BC, constructing and validating a prognostic model for BC patients. Immune landscapes and immunotherapy were further explored. Finally, in vitro experiments were conducted to assess the expression and function of key genes APOC1.

Results: In this study, we established and validated a prognostic signature based on eight methionine-related genes to predict overall survival (OS) in BC patients. Patients were further stratified into high-risk and low-risk groups according to prognostic risk score. Further analysis revealed significant differences between two groups in terms of pathway alterations, immune microenvironment characteristics, and immune checkpoint expression. Our study shed light on the relationship between methionine metabolism and immune infiltration in BC. APOC1, a key gene in the prognostic signature, was found to be upregulated in BC and closely associated with immune cell infiltration. Notably, APOC1 was primarily expressed in macrophages. Subsequent in vitro experiments demonstrated that silencing APOC1 reduced the generation of tumor-associated macrophages (TAMs) with an M2 phenotype while significantly decreasing the proliferation, invasion, and migration of MDA-MB-231 and MDA-MB-468 breast cancer cell lines.

Conclusion: We established a prognostic risk score consisting of genes associated with methionine metabolism, which helps predict prognosis and response to treatment in BC. The function of APOC1 in regulating macrophage polarization was explored.

Objective: This study aims to assess the diagnostic efficacy of a combined approach integrating chromosomal karyotyping, copy number variation sequencing (CNV-seq), and quantitative fluorescence polymerase chain reaction (QF-PCR) in detecting chromosomal abnormalities in high-risk pregnancies.

Methods: This retrospective study analyzed 617 high-risk pregnancies undergoing prenatal diagnosis from February 2023 to August 2024, with amniotic fluid samples concurrently analyzed using karyotyping, CNV-seq, and QF-PCR. We evaluated clinical characteristics, diagnostic yields, and inter-method concordance rates. Longitudinal follow-up assessed pregnancy outcomes and neonatal phenotypes, with particular emphasis on cases demonstrating diagnostic discrepancies or variants of uncertain clinical significance.

Results: The integrated approach detected chromosomal abnormalities in 12.5% (77/617) of cases, significantly higher than the rates achieved by karyotyping alone (9.7%) and CNV-seq/QF-PCR alone (8.3%) (p < 0.05). Karyotyping showed full concordance with CNV-seq and QF-PCR in detecting major chromosomal aneuploidies, identifying 21 cases of trisomy 21 and 4 cases of trisomy 18. CNV-seq uniquely identified additional pathogenic copy number variations in 2.1% of cases and variants of uncertain significance (VUS) in 3.2% of cases, both undetectable by conventional karyotyping. Subjects with high-risk non-invasive prenatal testing (NIPT) results had the highest abnormality detection rate (57.6%, p < 0.05). Follow-up data revealed pregnancy termination in 44 of 97 cases with chromosomal abnormalities. Notably, neonates carrying pathogenic CNVs inherited from asymptomatic parents demonstrated normal phenotypes.

Conclusion: The integration of karyotyping, CNV-seq, and QF-PCR provides superior diagnostic yield compared to individual testing strategies in high-risk pregnancies. Although karyotyping remains the gold standard for detecting major chromosomal aberrations, CNV-seq and QF-PCR enhance diagnostic precision through detection of submicroscopic variations. Multi-center studies with larger cohorts are needed to confirm these findings and clarify the clinical significance of uncertain variants.

Background: Patent foramen ovale (PFO) is a congenital defect between the atria, resulting in abnormal hemodynamics. We conducted a genome-wide association study (GWAS) to identify common genetic variants associated with PFO.

Methods: We performed a whole genome sequencing in a discovery cohort of 3,227 unrelated Chinese participants screened for PFO via contrast transthoracic echocardiography (cTTE). Single-nucleotide polymorphisms (SNPs) associated with PFO were further validated by Sanger sequencing and subsequently were evaluated in a validation cohort. Expression quantitative trait loci (eQTL) analysis was conducted using the GTEx database. Single-cell sequencing analyses with pseudotime trajectory modeling were employed to evaluate their expression in human fetal hearts.

Results: The case-control GWAS of discovery cohort ultimately included 517 cases and 517 demographically matched controls. Of the 7,040,407 variants assessed, we identified rs1227675732 (OR = 2.903; 95% CI, 1.961 to 4.297; p = 3.05 × 10^-8), rs62206790 (OR = 2.780; 95% CI, 1.864 to 4.146; p = 2.02 × 10^-7), rs879176184 (OR = 2.724; 95% CI, 1.822 to 4.073; p = 4.30 × 10^-7) and rs13115019 (OR = 2.437; 95% CI, 1.702 to 3.488; p = 5.80 × 10^-7) as high-risk variants for PFO, while rs57922961 (OR = 0.5081; 95% CI, 0.388 to 0.666; p = 6.82 × 10^-7) was identified as protective variant. These variations were replicated in the validation cohort (111 cases and 152 controls). Single-cell sequencing showed that CNOT2, KCNMB4, MLLT10, IGBP1, and FRG1 were highly expressed with significant changes during heart development.

Conclusion: The identification of susceptible loci for PFO might provide insights into the pathogenesis of PFO and contribute to understanding heart development.

Clinical trial registration: https://www.chictr.org.cn/showproj.html?proj=40590, identifier ChiCTR1900024623.