Frontiers in Genetics最新文献

Background and objective: TP53 mutation is an initiating event in tumorigenesis in many cancers. Mutant p53 expression is an important manifestation of TP53 mutations, however, this association has not yet been confirmed in esophageal squamous cell carcinoma (ESCC). This study comprised three components. The first was screening for TP53 mutations using whole-exome sequencing (WES) or whole-genome sequencing (WGS). The second was identifying mutant p53 expression by immunohistochemical (IHC) staining to explore the association between mutant p53 expression and TP53 mutations. The third was assessing the diagnostic value of mutant p53 expression in patients with ESCC.

Methods: Eighteen fresh ESCC specimens were collected for WES. For cases without TP53 mutations detected by WES, WGS was performed to confirm the results and identify additional mutations. These samples underwent p53 IHC staining, and p53 expression was assessed independently by two senior pathologists. The Kappa coefficient was used to evaluate interobserver consistency. An additional 60 ESCC samples and corresponding adjacent tissues were collected for IHC staining. The chi-square test was used to assess the diagnostic value of p53 expression.

Results: WES revealed TP53 mutations in 13/18 cases. WGS of the five WES-negative samples identified TP53 mutations in four of them. Overall, TP53 mutations were detected in 17/18 cases (94.44%). Mutant p53 expression was present in all ESCC cases, and the consistency rate between TP53 mutation and p53 protein expression was 94.44% (17/18). In the combined WES + WGS cohort, mutant p53 expression was detected in 18/18 (100.00%) patients with ESCC. In the IHC cohort, mutant p53 expression was detected in 60/60 (100.00%) patients with ESCC. In both cohorts, Type I mutant p53 expression was the most common subtype, followed by Type IV. Type IV mutant expression was not observed in the WES + WGS cohort. The Kappa value for the two pathologists to was 0.954 (0.911-1.000). The sensitivity and specificity of mutant p53 expression for diagnosing ESCC were 1.00 (0.95-1.00) and 1.00 (0.95-1.00), respectively.

Conclusion: Mutant p53 expression can serve as an alternative marker for TP53 mutation screening used WES or WGS. Mutant p53 expression shows high sensitivity and specificity in distinguishing ESCC and can assist in differentiating benign from malignant esophageal lesions. Five mutant p53 expression subtypes were identified in this study; however, their clinical significance requires further investigation.

CYP2C19 and CYP2D6 are two important pharmacogenes responsible for metabolising a wide range of medications. Both genes exhibit a high level of variation, which can lead to variable activity of the enzymes they encode, with risks of adverse drug reactions and treatment failure. Understanding this variation is therefore of great importance, but the full extent of variability in these genes is not yet documented, particularly for understudied populations. We employed targeted nanopore sequencing to identify genetic variants within CYP2C19 and CYP2D6 for a group of Māori individuals, largely affiliated with the Ngāti Porou iwi from Te Tairāwhiti (Gisborne), Aotearoa New Zealand. 135 CYP2D6 and 73 CYP2C19 genotypes were sequenced, with metaboliser phenotypes inferred for the majority of participants. CYP2D6 normal metabolisers make up 54% of the cohort and 45% of the cohort are CYP2C19 intermediate metabolisers. Nearly 20% had an uncertain CYP2D6 activity due to the prevalence of CYP2D6*71, which is of unknown functional impact. Understanding the extent of variation in these genes should contribute to equitable application of pharmacogenetic testing in Aotearoa New Zealand.

Restrictive cardiomyopathy (RCM) is the most severe type of cardiomyopathy in children with a very poor prognosis. RCM is often diagnosed between 6 and 10 years old and is predominantly of genetic origin. We conducted a retrospective study of 53 patients. The aim of our study was to determine whether outcomes are associated with the type of genetic variant. We compared the prognosis of patients with sarcomeric variants (n = 26) to those with non sarcomeric variants (n = 27). Our results showed no significant differences between the two groups at diagnosis in terms of heart failure symptoms, NT-proBNP levels, or hemodynamic parameters. However, survival without transplantation was significantly worse in the sarcomeric group (p = 0.003), which also exhibited greater disease severity. Furthermore, thrombotic events were more frequent in the sarcomeric group (p = 0.05). In conclusion, RCM caused by sarcomeric variants is associated with a poorer prognosis and a higher incidence of thrombotic events compared to non-sarcomeric RCM.

Osteogenesis imperfecta (OI), or brittle bone disease, is a rare congenital disorder characterized by bone fragility and increased fracture incidence mainly due to mutations in type I collagen or genes associated with collagen synthesis. Genetic and allelic heterogeneity underlie the phenotypic spectrum of OI yet all forms commonly feature early mortality stemming from pulmonary complications, the molecular cause for which has not been resolved. Using single-cell RNA sequencing (scRNAseq), we identified novel molecular and cellular mechanisms underlying the lung abnormalities observed in our Col1a1 ^Aga2/+ (Aga2) mouse, which recapitulates a moderate form of OI. Pulmonary tissues in OI models have consistently displayed a histological emphysematous phenotype, however the origin of this and the effect on lung cell development and function remains unknown. Using scRNAseq data derived from young and adult Aga2 lungs, we found significantly increased AT2 to AT1 cell transition (cells necessary for alveolar structure and gas exchange) in young Aga2 mice but decreased AT2 cell differentiation in adults. Further, adult Aga2 lungs show increased fibroblast activation and differentiation. Finally, our scRNAseq analysis revealed a chronic inflammation phenotype in the Aga2 lung with increased neutrophil and monocyte numbers, IL1B and TNF pathway activation, NOD-like receptor signaling activation, and expression of the NLRP3 inflammasome. Most importantly, we saw a significant decrease in the expression of Scgb1a1 in immune, epithelial, and fibroblast cells. Decreased expression of Scgb1a1 is associated with multiple lung diseases such as emphysema, chronic obstructive pulmonary disease (COPD), and asthma and has become an important therapeutic target for chronic lung inflammation. Clinical treatments specific to pulmonary complications in OI are non-existent and our results reveal that chronic inflammation could be a target to prevent the pulmonary insufficiency and early mortality observed in OI patients.

Background: Exome sequencing (ES) is increasingly used in prenatal diagnosis. However, its efficacy for isolated fetal growth restriction (FGR), especially across different levels of severity, is not well established. This study sought to evaluate and compare the diagnostic yield and clinical impact of trio-ES between isolated non-severe and severe FGR cases.

Methods: In this retrospective study, 164 singleton pregnancies with isolated FGR were stratified into non-severe FGR (estimated fetal weight [EFW] between the third and 10th percentiles) and severe FGR (EFW

Results: Pathogenic or likely pathogenic (P/LP) variants were identified via trio-ES in 8.3% (3/36) of non-severe FGR cases and 18.0% (16/89) of severe FGR cases. In the non-severe group, all detected P/LP variants were associated with high-risk phenotypes and led to termination of pregnancy. In the severe group, these variants were associated with moderate-to-severe disorders, and pregnancy outcomes were diverse (50% termination). Furthermore, the severe FGR cohort exhibited a higher prevalence of preeclampsia and abnormal umbilical artery Doppler waveforms compared to the non-severe group, with adverse outcomes attributable to both monogenic disorders and maternal-placental factors.

Conclusion: This stratified analysis demonstrates that ES provides substantial diagnostic value across the entire severity spectrum of isolated FGR, identifying clinically significant monogenic disorders in both severe and non-severe cases. These findings support the inclusion of ES in the diagnostic workup of isolated FGR, regardless of strict severity cut-offs. They also highlight the need for integrated genetic counseling to manage variants of uncertain significance and multifactorial risks, particularly in severe cases.

Introduction: Congenital cataract is a major cause of blindness and severe visual impairment in children. It may occur as an isolated ocular abnormality or in combination with microcornea, microphthalmia, aniridia, or glaucoma. It can also be part of syndromic conditions. Whole-exome sequencing (WES) is now recognized as an appropriate first-line approach for genetic testing in patients with congenital cataract. In this study, we use WES to characterize the genotype spectrum in a pediatric cataract cohort from southern China.

Methods: In this study, we aimed to clarify the genetic basis of congenital cataract in 40 families from southern China by WES. All candidate variants were confirmed by Sanger sequencing. After bioinformatic analysis, we prioritized rare or novel variants predicted to have moderate to damaging effects and assessed their segregation within each family.

Results: In this cohort of 40 probands with congenital cataract, pathogenic/likely pathogenic variants were identified in 15 (37.5%) individuals, including 6 sporadic cases and 9 familial cases. The identified variants involved 12 genes (CRYBB3, CRYBB2, CRYGS, CRYAA, GJA8, MIP, NHS, BCOR, COL11A1, PAX6, FTL, and FYCO1). In total, 15 pathogenic/likely pathogenic variants were detected, of which 7 were novel. Among genotype-positive patients, seven presented with syndromic cataract, whereas eight had non-syndromic cataract.

Discussion: This study performed WES in 40 probands with congenital cataracts from southern China and achieved a molecular diagnostic yield of 37.5%. Pathogenic/likely pathogenic variants were predominantly identified in crystallin genes, genes encoding lens membrane proteins, and genes implicated in syndromic forms of disease. Notably, a substantial proportion of apparently sporadic cases harbored variants suggestive of a de novo origin. These findings support the clinical utility of WES in clarifying the genetic basis of genetically heterogeneous congenital cataract. They also underscore the limitations of WES compared with whole-genome sequencing (WGS) and highlight the need for larger cohorts and functional validation of candidate variants.

Introduction: Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is a rare autosomal dominant familial gastric cancer syndrome. GAPPS is caused by pathogenic variant in the regulatory region of APC. This study describes the first Korean case of GAPPS associated with a novel likely pathogenic variant in APC promoter 1B region.

Methods: A 35-years-old female patient who have gastric polyposis extending from the fundus to the body of the stomach was evaluated. Sanger sequencing was performed to detect mutations in APC promoter 1B region. A familial segregation study and in vitro luciferase activity assay were conducted to assess the pathogenicity of the novel variant.

Results: A novel variant, c.-181dupC heterozygote, in APC promoter 1B region was detected. The same variant was found in her father, who underwent gastrectomy for gastric cancer. The in vitro functional study revealed a significant decrease in the expression of the APC promoter 1B variant in both HEK 293 TN and HeLa cells.

Conclusion: This is the first reported case of GAPPS in Korea, associated with a novel likely pathogenic variant in APC promoter 1B, linked to a significant reduction in gene expression.

Leukoencephalopathy with ataxia (LKPAT), also known as CLCN2-related leukoencephalopathy, is a rare autosomal recessive disorder caused by pathogenic variants in CLCN2, which encodes ClC-2, a ubiquitously expressed chloride channel protein. However, due to high variability in clinical presentation leading to underdiagnosis, very few cases have been reported since its first description in 2013. The prevalence and genotype-phenotype correlations of LKPAT remain unclear, as do the pathogenic mechanisms of CLCN2 variants. In this study, we reported a Chinese man who presented with dizziness, weakness of the left lower limb, and mild cerebellar ataxia. Notably, the patient had a history of azoospermia. Brain MRI showed symmetrical and confluent white matter abnormalities with hypointense signals on T1-weighted images and hyperintense signals on T2-weighted images. In this patient, a novel biallelic missense variant p.A506V was identified in CLCN2. Through in silico analysis, we observed that substitution of A506 with V506 altered hydrogen bond formation at chloride-binding sites. In addition, the A506V variant impacted the interaction of ClC-2 with GlialCAM, a ClC-2 auxiliary subunit that can physically bind ClC-2 and regulate its biophysical properties and subcellular localization in glial cells. Furthermore, we reviewed the literature and identified potential genotype-phenotype correlations in CLCN2-related diseases. Our results highlight the need for CLCN2 genetic analysis to establish a definitive diagnosis when strong diagnostic clues are present. This study expands the genotypic spectrum of LKPAT, indicates the potential pathogenesis of the CLCN2 A506V variant, and provides valuable insights into further investigation into therapeutics of CLCN2-related leukoencephalopathy.

Cardiovascular disease (CVD) remains the leading cause of worldwide morbidity and mortality. Studies have found that there is a significant genetic component contributing to CVD development. Advances in genome sequencing technologies have revolutionized the identification of disease-causing variants in the human genome. With the development of whole genome sequencing (WGS), the understanding of these variants has been deepened as it enables comprehensive detection of many variants in the genome including structural variants (SVs). SVs are large genomic variants that are present in the genome of an organism and play a significant role in disease. Numerous techniques are being used to detect SVs with varying accuracy levels. Due to the limited number of focused research studies on SVs and CVD, there is a rich opportunity for further investigation with the aim of utilizing SV data in disease diagnosis and treatment plans. Emerging evidence highlights the role of SVs in CVD and the importance of adopting WGS approaches to unravel the genetic architecture of CVD. Moreover, integrating SV data with population scale epidemiology and advanced risk prediction models would enhance CVD prevention by enabling more personalized treatment strategies. This review aims to describe the different types of SVs and their involvement in CVD development and then to discuss WGS-based SV detection methods and future clinical implementations. We also report an overview of the SVs identified across various CVD types and different bioinformatics tools that can be used to detect SVs in WGS data.

Background: Oral squamous cell carcinoma (OSCC) remains a major health burden in India, yet region-specific genomic data are limited. This study aimed to characterize the mutational landscape of OSCC patients from the southwest coast of Karnataka using FFPE tissues and assess potential clinical correlations.

Methods: Whole-exome sequencing was performed on tumor and adjacent normal FFPE samples from 21 OSCC patients. Variants were annotated using multiple clinical databases, and stratified analyses were conducted across clinicopathological parameters including age, sex, tumor site, and TNM stage.

Results: We identified extensive inter-patient variability in clinically relevant mutations, with intronic and missense variants being most frequent. A core set of 21 genes including ABCB1, CD44, IL6, PADI2, and VKORC1-carried pathogenic or drug-response variants in all patients. Ten tumor-exclusive mutations were observed, including TLR1 rs5743618, present in 100% of tumors. Pathway and network analyses highlighted enrichment in p53 signaling, immune pathways, and platinum-drug resistance. Stratified analyses showed no significant differences in mutation burden across TNM stages (Kruskal-Wallis p = 0.952), nodal status (p = 0.460), age, or sex. Polygenic risk score estimation revealed that 15 of 21 patients belonged to the highest-risk quartile, suggesting strong inherited susceptibility.

Conclusion: FFPE-based genomic profiling successfully captured key OSCC-associated alterations and revealed region-specific mutation signatures. The predominance of germline and pharmacogenomic variants and strong PRS enrichment underscore the potential of incorporating hereditary risk assessment and targeted therapy selection into OSCC management strategies in this population.