Molecular Genetics and Genomics最新文献

Root nodule symbiosis is traditionally recognized in the Fabales, Fagales, Cucurbitales, and Rosales orders within the Rosid I clade of angiosperms. However, ambiguous root nodule formation has been reported in Zygophyllaceae and Roystonea regia (Arecaceae), although a detailed analysis has yet to be conducted. We aimed to perform morphological analyses of root structures in these plants and utilize metagenomic techniques to identify and characterize the bacterial populations within the nodule-like structures. We collected root samples of Tribulus terrestris (Zygophyllaceae) and Roystonea regia from West Asia and the Caribbean, respectively. We conducted detailed morphological analyses of nodule-like structures, isolated and genome-sequenced the endophytes, and employed metagenomic techniques to identify the bacterial populations within these formations. We observed nodule-like structures in both plant species. Symbiosomes, which are hallmark structures of nodulating plants, were not detected. Metagenome sequence data analysis revealed potential nodulating and nitrogen-fixing bacteria in the nodule-like structures of both species. Canonical nodulation and nitrogen-fixation genes were identified in microbes associated with the nodules. However, the phylogenomic analysis showed that the bacteria isolated from T. terrestris and R. regia are within Gammaproteobacteria and Bacilli, which are not typically known as nodulating bacteria. The observed structures differ significantly from traditional nodules found in legumes and actinorhizal plants, suggesting unique characteristics with hosting nitrogen-fixing bacteria. Although bacteria identified through in silico analysis or culture are well-known nitrogen-fixers, their specific role in root nodule formation remains to be investigated.

Patients with multiple sclerosis (MS) face a heightened risk of developing chronic obstructive pulmonary disease (COPD). Despite this widely reported association, the pathogenic contributors and processes that may favor the development of COPD in MS patients have yet to be identified. Recent studies have suggested peripheral blood leukocytes as a potential link between COPD and autoimmune disorders. Therefore, this study aimed to unveil shared molecular signatures between MS and COPD using blood transcriptomes. To this end, gene expression datasets obtained from MS and COPD blood specimens were retrieved from the Gene Expression Omnibus (GEO) database. By integrating datasets belonging to each disorder, differentially expressed genes (DEGs) were determined for each disease. Then, the protein-protein interaction (PPI) network was constructed for shared DEGs between MS and COPD. Subsequently, the network was analyzed to identify hub genes and key regulatory miRNAs. The integrated data for MS encompassed 51 samples (28 from MS patients and 23 from controls), and the integrated data for COPD included 450 samples (275 from COPD patients and 175 from controls). A total of 246 genes were found to exhibit identical directions of expression in both MS and COPD. By applying a high confidence threshold (0.7), a PPI network with 74 nodes was constructed. TP53, H4C6, SNRPE, and RPS11 were identified as hub genes according to the degree measure. In addition, 8 miRNAs were identified as key regulators, each interacting with 6 mRNAs. Among these miRNAs, miR-218-5p and miR-142-5p have been previously reported to contribute to the pathogenesis of these diseases, and here they were identified as key regulators of the shared PPI network, suggesting a potential epigenetic link between MS and COPD. In conclusion, the results highlighted the potential role of peripheral blood leucocytes as a bridge between MS and COPD. These findings broaden our understanding of pathogenic contributors linking MS and COPD. While this transcriptomics study identified multiple key players, such as TP53, miR-218-5p, and miR-142-5p, the assessment of their therapeutic efficacy demands further experimental studies.

Our study examined the relationships and interactions among 30 genes related to the NOD-like receptor protein 3 (NLRP3) inflammasome. We identified 368 interconnections between these 30 genes, with NLRP3 participating in 38 interactions. The potential roles of these genes in atherosclerosis were evaluated based on protein-protein interaction networks and coexpression analysis. We identified differential expression in 20 genes, five of which were significantly upregulated: P2RX7, CASP1, CD36, GBP5, and PYCARD. We also observed a strong positive association between P2RX7 and PYCARD and as a notable negative association between RELA and CD36. Furthermore, our analysis revealed a clear association between the expression of inflammasome-associated genes and immune cell infiltration in disease specimens. To diagnose AS, a logistic regression model based on six inflammasome-related genes, achieved an Area under the curve of 0.996, indicating excellent diagnostic performance. Genomic enrichment analysis indicated that inflammasome-related genes were primarily involved in various pathways, such as hypertrophic cardiomyopathy and ribosomal function. To validate our findings, we confirmed the expression of risk genes in AS cells using qRT-PCR and Western blot techniques. Additionally, we observed a shift toward M2 polarization in THP-1 macrophages upon P2RX7 knockdown, further supporting our findings.

Tuberous sclerosis complex (TSC) is a rare genetic disorder characterized by the formation of benign tumors in various organs, particularly in the central nervous system. We aimed to delineate the molecular profile of Turkish individuals diagnosed with TSC by analyzing the TSC1 and TSC2 genes using next-generation sequencing (NGS). Sophia Genetics' Sophia Inherited Disease Panel was used to perform NGS on 22 individuals diagnosed with TSC and to identify pathogenic variants in the TSC1 and TSC2 genes. Among the 22 cases, mutations were found in 3 (13.6%) for TSC1 and in 16 (73%) for TSC2, while 3 (13.6%) exhibited no detectable mutations. Notably, one individual with a TSC2 mutation presented with angiofibroma, ungual fibroma, and pitted dental enamel, while another had cardiac rhabdomyoma. Autism spectrum disorders were observed in 6 (27%) with TSC2 mutations, including one with autistic behavior. Abnormal motor development was noted in 3 (13.6%), of which 2 had TSC2 mutations. Severe intellectual disability was found in 3 (13.6%) with TSC2 mutations, and developmental delay was seen in 2 (9%) with TSC2 mutations. Epileptic encephalopathy occurred in 3 (13.6%), with 2 having TSC2 mutations. Additionally, 6 (27%) exhibited drug resistance for focal seizures, with 5 of them having TSC2 mutations. These findings are consistent with other research indicating that TSC2 mutations are associated with a more severe phenotypic range compared to TSC1 mutations. Moreover, our analysis showed that some people with TSC1/TSC2 mutations did not match diagnostic criteria. This highlights the importance of genetic testing and molecular profiling in understanding the clinical variability and aiding in the management of TSC patients.

Low-frequency non-syndromic hearing loss (LFNSHL) is a rare auditory disorder affecting frequencies ≤ 2000 Hz. To elucidate its genetic basis, we conducted whole-exome sequencing on nine Chinese families (31 affected individuals) with LFNSHL. Four heterozygous pathogenic variants, including two novel variants, were identified in common LFNSHL-related genes (WFS1, DIAPH1) and less common genes (TNC, EYA4), achieving a 44% genetic diagnosis rate. All genetically diagnosed patients had early adulthood-onset hearing loss except for one WFS1 variant case, and all exhibited progressive hearing loss. Our findings indicate that LFNSHL is predominantly inherited in an autosomal dominant manner. Further review showed that WFS1 mutations typically cause childhood-onset LFNSHL, while DIAPH1 and EYA4 mutations result in adulthood-onset LFNSHL; interestingly, WFS1 mutations generally progress to moderate hearing loss, milder than DIAPH1, TNC, and EYA4 mutations. Additionally, tinnitus was more prevalent in patients with WFS1, DIAPH1, and EYA4 mutations than those with TNC mutations. Notably, hearing loss deteriorated at all frequencies, becoming markedly severe after age 50 for TNC and WFS1 mutations, and after age 40 for EYA4 mutations. Mutations in WFS1 were predominantly missense, with the p.Ser807 codon and the protein's C-terminal intracytoplasmic domain identified as mutation hotspots. Comparative analysis revealed a higher incidence of bilateral symmetrical progressive LFNSHL in genetically diagnosed patients than those without. This study, the first to investigate LFNSHL genetics in a Chinese cohort, underscores the complex genetic landscape and phenotypic variability of LFNSHL, providing valuable insights for future diagnostic and therapeutic strategies.

Objective: . Despite the establishment of a link between telomere status and carcinogenesis, lack of a consensus in the cancer specific pattern of telomere length has a severe impact on the use of relative telomere length (RTL) in cancer diagnosis. The disparity in assessing the relationship between telomere length and cancer risk is complex and may vary as it is influenced by other factors. The objective of this study is to thoroughly examine the intricate relationship between telomere length and cancer incidence in Papillary Thyroid Cancer (PTC) depending on the tumor type, stage, patients' sex and age. Therefore, the current study is focused on the association of RTL in PTC patients with different clinicopathological characteristics and compared with controls to determine the risk of PTC and expected survival time after surgery.

Method: . This study included 126 patients with PTC and 80 controls. RTL in thyroid tissues was measured using quantitative (q) PCR. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using logistic regression analysis. Kaplan-Meier and Cox regression were used to analyze postsurgical outcomes.

Result: . The RTL of patients was significantly shorter than that of controls. A short RTL was significantly correlated with an elevated risk of PTC in patients aged ≥ 55 years, female sex, classic subtype, and tumor size > 2 cm. A short RTL did not affect the overall survival of patients with PTC; however, it was associated with poor survival in patients with tumor size > 2 cm and tumor invasion.

Conclusion: . This unique study combines the use of RTL with various clinicopathological features of patients with PTC. In conclusion, RTL is a promising tumor marker that correlates with the clinical characteristics of patients with PTC. Specifically, RTL < 0.6 could be used with age, sex, tumor size > 2 cm and tumor invasion to predict the risk of PTC development and prognosis of the disease. This study will open new horizon in the use of molecular marker such as RTL for understanding its association with increased cancer risk in patients with different clinicopathological features.

The brown pencilfish, Nannostomus eques is a lebiasinid harvested for ornamental purposes; however, its complete mitochondrial genome sequence is still unknown. To enrich the molecular genetic information pertaining to Nannostomus, we present here the first report of the complete mitochondrial genome sequence of Nannostomus eques and compare it with Nannostomus beckfordi. The total lengths of the N. eques and N. beckfordi mitochondrial genomes were 16,673 bp and 16,742 bp, respectively, and there was a double-stranded ring with a heavy chain and a light chain in the whole structures of both. We used PhyloSuite v1.2.1 to construct the maximum likelihood and Bayesian Analysis trees based on tRNAs, rRNAs, and protein-coding genes (PCGs) data and compared them with other Nannostomus species by referring to other studies. Our study found that N. beckfordi has a closer genetic relationship with N. eques than with Lebiasina astrigata, which belongs to the same family, and we discovered some similarities and even rules in Nannostomus species. Our study provides a molecular basis for the conservation and sustainable use of Nannostomus species.

This paper describes a novel methodology based on GWAS filtering, aimed to find novel phenotypes associated to genetic loci independently of canonical risk factors using the large database of UK Biobank. Genome wide association studies (GWAS) is an untargeted methodology able to identify novel gene variants associated with diseases. Novel gene-phenotype associations might be discovered by this method. UKBiobank was interrogated by an automated routine to search associations between hundreds of phenotypes and single nucleotide polymorphisms (SNPs) resulting from GWAS, using Cardiovascular Disease as investigated trait. Six gene variants associated with CVD, independently of canonical risk factors, were identified using a variants database of more than 400k genotyped subjects (rs9349379 PHACTR1;intragenic_variant, rs74617384 LPA; intron_variant, rs4977574 CDKN2B-AS1;intron_variant, rs11191846 STN1;intron_variant, rs3184504, SH2B3;missense_variant, rs2929155 ADAMTS7;synonymous_variant). Novel clinical and biochemical phenotypes have been associated to the variants. The phenotypical characterization of the loci helped to propose mechanistic links that could explain their connection to CVD.

Telomeres, which are situated at the terminal ends of chromosomes, undergo a reduction in length with each cellular division, ultimately reaching a critical threshold that triggers cellular senescence. Cancer cells circumvent this senescence by utilizing telomere maintenance mechanisms (TMMs) that grant them a form of immortality. These mechanisms can be categorized into two primary processes: the reactivation of telomerase reverse transcriptase and the alternative lengthening of telomeres (ALT) pathway, which is dependent on homologous recombination (HR). Various strategies have been developed to inhibit telomerase activation in 85-95% of cancers, including the use of antisense oligonucleotides such as small interfering RNAs and endogenous microRNAs, agents that simulate telomere uncapping, expression modulators, immunotherapeutic vaccines targeting telomerase, reverse transcriptase inhibitors, stabilization of G-quadruplex structures, and gene therapy approaches. Conversely, in the remaining 5-15% of human cancers that rely on ALT, mechanisms involve modifications in the chromatin environment surrounding telomeres, upregulation of TERRA long non-coding RNA, enhanced activation of the ataxia telangiectasia and Rad-3-related protein kinase signaling pathway, increased interactions with nuclear receptors, telomere repositioning driven by HR, and recombination events between non-sister chromatids, all of which present potential targets for therapeutic intervention. Additionally, combinatorial therapy has emerged as a strategy that employs selective agents to simultaneously target both telomerase and ALT, aiming for optimal clinical outcomes. Given the critical role of anti-TMM strategies in cancer treatment, this review provides an overview of the latest insights into the structure and function of telomeres, their involvement in tumorigenesis, and the advancements in TMM-based cancer therapies.

Flavin-containing monooxygenases (FMOs) are present in most organisms including plants, fungi, bacteria, invertebrates and vertebrates, where they catalyse the oxidative metabolism of a range of xenobiotics and endogenous metabolites. FMOs have been associated with ageing and longevity in the mouse and in C. elegans. As all five FMOs of C. elegans share an evolutionary root with mouse and human FMO5, it was of interest to discover if effects on ageing and longevity persisted across the whole group. We therefore investigated the impact of fmo gene knockout (KO) in C. elegans. We found that fmo-1, fmo-3 and fmo-4 KO significantly extended C. elegans lifespan relative to wild type and, as previously reported, FMO-2 over-expression did likewise. The transcription levels of C. elegans fmo genes were determined throughout the life cycle (embryo, larva and adult) in wild type and in each mutant to discover if their expression was related to stages in ageing, and expression levels were compared to those in human and mouse. In wild type worms, fmo-1 and fmo-4 were the mostly highly transcribed genes (especially at the larval stage), whereas fmo-2 and fmo-3 were the least transcribed, at all stages. Notably, the knockout of fmo-4 led to a 17- to 30-fold up-regulation of fmo-2, along with significantly increased levels of the other fmos. This parallels recent findings in the long-lived C. elegans tald-1 mutant where fmo-2 was also significantly up-regulated and reinforces its importance in lifespan extension.