Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 502.483
Filter
1.
Theor Appl Genet ; 137(7): 151, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38849610

ABSTRACT

Dwarfing is an ideal agronomic trait in crop breeding, which can improve lodging resistance and increase crop productivity. In this study, we identified a dwarf mutant cp-3 from an EMS-mutagenized population, which had extremely short internodes, and the cell length and number of internodes were significantly reduced. Meanwhile, exogenous GA3 treatment partially rescued the plant height of the cp-3. Inheritance analysis showed that the cp-3 mutant was regulated via a recessive nuclear locus. A candidate gene, CsERECTA, encoding an LRR receptor-like serine/threonine-protein kinase, was cloned through a map-based cloning strategy. Sequence analysis showed that a nucleotide mutation (C ~ T) in exon 26 of CsERECTA led to premature termination of the protein. Subsequently, two transgenic lines were generated using the CRISPR/Cas9 system, and they showed plant dwarfing. Plant endogenous hormones quantitative and RNA-sequencing analysis revealed that GA3 content and the expression levels of genes related to GA biosynthesis were significantly reduced in Cser knockout mutants. Meanwhile, exogenous GA3 treatment partially rescued the dwarf phenotype of Cser knockout mutants. These findings revealed that CsERECTA controls stem elongation by regulating GA biosynthesis in cucumber.


Subject(s)
Cucumis sativus , Gene Expression Regulation, Plant , Gibberellins , Phenotype , Plant Proteins , Cucumis sativus/genetics , Cucumis sativus/growth & development , Gibberellins/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Plants, Genetically Modified/growth & development , Genes, Plant , Plant Stems/growth & development , Plant Stems/genetics , Mutation , Cloning, Molecular
2.
Curr Microbiol ; 81(7): 215, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38849666

ABSTRACT

Non-tailed icosahedral phages belonging to families Fiersviridae (phages MS2 and Qbeta), Tectiviridae (PRD1) and Microviridae (phiX174) have not been considered in detail so far as potential antibacterial agents. The aim of the study was to examine various aspects of the applicability of these phages as antibacterial agents. Antibacterial potential of four phages was investigated via bacterial growth and biofilm formation inhibition, lytic spectra determination, and phage safety examination. The phage phiX174 was combined with different classes of antibiotics to evaluate potential synergistic interactions. In addition, the incidence of phiX174-insensitive mutants was analyzed. The results showed that only phiX174 out of four phages tested against their corresponding hosts inhibited bacterial growth for > 90% at different multiplicity of infection and that only this phage considerably prevented biofilm formation. Although all phages show the absence of potentially undesirable genes, they also have extremely narrow lytic spectra. The synergism was determined between phage phiX174 and ceftazidime, ceftriaxone, ciprofloxacin, macrolides, and chloramphenicol. It was shown that the simultaneous application of agents is more effective than successive treatment, where one agent is applied first. The analysis of the appearance of phiX174 bacteriophage-insensitive mutants showed that mutations occur with a frequency of 10-3. The examined non-tailed phages have a limited potential for use as antibacterial agents, primarily due to a very narrow lytic spectrum and the high frequency of resistant mutants appearance, but Microviridae can be considered in the future as biocontrol agents against susceptible strains of E. coli in combinations with conventional antimicrobial agents.


Subject(s)
Anti-Bacterial Agents , Biofilms , Anti-Bacterial Agents/pharmacology , Biofilms/drug effects , Biofilms/growth & development , Bacteriophages/genetics , Bacteriophages/physiology , Escherichia coli/virology , Escherichia coli/drug effects , Bacteriophage phi X 174/drug effects , Bacteriophage phi X 174/genetics , Bacteria/drug effects , Bacteria/virology , Mutation
3.
Am J Case Rep ; 25: e943466, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38822519

ABSTRACT

BACKGROUND Various resistance mechanisms of the epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) have been reported, and approximately half of the cases show a T790M point mutation as resistance to EGFR-TKI. In addition, 3-14% of cases of non-small cell lung cancer transform into small cell lung carcinoma (SCLC) during treatment. However, there are few reported cases in which 2 mechanisms of resistance have been observed simultaneously. This report describes a 66-year-old man with initial presentation of stage IIA right-sided lung adenocarcinoma with EGFR gene exon 21 L858R mutation and 3 years of stable disease. During treatment with erlotinib, the patient developed SCLC and adenocarcinoma with EGFR exon 21 L858R and exon 20 T790M mutation. CASE REPORT A 66-year-old man underwent right pneumonectomy plus nodal dissection 2a for right hilar lung cancer and was diagnosed with an EGFR exon21 L858R mutated lung adenocarcinoma. Three years later, pleural dissemination was observed in the right chest wall. Although erlotinib was continued for 52 months, new metastases to the right ribs were detected. Chest wall tumor resection was performed. Based on the World Health Organization classification, the patient was diagnosed with combined SCLC, with EGFR exon21 L858R and exon20 T790M mutation. The patient received 4 cycles of carboplatin plus etoposide, 14 cycles of amrubicin, and 2 cycles of irinotecan. Chemotherapy continued for 25 months. CONCLUSIONS Long-term survival was achieved by chemotherapy after transformation. Since EGFR mutation-positive lung cancer shows a variety of acquired resistances, it is important to consider the treatment strategy of performing re-biopsy.


Subject(s)
Adenocarcinoma of Lung , Adenocarcinoma , ErbB Receptors , Erlotinib Hydrochloride , Lung Neoplasms , Small Cell Lung Carcinoma , Aged , Humans , Male , Adenocarcinoma/drug therapy , Adenocarcinoma/genetics , Adenocarcinoma of Lung/drug therapy , Adenocarcinoma of Lung/genetics , Drug Resistance, Neoplasm , ErbB Receptors/genetics , Erlotinib Hydrochloride/therapeutic use , Lung Neoplasms/drug therapy , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Mutation , Small Cell Lung Carcinoma/genetics , Small Cell Lung Carcinoma/drug therapy , Small Cell Lung Carcinoma/pathology , /therapeutic use
4.
Alzheimers Res Ther ; 16(1): 127, 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38872230

ABSTRACT

BACKGROUND: Our study aims to evaluate the genetic and phenotypic spectrum of Frontotemporal dementia (FTD) gene variant carriers in Chinese populations, investigate mutation frequencies, and assess the functional properties of TBK1 and OPTN variants. METHODS: Clinically diagnosed FTD patients underwent genetic analysis through exome sequencing, repeat-primed polymerase chain reaction, and Sanger sequencing. TBK1 and OPTN variants were biologically characterized in vitro using immunofluorescence, immunoprecipitation, and immunoblotting analysis. The frequencies of genes implicated in FTD in China were analyzed through a literature review and meta-analysis. RESULTS: Of the 261 Chinese FTD patients, 61 (23.4%) carried potential causative variants in FTD-related genes, including MAPT (n = 17), TBK1 (n = 7), OPTN (n = 6), GRN (n = 6), ANXA11 (n = 4), CHMP2B (n = 3), C9orf72 GGGGCC repeats (n = 2), CYLD (n = 2), PRNP (n = 2), SQSTM1 (n = 2), TARDBP (n = 2), VCP (n = 1), CCNF (n = 1), CHCHD10 (n = 1), SIGMAR1 (n = 1), CHCHD2 (n = 1), FUS (n = 1), TMEM106B (n = 1), and UBQLN2 (n = 1). 29 variants can be considered novel, including the MAPT p.D54N, p.E342K, p.R221P, p.T263I, TBK1 p.E696G, p.I37T, p.E232Q, p.S398F, p.T78A, p.Q150P, p.W259fs, OPTN p.R144G, p.F475V, GRN p.V473fs, p.C307fs, p.R101fs, CHMP2B p.K6N, p.R186Q, ANXA11 p.Q155*, CYLD p.T157I, SQSTM1 p.S403A, UBQLN2 p.P509H, CCNF p.S160N, CHCHD10 p.A8T, SIGMAR1 p.S117L, CHCHD2 p.P53fs, FUS p.S235G & p.S236G, and TMEM106B p.L144V variants. Patients with TBK1 and OPTN variants presented with heterogeneous clinical phenotypes. Functional analysis demonstrated that TBK1 I37T and E232Q mutants showed decreased autophosphorylation, and the OPTN phosphorylation was reduced by the TBK1 I37T mutant. The OPTN-TBK1 complex formation was enhanced by the TBK1 E696G mutant, while OPTN R144G and F475V mutants exhibited reduced recruitment to autophagosomes compared to the wild-type. The overall frequency of TBK1 and OPTN in Chinese FTD patients was 2.0% and 0.3%, respectively. CONCLUSIONS: Our study demonstrates the extensive genetic and phenotypic heterogeneity of Chinese FTD patients. TBK1 mutations are the second most frequent cause of clinical FTD after MAPT in the Chinese.


Subject(s)
Cell Cycle Proteins , Frontotemporal Dementia , Membrane Transport Proteins , Protein Serine-Threonine Kinases , Transcription Factor TFIIIA , Aged , Female , Humans , Male , Middle Aged , Cell Cycle Proteins/genetics , China/epidemiology , East Asian People/genetics , Frontotemporal Dementia/genetics , Genetic Predisposition to Disease/genetics , Membrane Transport Proteins/genetics , Mutation , Protein Serine-Threonine Kinases/genetics , Transcription Factor TFIIIA/genetics
5.
Blood Cancer J ; 14(1): 97, 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38871702

ABSTRACT

The evaluation of measurable residual disease (MRD) in acute myeloid leukemia (AML) using comprehensive mutation analysis by next-generation sequencing (NGS) has been investigated in several studies. However controversial results exist regarding the detection of persisting mutations in DNMT3A, TET2, and ASXL1 (DTA). Benchmarking of NGS-MRD taking into account other molecular MRD strategies has to be done. Here, we performed error-corrected-NGS-MRD in 189 patients homogeneously treated in the ALFA-0702 study (NCT00932412). Persistence of non-DTA mutations (HR = 2.23 for RFS and 2.26 for OS), and DTA mutations (HR = 2.16 for OS) were associated with poorer prognosis in multivariate analysis. Persistence of at least two mutations in complete remission (CR) was associated with a higher cumulative incidence of relapse (CIR) (HR = 3.71, p < 0.0001), lower RFS (HR = 3.36, p < 0.0001) and OS (HR = 3.81, p = 0.00023) whereas persistence of only one mutation was not. In 100 analyzable patients, WT1-MRD, but not NGS-MRD, was an independent factor for RFS and OS. In the subset of 67 NPM1 mutated patients, both NPM1 mutation detection (p = 0.0059) and NGS-MRD (p = 0.035) status were associated with CIR. We conclude that detectable NGS-MRD including DTA mutations correlates with unfavorable prognosis in AML. Its integration with alternative MRD strategies in AML management warrants further investigations.


Subject(s)
High-Throughput Nucleotide Sequencing , Leukemia, Myeloid, Acute , Mutation , Neoplasm, Residual , Nucleophosmin , Humans , Leukemia, Myeloid, Acute/genetics , Leukemia, Myeloid, Acute/mortality , Leukemia, Myeloid, Acute/therapy , Female , Male , Middle Aged , Adult , Aged , Young Adult , Prognosis , DNA Methyltransferase 3A , Aged, 80 and over , DNA (Cytosine-5-)-Methyltransferases/genetics , Adolescent , Repressor Proteins/genetics , DNA Mutational Analysis
6.
Nat Commun ; 15(1): 5053, 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38871684

ABSTRACT

Childhood radioactive iodine exposure from the Chornobyl accident increased papillary thyroid carcinoma (PTC) risk. While cervical lymph node metastases (cLNM) are well-recognized in pediatric PTC, the PTC metastatic process and potential radiation association are poorly understood. Here, we analyze cLNM occurrence among 428 PTC with genomic landscape analyses and known drivers (131I-exposed = 349, unexposed = 79; mean age = 27.9 years). We show that cLNM are more frequent in PTC with fusion (55%) versus mutation (30%) drivers, although the proportion varies by specific driver gene (RET-fusion = 71%, BRAF-mutation = 38%, RAS-mutation = 5%). cLNM frequency is not associated with other characteristics, including radiation dose. cLNM molecular profiling (N = 47) demonstrates 100% driver concordance with matched primary PTCs and highly concordant mutational spectra. Transcriptome analysis reveals 17 differentially expressed genes, particularly in the HOXC cluster and BRINP3; the strongest differentially expressed microRNA also is near HOXC10. Our findings underscore the critical role of driver alterations and provide promising candidates for elucidating the biological underpinnings of PTC cLNM.


Subject(s)
Chernobyl Nuclear Accident , Iodine Radioisotopes , Lymphatic Metastasis , Mutation , Thyroid Cancer, Papillary , Thyroid Neoplasms , Humans , Thyroid Cancer, Papillary/genetics , Thyroid Cancer, Papillary/pathology , Lymphatic Metastasis/genetics , Male , Adult , Female , Thyroid Neoplasms/genetics , Thyroid Neoplasms/pathology , Adolescent , Proto-Oncogene Proteins B-raf/genetics , Young Adult , Lymph Nodes/pathology , Proto-Oncogene Proteins c-ret/genetics , Child , Genomics , Middle Aged , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism , Gene Expression Profiling , MicroRNAs/genetics , MicroRNAs/metabolism , Neoplasms, Radiation-Induced/genetics , Neoplasms, Radiation-Induced/pathology , Neck/pathology , Gene Expression Regulation, Neoplastic
7.
Nat Commun ; 15(1): 4871, 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38871738

ABSTRACT

The phenomenon of mixed/heterogenous treatment responses to cancer therapies within an individual patient presents a challenging clinical scenario. Furthermore, the molecular basis of mixed intra-patient tumor responses remains unclear. Here, we show that patients with metastatic lung adenocarcinoma harbouring co-mutations of EGFR and TP53, are more likely to have mixed intra-patient tumor responses to EGFR tyrosine kinase inhibition (TKI), compared to those with an EGFR mutation alone. The combined presence of whole genome doubling (WGD) and TP53 co-mutations leads to increased genome instability and genomic copy number aberrations in genes implicated in EGFR TKI resistance. Using mouse models and an in vitro isogenic p53-mutant model system, we provide evidence that WGD provides diverse routes to drug resistance by increasing the probability of acquiring copy-number gains or losses relative to non-WGD cells. These data provide a molecular basis for mixed tumor responses to targeted therapy, within an individual patient, with implications for therapeutic strategies.


Subject(s)
Chromosomal Instability , ErbB Receptors , Lung Neoplasms , Mutation , Tumor Suppressor Protein p53 , Humans , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism , Animals , Mice , Lung Neoplasms/genetics , Lung Neoplasms/drug therapy , Lung Neoplasms/pathology , ErbB Receptors/genetics , ErbB Receptors/metabolism , ErbB Receptors/antagonists & inhibitors , Drug Resistance, Neoplasm/genetics , Cell Line, Tumor , Protein Kinase Inhibitors/pharmacology , Protein Kinase Inhibitors/therapeutic use , Adenocarcinoma of Lung/genetics , Adenocarcinoma of Lung/drug therapy , Adenocarcinoma of Lung/pathology , Molecular Targeted Therapy/methods , Female , DNA Copy Number Variations , Male
8.
Elife ; 132024 Jun 03.
Article in English | MEDLINE | ID: mdl-38829031

ABSTRACT

Connexins allow intercellular communication by forming gap junction channels (GJCs) between juxtaposed cells. Connexin26 (Cx26) can be regulated directly by CO2. This is proposed to be mediated through carbamylation of K125. We show that mutating K125 to glutamate, mimicking the negative charge of carbamylation, causes Cx26 GJCs to be constitutively closed. Through cryo-EM we observe that the K125E mutation pushes a conformational equilibrium towards the channel having a constricted pore entrance, similar to effects seen on raising the partial pressure of CO2. In previous structures of connexins, the cytoplasmic loop, important in regulation and where K125 is located, is disordered. Through further cryo-EM studies we trap distinct states of Cx26 and observe density for the cytoplasmic loop. The interplay between the position of this loop, the conformations of the transmembrane helices and the position of the N-terminal helix, which controls the aperture to the pore, provides a mechanism for regulation.


Subject(s)
Carbon Dioxide , Connexin 26 , Cryoelectron Microscopy , Protein Conformation , Humans , Carbon Dioxide/metabolism , Connexin 26/metabolism , Connexin 26/genetics , Connexins/metabolism , Connexins/genetics , Connexins/chemistry , Gap Junctions/metabolism , Mutation
9.
Ideggyogy Sz ; 77(5-6): 207-211, 2024 May 30.
Article in Hungarian | MEDLINE | ID: mdl-38829246

ABSTRACT

Background - Leukodystrophies, a hete­ro­­ge­neous group of brain and spinal cord dis­orders, often pose challenges in es­tab­li­shing molecular etiology. Vanishing White Matter Disease (VWMD) is a rare sub­type of leu­ko­dys­trophies presenting with characteristic clinical and MRI features, ne­ver­theless, achieving diag­nostic certainty requires genetic studies.

Case presentation - Our patient is a nine year old girl, who developed progressive gait difficulties at around 3-4 years of age. Her brain MRI showed confluent lesions with in­­creased signal intensity in the cerebral and cerebellar white matter on T2/FLAIR se­quen­ces, within which hypointense regions ap­peared with signal intensity resembling that of the cerebrospinal fluid on T1 sequences. Whole exome sequencing identified a homozygous likely pathogenic variant within the EIF2B5 gene in the proband, which was present in a heterozygous state in both asymptomatic parents. Having the clinical and molecular genetic diagnosis established, we explored therapeutic possibilities for the patient.

Conclusion - VWMD is a severe form of leukodystrophies with little or no disease modifying therapy available until recently. A better understanding of its molecular pathogenesis offers some hope for new inventive therapies. 

.


Subject(s)
Eukaryotic Initiation Factor-2B , Leukoencephalopathies , Mutation , Humans , Leukoencephalopathies/genetics , Leukoencephalopathies/diagnostic imaging , Leukoencephalopathies/pathology , Female , Eukaryotic Initiation Factor-2B/genetics , Child , Magnetic Resonance Imaging , White Matter/diagnostic imaging , White Matter/pathology
11.
Mol Biol Evol ; 41(6)2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38829800

ABSTRACT

It is commonly thought that the long-term advantage of meiotic recombination is to dissipate genetic linkage, allowing natural selection to act independently on different loci. It is thus theoretically expected that genes with higher recombination rates evolve under more effective selection. On the other hand, recombination is often associated with GC-biased gene conversion (gBGC), which theoretically interferes with selection by promoting the fixation of deleterious GC alleles. To test these predictions, several studies assessed whether selection was more effective in highly recombining genes (due to dissipation of genetic linkage) or less effective (due to gBGC), assuming a fixed distribution of fitness effects (DFE) for all genes. In this study, I directly derive the DFE from a gene's evolutionary history (shaped by mutation, selection, drift, and gBGC) under empirical fitness landscapes. I show that genes that have experienced high levels of gBGC are less fit and thus have more opportunities for beneficial mutations. Only a small decrease in the genome-wide intensity of gBGC leads to the fixation of these beneficial mutations, particularly in highly recombining genes. This results in increased positive selection in highly recombining genes that is not caused by more effective selection. Additionally, I show that the death of a recombination hotspot can lead to a higher dN/dS than its birth, but with substitution patterns biased towards AT, and only at selected positions. This shows that controlling for a substitution bias towards GC is therefore not sufficient to rule out the contribution of gBGC to signatures of accelerated evolution. Finally, although gBGC does not affect the fixation probability of GC-conservative mutations, I show that by altering the DFE, gBGC can also significantly affect nonsynonymous GC-conservative substitution patterns.


Subject(s)
Evolution, Molecular , Gene Conversion , Models, Genetic , Recombination, Genetic , Selection, Genetic , Genetic Fitness , Mutation , Base Composition , Genetic Linkage
12.
Gen Comp Endocrinol ; 355: 114563, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38830459

ABSTRACT

Investigating the principles of fish fat deposition and conducting related research are current focal points in fish nutrition. This study explores the endocrine regulation of LEAP2 and GHSR1a in zebrafish by constructing mutantmodels andexamining the effects of the endocrine factors LEAP2 and its receptor GHSR1a on zebrafish growth, feeding, and liver fat deposition. Compared to the wild type (WT), the mutation of LEAP2 results in increased feeding and decreased swimming in zebrafish. The impact is more pronounced in adult female zebrafish, characterized by increased weight, length, width, and accumulation of lipid droplets in the liver.Incontrast, deficiency in GHSR1a significantly reduces the growth of male zebrafish and markedly decreases liver fat deposition.These research findings indicate the crucial roles of LEAP2 and GHSR1a in zebrafish feeding, growth, and intracellular fat metabolism. This study, for the first time, investigated the endocrine metabolic regulation functions of LEAP2 and GHSR1a in the model organism zebrafish, providing initial insights into their effects and potential mechanisms on zebrafish fat metabolism.


Subject(s)
CRISPR-Cas Systems , Lipid Metabolism , Receptors, Ghrelin , Zebrafish , Animals , Zebrafish/genetics , Zebrafish/metabolism , Receptors, Ghrelin/genetics , Receptors, Ghrelin/metabolism , Lipid Metabolism/genetics , CRISPR-Cas Systems/genetics , Male , Female , Zebrafish Proteins/genetics , Zebrafish Proteins/metabolism , Mutation
13.
Orphanet J Rare Dis ; 19(1): 226, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38844942

ABSTRACT

BACKGROUND: Waardenburg syndrome (WS) is a rare genetic disorder mainly characterized by hearing loss and pigmentary abnormalities. Currently, seven causative genes have been identified for WS, but clinical genetic testing results show that 38.9% of WS patients remain molecularly unexplained. In this study, we performed multi-data integration analysis through protein-protein interaction and phenotype-similarity to comprehensively decipher the potential causative factors of undiagnosed WS. In addition, we explored the association between genotypes and phenotypes in WS with the manually collected 443 cases from published literature. RESULTS: We predicted two possible WS pathogenic genes (KIT, CHD7) through multi-data integration analysis, which were further supported by gene expression profiles in single cells and phenotypes in gene knockout mouse. We also predicted twenty, seven, and five potential WS pathogenic variations in gene PAX3, MITF, and SOX10, respectively. Genotype-phenotype association analysis showed that white forelock and telecanthus were dominantly present in patients with PAX3 variants; skin freckles and premature graying of hair were more frequently observed in cases with MITF variants; while aganglionic megacolon and constipation occurred more often in those with SOX10 variants. Patients with variations of PAX3 and MITF were more likely to have synophrys and broad nasal root. Iris pigmentary abnormality was more common in patients with variations of PAX3 and SOX10. Moreover, we found that patients with variants of SOX10 had a higher risk of suffering from auditory system diseases and nervous system diseases, which were closely associated with the high expression abundance of SOX10 in ear tissues and brain tissues. CONCLUSIONS: Our study provides new insights into the potential causative factors of WS and an alternative way to explore clinically undiagnosed cases, which will promote clinical diagnosis and genetic counseling. However, the two potential disease-causing genes (KIT, CHD7) and 32 potential pathogenic variants (PAX3: 20, MITF: 7, SOX10: 5) predicted by multi-data integration in this study are all computational predictions and need to be further verified through experiments in follow-up research.


Subject(s)
Microphthalmia-Associated Transcription Factor , SOXE Transcription Factors , Waardenburg Syndrome , Waardenburg Syndrome/genetics , Humans , Microphthalmia-Associated Transcription Factor/genetics , Microphthalmia-Associated Transcription Factor/metabolism , SOXE Transcription Factors/genetics , SOXE Transcription Factors/metabolism , PAX3 Transcription Factor/genetics , PAX3 Transcription Factor/metabolism , Mice , Animals , Phenotype , Genotype , Mutation/genetics
14.
Hum Genomics ; 18(1): 59, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38844983

ABSTRACT

BACKGROUND: Hereditary hearing loss is a rare hereditary condition that has a significant presence in consanguineous populations. Despite its prevalence, hearing loss is marked by substantial genetic diversity, which poses challenges for diagnosis and screening, particularly in cases with no clear family history or when the impact of the genetic variant requires functional analysis, such as in the case of missense mutations and UTR variants. The advent of next-generation sequencing (NGS) has transformed the identification of genes and variants linked to various conditions, including hearing loss. However, there remains a high proportion of undiagnosed patients, attributable to various factors, including limitations in sequencing coverage and gaps in our knowledge of the entire genome, among other factors. In this study, our objective was to comprehensively identify the spectrum of genes and variants associated with hearing loss in a cohort of 106 affected individuals from the UAE. RESULTS: In this study, we investigated 106 sporadic cases of hearing impairment and performed genetic analyses to identify causative mutations. Screening of the GJB2 gene in these cases revealed its involvement in 24 affected individuals, with specific mutations identified. For individuals without GJB2 mutations, whole exome sequencing (WES) was conducted. WES revealed 33 genetic variants, including 6 homozygous and 27 heterozygous DNA changes, two of which were previously implicated in hearing loss, while 25 variants were novel. We also observed multiple potential pathogenic heterozygous variants across different genes in some cases. Notably, a significant proportion of cases remained without potential pathogenic variants. CONCLUSIONS: Our findings confirm the complex genetic landscape of hearing loss and the limitations of WES in achieving a 100% diagnostic rate, especially in conditions characterized by genetic heterogeneity. These results contribute to our understanding of the genetic basis of hearing loss and emphasize the need for further research and comprehensive genetic analyses to elucidate the underlying causes of this condition.


Subject(s)
Connexin 26 , Exome Sequencing , Hearing Loss , Humans , Male , Female , Hearing Loss/genetics , Hearing Loss/epidemiology , Connexin 26/genetics , Adult , United Arab Emirates/epidemiology , Child , Mutation/genetics , Adolescent , High-Throughput Nucleotide Sequencing , Genetic Testing , Middle Aged , Young Adult , Child, Preschool , Connexins/genetics , Genetic Predisposition to Disease , Heterozygote , Homozygote
15.
Brief Bioinform ; 25(4)2024 May 23.
Article in English | MEDLINE | ID: mdl-38833323

ABSTRACT

The emergence and rapid spread of SARS-CoV-2 prompted the global community to identify innovative approaches to diagnose infection and sequence the viral genome because at several points in the pandemic positive case numbers exceeded the laboratory capacity to characterize sufficient samples to adequately respond to the spread of emerging variants. From week 10, 2020, to week 13, 2023, Slovenian routine complete genome sequencing (CGS) surveillance network yielded 41 537 complete genomes and revealed a typical molecular epidemiology with early lineages gradually being replaced by Alpha, Delta, and finally Omicron. We developed a targeted next-generation sequencing based variant surveillance strategy dubbed Spike Screen through sample pooling and selective SARS-CoV-2 spike gene amplification in conjunction with CGS of individual cases to increase throughput and cost-effectiveness. Spike Screen identifies variant of concern (VOC) and variant of interest (VOI) signature mutations, analyses their frequencies in sample pools, and calculates the number of VOCs/VOIs at the population level. The strategy was successfully applied for detection of specific VOC/VOI mutations prior to their confirmation by CGS. Spike Screen complemented CGS efforts with an additional 22 897 samples sequenced in two time periods: between week 42, 2020, and week 24, 2021, and between week 37, 2021, and week 2, 2022. The results showed that Spike Screen can be applied to monitor VOC/VOI mutations among large volumes of samples in settings with limited sequencing capacity through reliable and rapid detection of novel variants at the population level and can serve as a basis for public health policy planning.


Subject(s)
COVID-19 , High-Throughput Nucleotide Sequencing , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Humans , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , High-Throughput Nucleotide Sequencing/methods , COVID-19/virology , COVID-19/diagnosis , COVID-19/epidemiology , Spike Glycoprotein, Coronavirus/genetics , Mutation , Genome, Viral , Slovenia/epidemiology
16.
Clin Epigenetics ; 16(1): 76, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38845031

ABSTRACT

Tatton-Brown-Rahman syndrome (TBRS) is a rare congenital genetic disorder caused by autosomal dominant pathogenic variants in the DNA methyltransferase DNMT3A gene. Typical TBRS clinical features are overgrowth, intellectual disability, and minor facial anomalies. However, since the syndrome was first described in 2014, a widening spectrum of abnormalities is being described. Cardiovascular abnormalities are less commonly reported but can be a major complication of the syndrome. This article describes a family of three individuals diagnosed with TBRS in adulthood and highlights the variable expression of cardiovascular features. A 34-year-old proband presented with progressive aortic dilatation, mitral valve (MV) regurgitation, left ventricular (LV) dilatation, and ventricular arrhythmias. The affected family members (mother and brother) were diagnosed with MV regurgitation, LV dilatation, and arrhythmias. Exome sequencing and computational protein analysis suggested that the novel familial DNMT3A mutation Ser775Tyr is located in the methyltransferase domain, however, distant from the active site or DNA-binding loops. Nevertheless, this bulky substitution may have a significant effect on DNMT3A protein structure, dynamics, and function. Analysis of peripheral blood cfDNA and transcriptome showed shortened mononucleosome fragments and altered gene expression in a number of genes related to cardiovascular health and of yet undescribed function, including several lncRNAs. This highlights the importance of epigenetic regulation by DNMT3A on cardiovascular system development and function. From the clinical perspective, we suggest that new patients diagnosed with congenital DNMT3A variants and TBRS require close examination and follow-up for aortic dilatation and valvular disease because these conditions can progress rapidly. Moreover, personalized treatments, based on the specific DNMT3A variants and the different pathways of their function loss, can be envisioned in the future.


Subject(s)
DNA (Cytosine-5-)-Methyltransferases , DNA Methyltransferase 3A , Pedigree , Humans , DNA Methyltransferase 3A/genetics , Adult , Male , DNA (Cytosine-5-)-Methyltransferases/genetics , Female , Cardiomyopathies/genetics , Aortic Diseases/genetics , Exome Sequencing/methods , Intellectual Disability/genetics , Mutation
17.
Sci Adv ; 10(23): eadj0787, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38848368

ABSTRACT

Somatic mutations in T cells can cause cancer but also have implications for immunological diseases and cell therapies. The mutation spectrum in nonmalignant T cells is unclear. Here, we examined somatic mutations in CD4+ and CD8+ T cells from 90 patients with hematological and immunological disorders and used T cell receptor (TCR) and single-cell sequencing to link mutations with T cell expansions and phenotypes. CD8+ cells had a higher mutation burden than CD4+ cells. Notably, the biggest variant allele frequency (VAF) of non-synonymous variants was higher than synonymous variants in CD8+ T cells, indicating non-random occurrence. The non-synonymous VAF in CD8+ T cells strongly correlated with the TCR frequency, but not age. We identified mutations in pathways essential for T cell function and often affected lymphoid neoplasia. Single-cell sequencing revealed cytotoxic TEMRA phenotypes of mutated T cells. Our findings suggest that somatic mutations contribute to CD8+ T cell expansions without malignant transformation.


Subject(s)
CD8-Positive T-Lymphocytes , Mutation , Receptors, Antigen, T-Cell , Humans , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/metabolism , Adult , Single-Cell Analysis , Male , Female , Middle Aged , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism , Gene Frequency , Phenotype , Aged
18.
Crit Rev Immunol ; 44(6): 37-47, 2024.
Article in English | MEDLINE | ID: mdl-38848292

ABSTRACT

BACKGROUND: Estrogen receptor (ER) signaling plays an important role in the development and functional differentiation of the breast and participates in the process of breast cancer. Activated ER can affect various aspects of the cell's behavior, including proliferation, via modulating the expression of many downstream target genes. Phosphorylation is one of the activation pathways of ER. However, the relationship between estrogen receptor phosphorylation sites and breast development and carcinogenesis is not clear. METHODS: Using Crisper-Cas9 gene editing technology, we constructed ER S309A mutant mice. Using carmine staining of the mammary gland of mice at different developmental stages, we examined the breast development of ER S309A mice. Using hematoxylin-eosin (HE) staining of vaginal smears of mice at the same time for 5 consecutive days, we measured the vaginal epithelial keratinocytes. RESULTS: We established ER S309A mutant mice and observed breast defects in ER S309A mice. In addition, we observed decreased reproductive ability, and estrous cycle disorder in ER S309A mice. The number of vaginal epithelial keratino-cytes in the estrous cycle of ER S309A mice was decreased. CONCLUSION: These results suggest that the phosphorylation site of ER at Serine 309 is important for ER function and breast development.


Subject(s)
Serine , Animals , Female , Mice , Phosphorylation , Serine/metabolism , Humans , Receptors, Estrogen/metabolism , Receptors, Estrogen/genetics , Breast/growth & development , Breast/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Mammary Glands, Animal/metabolism , Mammary Glands, Animal/growth & development , Mutation
19.
JCO Precis Oncol ; 8: e2300640, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38848517

ABSTRACT

PURPOSE: The choice of threshold and reliability of high tumor mutational burden (TMB) to predict outcomes and guide treatment choice for patients with metastatic melanoma receiving first-line immune checkpoint inhibitor (ICI) therapy in the real world is not well known. METHODS: Using a deidentified nationwide (US-based) melanoma clinicogenomic database, we identified a real-world cohort of patients with metastatic melanoma (N = 497) who received first-line monotherapy anti-PD-1 (n = 240) or dual anti-PD-1 and anti-CTLA-4 ICI (n = 257) and had a tissue-based comprehensive genomic profiling test TMB score. RESULTS: TMB-high (TMB-H; ≥10 mutations per megabase [muts/Mb], n = 352, 71%) was independently predictive of superior real-world progression-free survival and overall survival versus TMB-low (<10 mut/Mb, n = 145, 29%) in both mono ICI (hazard ratio [HR], 0.45 [95% CI, 0.32 to 0.63]; P < .001; HR, 0.61 [95% CI, 0.41 to 0.90]; P = .01, respectively) and dual ICI (HR, 0.67 [95% CI, 0.49 to 0.90]; P = .009; HR, 0.61 [95% CI, 0.42 to 0.88]; P = .007, respectively) patients. Dual ICI offered no significant advantage in BRAFwt patients and unexpectedly demonstrated greatest benefit in the TMB 10-19 mut/Mb group, identifying a TMB-very high (≥20 mut/Mb, n = 247, 50%) BRAFmut patient subgroup for whom mono ICI may be preferable. CONCLUSION: TMB-H predicts superior outcomes on ICI while coassessment of BRAF status and TMB may inform first-line regimen choice.


Subject(s)
Immune Checkpoint Inhibitors , Melanoma , Mutation , Humans , Melanoma/drug therapy , Melanoma/genetics , Melanoma/secondary , Melanoma/mortality , Immune Checkpoint Inhibitors/therapeutic use , Male , Female , Middle Aged , Aged , Adult , Aged, 80 and over , Treatment Outcome
SELECTION OF CITATIONS
SEARCH DETAIL
...