Project description:To explore the genetic cause of a Chinese woman with fetal hydrocephalus X-linked hydrocephalus (XLH), a genetic disorder, has an incidence of 1/30,000 male births. The great proportion of XLH is ascribed to loss of function mutations of L1 cell adhesion molecule gene (L1CAM), but silent mutations in L1CAM with pathogenic potential were rare, and were usually ignored especially in WES detection. In the present study, we describe a novel silent L1CAM mutation in a Chinese pregnant woman reporting continuous five times pregnancies with fetal hydrocephalus. After fetal blood sampling, we found c.453G>T (p.Gly151=) in L1CAM gene of the fetus by whole exome sequencing (WES), RT-PCR of the mRNA from cord blood mononuclear cells and subsequent sequence analysis identified the mutation created a potential 5' splice site consensus sequence, which would result in an in-frame deletion of 72 bp from exon 5 and 24 amino acids of the L1CAM protein. Heterozygous mutations were confirmed in analyzing DNA and mRNA from peripheral blood mononuclear cells of the woman, and, a severe L1 syndrome was confirmed by fetal ultrasound scan and MRI. Our study first indicated c.453G>T (p.Gly151=) in L1CAM could be disease causing for hydrocephalus, which would aid in genetic counseling for the prenatal diagnosis of hydrocephalus. Meanwhile, it suggested some silent mutations detected in WES should not be ignored, splicing predictions of these mutations were necessary.
Project description:We identified a novel germline mutation of the microphthalmia-associated transcription factor (MITF - E318K). This mutation was found to be present in numerous melanoma families, as well as the general population, where its association with melanoma has a significant effect. We determined the effect of the E318K mutation on global MITF target gene transcription. We developed a tetracycline-inducible system for expression of wild type MITF or the E318K variant in melanoma cell lines with constitutively low or undetectable levels of endogenous MITF (HT144 and C32). We examined whole-genome expression profiles in these cells following induction of either wild-type or E318K MITF for 48 hours. Analysis suggests that the MITF E318K mutant exhibits differential transcriptional activity against some, though not all, target genes. Expression profiling by array
Project description:Introduction: Although sequence variants in FAT1 have been identified in patients with distinct renal disease, definitive proof of causality in human disease is meager. Methods: A 35-year-old Chinese female with microscopic hematuria and proteinuria underwent a renal biopsy to identify the underlying cause. Whole-exome sequencing (WES) with homozygosity mapping revealed genetic factors, and patient-derived primary urinary epithelial cells confirmed the renal agenesis phenotype. RNA sequencing, immunofluorescence staining, and immunoblotting were used to explore the mechanisms involved. Results: The patient, whose parents are cousins, exhibited a syndrome featuring ptosis, corneal dystrophy, macular degeneration and right feet syndactyly, with glomerulotubular nephropathy. A homozygous frameshift mutation in FAT1 (NM_005245: c.7444_7445delGT) was identified. Structural prediction, immunohistochemistry, and Western blot analyses confirmed that the mutation caused translational repression of FAT1. RNA-seq analysis revealed significant dysregulation of cell adhesion and the Rap1 signaling pathway. Immunofluorescence showed a marked loss of intercellular β-catenin junctions and cytoskeletal disruption in patient-derived primary urinary epithelial cells. Pull-down assays demonstrated that these effects were associated with a reduction in activated Rap1 levels. Conclusion: This study presents compelling evidence that the homozygous FAT1 frameshift mutation (c.7444_7445delGT, p.Val2482fs) is causally associated with nephropathy and congenital anomalies. The mutation likely leads to the degradation of transcribed mRNA, which in turn impairs protein expression. These findings underscore the critical role of FAT1 in renal development and offer new insights into the molecular mechanisms underlying these conditions.
Project description:This study aims to confirm the pathogenic role of the AFG3L2 F175S mutation in dominant optic atrophy (DOA) and elucidate its molecular mechanisms disrupting mitochondrial morphology and function.
Project description:POC1A encodes a WD repeat protein localizing to centrioles and spindle poles and associated with Short stature, onychodysplasia, facial dysmorphism and hypotrichosis (SOFT) syndrome (OMIM #614813). In our study, we reported on two patients with primordial dwarfism (PD) from the same family. We utilized Whole Exome Sequencing (WES) in the patients to screen all PD related genes and to define putative novel candidate genes. A novel homozygous p.T120A missense mutation was detected in POC1A, a known causative gene of SOFT syndrome, and confirmed using Sanger sequencing. To confirm the pathogenicity of the detected mutation, primary fibroblast cultures obtained from the patients and a control individual were used. Gene expression profiles of the fibroblast cultures were taken. We performed gene expression arrays on fibroblasts cultured from patients with SOFT syndrome and POC1A mutation and compared their expression profiles to that of control fibroblast cells.
Project description:Background: In vitro models are an essential tool towards understanding the molecular characteristics of colorectal cancer (CRC) and the testing of therapies for CRC. To this end we established 21 novel CRC cell lines of which six were derived from liver metastases. Extensive genetic, genomic, transcriptomic and methylomic profiling was performed in order to characterize these new cell lines and all data is made publically available. Additionally, sensitivity of oxaliplatin was tested as a measure for chemotherapy resistance. Results: DNA copy-number alterations (CNA) were compared between primary and metastasis derived cell lines. In concordance with previous studies copy-number gain of chr20, and loss of chr8p were found highly specific for liver metastases. Previously reported BRAF-mutation associated DNA methylation profiles could be validated on the genome-wide DNA methylation profiles of these cell lines. 47.6% of the loci previously reported to associate with BRAF mutation status were reproduced in this dataset. When examining the gene expression profiles in conjunction with these DNA methylation results, we identified 20 genes of which the gene expression correlated with the DNA methylation status, including MEIS1, LRAT and STC2. These genes have previously been reported to be subject to transcriptional regulation through DNA hypermethylation, validating our approach. Conclusions: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC. 21 CRC cell lines were analyzed
Project description:Gene expression array utilizes the advantage of the big number of the significantly changed genes creating transcriptional profiles of known mutations. Creating gene expression profiles of the animal models with known genetic defect provides great opportunity for further investigation human diseases with unknown etiology. Motheaten mice with mutation in protein tyrosine phosphatase Ptpn6 have massive neutrophilic infiltration within the skin followed by autoinflammatory and autoimmune systemic pathology resembling similarity to neutrophilic dermatoses in human. Keywords: genetic modification We performed microarray study on motheaten mice with novel mutation (meb2) in protein tyrosine phosphatase non-receptor-6 (Ptpn6) in with 5 sick bone marrow samples and 5 wild type controls and found significant difference between these two groups.
Project description:A mouse model utilizing knock in strategy to coexpress both oncogenic ErbB2 (NeuNT) and a PI3KCA mutation H1047R Microarray was used to determine gene expression change due to H1047R mutation by comparison between ErbB2 KI tumors expressing either wild type or mutant allele.
Project description:We found a novel MEN1 p. R21Afs mutaion in a multiple endocrine neoplasia type 1 family. To investigate the pathogenic function of p.R21Afs MEN1 mutation, the leukocyte transcriptoma profilings derived from MEN1 patients with heterozygote p.R21Afs MEN1 mutation was compared with the unaffected relatives without p.R21Afs MEN1 mutation.