Homozygosity mapping in a consanguineous family with osteogenesis imperfecta (OI)
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE21958 | GEO | 2010/11/01
SECONDARY ACCESSION(S): PRJNA126763
REPOSITORIES: GEO
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Project description:Homozygosity mapping using genome-wide SNP arrys is a useful tool to map causative genes of mendelian disorders in consanguineous patients To search for LOH (loss of heterozygosity) regions we hybridized genomic DNA from a OI patient and a normal sibling against Human610quad beadarrays from Illumina (www.illumina.com). Genotyping data was analyzed with BeadStudio software (www.illumina.com) Genomic DNAs from OI affected individual and non-affected sibling were hybridized each on an Illumina Human610Quad Genotyping BeadChip. Image data was analyzed using Beadstudio 3.1.3 software. CNV and LOH (larger than 1 Mb) analysis was performed using the cnvPartition 2.3.4. It was considered as a region of interest those showing LOH in the affected individual but not in the non-affected sibling.
2010-11-01 | E-GEOD-21958 | biostudies-arrayexpress
Project description:Homozygosity mapping in a consanguineous family with osteogenesis imperfecta (OI)
| PRJNA126763 | ENA
Project description:Osteogenesis Imperfecta (OI) is a genetic, rare disease characterized by bone fragility, with a wide range in the severity of clinical manifestations. The majority of the cases are due to mutations in COL1A1 or COL1A2 genes which code for the type I collagen molecule. Mesenchymal stem cells (MSCs), as the progenitors of the osteoblasts, the main type I collagen secreting cell type in the bone, have been proposed and tested as an innovative therapy for OI with promising but transient outcomes. In this study, we performed a phase I clinical trial based on reiterative infusions of histocompatible MSCs in two pediatric patients affected by severe and moderate OI. The aim of this study was to assess the safety and effectiveness of this cell therapy in non-immunosuppressed OI patients. The host response to MSCs was also evaluated by collecting the sera from OI patients before, along and after the cell therapy. The results of this clinical trial are twofold: the sequential administration of MSCs is safe and improve the bone parameters and quality of life of OI patients. Moreover, MSCs therapy elicits a pro-osteogenic paracrine response in patients, especially noticeable in that affected by severe OI. These results indicate the feasibility and potential of reiterative MSCs infusion for OI and highlight the paracrine response shown by OI patients as a consequence of MSCs treatment. Study design and patients: The Mesenchymal Stem Cell Therapy for the Treatment of Osteogenesis Imperfecta (TERCELOI) study (www.clinical trials.gov: # NCT02172885, EudraCT number: 2012-002553-38) is an independent multi-center Phase I clinical trial to evaluate the feasibility, safety and potential efficacy of infused sibling HLA-matched MSCs in non-immunosuppressed children with OI. PBMCs isolation and serum collection: Venous blood samples were collected before the cell therapy (basal serum), along the cell therapy (1 week, 1 month and 4 months after each MSCs infusion) and during the follow-up period (1 and 2 years after the fifth and last MSCs infusion). MLR assay: PBMCs isolated from patients were resuspended in PBS+FBS (5%) and stained with carboxyfluoroscein succinate-ester (CFSE) (Molecular Probes, USA). Bone mineral density: Bone mineral density (BMD) at the lumbar spine (LS) from L1 to L4, was measured by dual energy x-ray absorptiometry (DXA) on a whole-body scanner within a pediatric platform (Hologic QDR densitometer). Raw measurements were converted to Z-scores for analysis using reference standards for age and pubertal status. OI-MSCs isolation and characterization and culture: OI-MSCs were derived from discarded and donated bone fragments of OI pediatric patients undergoing corrective surgery. All patients suffered Type III-IV OI, with mutations in either COL1A1 or COL1A2 genes. The donation was approved by the Basque Clinical Research Ethics Committee. Briefly, bone chips were mechanically flushed with PBS and then cut into small pieces to extrude cells without the use of enzymes. The cut bone pieces were let undisturbed during 14 days until OI-MSCs migrated to cell culture plate. OI-MSCs were assessed for the expression of CD105, CD90 and CD73 and the absence of CD14, CD34, CD45, CD19 and HLA-DR. MSCs were also tested for their potential to differentiate to osteoblasts and adipocytes using specific cell culture media. OI-MSCs were cultured under standard growth medium (DMEM low glucose with glutamax (Gibco), penicillin/streptomycin (Gibco) and fetal bovine serum at 10% (Sigma-Aldrich, USA). Osteogenesis induction medium (OIM) was composed of standard medium plus ascorbic acid 0.2 mM, beta-glycerophosphate 10 mM, and dexamethasone 10 nM (all from Sigma-Aldrich). When specified, FBS was replaced by P01 and P02 serum samples at 2.5%. RNAseq and Q-PCR validation: OI-MSCs from 10 OI pediatric patients were seeded in 96-well plates (1 000 cells/well) and the following day cultured in the presence of OIM. Next, total RNA was isolated with the AllPrep kit (QIAGEN, USA). cDNA library (TrueSeq stranded Total cDNA library, Illumina, USA) and sequencing at HiSeq 4000 (PE100nt, 50 million reads/sample).
2021-01-22 | GSE157587 | GEO
Project description:Osteocytes are long-lived, highly interconnected, terminally differentiated osteoblasts which reside within mineralized bone matrix. They constitute about 95% of adult bone cells and play important functions in the regulation of bone remodeling, phosphate homeostasis, and mechanical stimuli sensing and response. However, the role of osteocytes in the pathogenesis of congenital diseases of bone such as osteogenesis imperfecta (OI) is poorly understood. This study characterized in vivo transcriptional changes in osteocytes from the CrtapKO and oim/oim mouse models of OI, using RNA-sequencing on osteocyte-enriched cortical bone from femur and tibia. These models were chosen because they mimic two types of OI with different genetic mutations which result in distinct type I collagen defects. Hundreds of transcripts were dysregulated in either model of OI compared to WT, but 281 of these were similarly up- or down-regulated in both. Conversely, very few transcripts were differentially expressed between the CrtapKO and oim/oim mice, indicating that distinct alterations in type I collagen can lead to shared pathogenic processes and similar phenotypic outcomes. Bioinformatics analyses identified several critical hubs of dysregulation that were enriched in annotation terms such as development and differentiation, ECM and collagen fibril organization, cell adhesion, signaling, regulatory processes, pattern binding, chemotaxis, and cell projections. The data further indicated alterations in important signaling pathways such as WNT and TGF-β. Overall, our study suggested that the osteocyte transcriptome is broadly dysregulated in OI, that transcriptomic alterations in OI can be strikingly similar despite arising from different genetic mutations, and that the potential consequences of osteocyte dysregulation deserve further investigation.
2020-07-21 | GSE154748 | GEO
Project description:Purpose: The main objective of this pilot study was to compare blood transcriptional landscape of OI patients with COL1A1 pathogenic variants and their healthy relatives, in order to find out different gene expression and dysregulated molecular pathways in OI. Methods: We performed RNA sequencing analysis of the whole blood in seven individuals affected with different OI severity and their five unaffected relatives from the three families. The data was analyzed using edgeR package of R Bioconductor. Functional profiling and pathway analysis of the identified differently expressed genes was performed with g:GOSt and MinePath web-based tools. Results: We identified 114 differently expressed genes. The expression of 79 genes was up-regulated, while 35 genes were down-regulated. The functional analysis identified a presence of dysregulated interferon signaling pathways (IFI27, IFITM3, RSAD12, GBP7). Additionally, the expressions of the genes related to extracellular matrix organization, Wnt signaling, vitamin D metabolism and MAPK-ERK 1/2 pathways were also altered. Conclusions: The current pilot study successfully captured the differential expression of inflammation and bone metabolism pathways in OI patients.
2020-10-28 | GSE160207 | GEO
Project description:Osteogenesis imperfecta (OI) is a rare bone disease that is associated with fractures and low bone mass. Sclerostin inhibition is being evaluated as a potential approach to increase bone mass in OI. We had previously found that in Col1a1Jrt/+ mice, a model of severe OI, treatment with an anti-sclerostin antibody had a minor effect on the skeletal phenotype. In the present study, we assessed the effect of genetic sclerostin inactivation in the Col1a1Jrt/+ mouse. We crossed Col1a1Jrt/+ mice with Sost knockout mice to generate Sost-deficient Col1a1Jrt/+ mice and assessed differences between Col1a1Jrt/+ mice with homozygous Sost deficiency and Col1a1Jrt/+ mice with heterozygous Sost deficiency. We found that Col1a1Jrt/+ mice with homozygous Sost deficiency had higher body mass, femur length, trabecular bone volume, cortical thickness and periosteal diameter as well as increased biomechanical parameters of bone strength. Differences between genotypes were larger at the age of 14 weeks than at 8 weeks of age. Transcriptome analysis of RNA extracted from the tibial diaphysis revealed only 5 differentially regulated genes. Thus, genetic inactivation of Sost increased bone mass and strength in the Col1a1Jrt/+ mouse. It appears from these observations that the degree of Sost suppression that is required for eliciting a beneficial response can vary with the genetic cause of OI.
2023-04-04 | GSE220601 | GEO
Project description:Osteogenesis imperfecta (OI) is a rare inherited connective tissue dysplasia characterized with skeletal fragility, recurrent fractures and bone deformity, predominantly caused by mutations in the genes COL1A1 or COL1A2 that encode the chains of type I collagen. In the present study, clinical manifestations and genetic variants were analysed from 188 Chinese OI patients, majority of which are of southern China origin. By targeted sequencing, 64 and 58 OI patients were found carrying mutations in COL1A1 and COL1A2 respectively, including 12 novel COL1A1 and 8 novel COL1A2 variants. We identified a COL1A1 hotspot (c.G2461A; p.G821S) in 8 patients and validated two novel splicing mutations. A diverse mutational and phenotypic spectrum was observed, coupling with heterogeneity observed in the transcriptomic data (n=6) derived from osteoblasts of our cohort. Missense mutations were significantly associated (χ2 p=0.0096) with a cluster of patients with more severe clinical phenotypes. Additionally, the severity of OI was more correlated with the quality of bones, rather than the bone mineral density. Bone density is most responsive to bisphosphonate (BP) treatment during the juvenile stage (10-15 y/o). In contrast, height is not responsive to bisphosphonate treatment. Our findings expand the mutational spectrum of type I collagen genes and the genotype-phenotype correlation in Chinese OI patients. The observation of effective BP treatment in an age-specific manner may help to improve OI patient management.
2022-01-10 | GSE186141 | GEO
Project description:Sequencing of a Fleckvieh animal for dominant Osteogensis imperfecta
| PRJEB12324 | ENA
Project description:In this study, we use transcriptomic approaches, to delineate a non-coding TAPT1 mutation (c.1237-52G>A) resulting in a protein-null allele, that segregated with a congenital recessive disease recessive consisting of Osteogenesis Imperfecta (OI) and neonatal progeria.
2023-01-20 | GSE197118 | GEO
Project description:In this study, we use transcriptomic approaches, to delineate a non-coding TAPT1 mutation (c.1237-52G>A) resulting in a protein-null allele, that segregated with a congenital recessive disease recessive consisting of Osteogenesis Imperfecta (OI) and neonatal progeria.
2023-01-20 | GSE197119 | GEO