Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

47 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq on PBMC of two patients with a novel syndromic entity combining immunodeficiency, lymphoproliferation and HLH-like phenotypes, and three age and sex-matched controls for each patient.

ABSTRACT: The study describes two independent cases of NCKAP1L-deficiency, both carrying homozygous non-sense or splice variants in the NCKAP1L gene. The patients presented a phenotype of immunodeficiency, lymphoproliferation and hyperinflammation with features of Hemophagocytic Lymphohistiocytosis (HLH).

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Raphael Carapito

PROVIDER: E-MTAB-8524 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNAseq on PBMC of three patients with Familial Hemophagocytic Lymphohistiocytosis Type 5 (FHL5) and three age and sex-matched controls

Project description:RNAseq on PBMC of three patients with Familial Hemophagocytic Lymphohistiocytosis Type 5 (FHL5) and three age and sex-matched controls.

2020-03-31 | E-MTAB-8875 | biostudies-arrayexpress

A de novo mutation in ITPR3 causes severe combined immunodeficiency

Project description:This study reports two unrelated patients with a combined immunodeficiency. Whole-exome sequencing of both patients, their healthy parents and siblings identified a single de novo missense variant in ITPR3 (NM_002224.3:c.7570C>T, p.Arg2524Cys) in both index cases. While the mRNA level in patients remained the same as in healthy siblings and controls, the level of protein expression was diminished. It was also shown that the ITPR3 heterozygous p.Arg2524Cys mutation impairs calcium flux function in dermal fibroblast of one patient and in a knock-in Jurkat T cell line. Two additional patients with related phenotypes and the same mutation were further identified and described in the study. The present dataset corresponds to the RNAseq performed on PBMC of patient 2 of the study and healthy controls.

2023-01-02 | E-MTAB-12432 | biostudies-arrayexpress

Immature cell populations and an erythropoiesis gene expression signature in systemic juvenile idiopathic arthritis: Implications for pathogenesis

Project description:Objective. Previous observations suggest that active systemic juvenile idiopathic arthritis (sJIA) is associated with a prominent erythropoiesis gene expression signature. The aim of this study was to determine the association of this signature with peripheral blood mononuclear cell (PBMC) subpopulations and its specificity for sJIA as compared to related conditions. 125 patients with JIA (18 sJIA and 107 non-sJIA) and 29 controls were studied. PBMC were isolated and analyzed for multiple surface antigens by flow cytometry and for gene expression profiles. The proportions of different PBMC subpopulations were compared among sJIA, non-sJIA patients and controls and subsequently correlated with the strength of the erythropoiesis signature. Additional gene expression data from patients with familial hemophagocytic lymphohistiocytosis (FHLH) and from a published sJIA cohort were analyzed to determine if the erythropoiesis signature was present. Keywords: Patient Vs Control, reassassment of phenotype Peripheral blood samples were obtained from 29 healthy children and 125 children with JIA . RNA was purified from Ficoll-isolated mononuclear cells, fluorescently labeled and then hybridized to Affymetrix U133 Plus 2.0 GeneChips. Data were analyzed using ANOVA at a 5% false discovery rate threshold after Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization.

2010-07-30 | E-GEOD-21521 | biostudies-arrayexpress

Expression data of wild-type and perforin-knockout CAR-T cell

Project description:Murine chimeric antigen receptor transduced T cells (CAR-T cells) deficient in perforin recapitulate hemophagocytic lymphohistiocytosis (HLH)-like toxicities occuring in human CAR-T recipients. We used microarray to describe gene expression profiles of wild-type and perforin-deficient CAR-T cells.

2020-10-07 | GSE130929 | GEO

Gene Expression Profiling of Peripheral Blood Mononuclear Cells from Children With Active Hemophagocytic Lymphohistiocytosis

Project description:Familial hemophagocytic lymphohistiocytosis (FHL) is a rare, genetically heterogeneous autosomal recessive immune disorder that results when the critical regulatory pathways that mediate immune defense mechanisms and the natural termination of immune/inflammatory responses are disrupted or overwhelmed. In order to advance the understanding of FHL, we performed gene expression profiling of peripheral blood mononuclear cells (PBMCs) from 11 children with untreated FHL. Total RNA was isolated and gene expression levels were determined using microarray analysis. Comparisons between patients with FHL and normal pediatric controls (n = 30) identified 915 down-regulated and 550 up-regulated genes with 2.5-fold difference in expression (P = 0.05). The expression of genes associated with natural killer cell functions, innate and adaptive immune responses, pro-apoptotic proteins, and B- and T-cell differentiation were down-regulated in patients with FHL. Genes associated with the canonical pathways of IL-6, IL-10 IL-1, IL-8, TREM1, LXR/RXR activation, and PPAR signaling and genes encoding of anti-apoptotic proteins were overexpressed in patients with FHL. This, first study of genome-wide expression profiling in children with FHL demonstrates the complexity of gene expression patterns, which underly the immunobiology of FHL. 11 Patients and 33 controls

2011-12-12 | E-GEOD-26050 | biostudies-arrayexpress

Homo sapiens

Project description:Next Generation Mendelian Genetics: Familial Hemophagocytic Lymphohistiocytosis

| PRJNA173802 | ENA

Homo sapiens

Project description:Next Generation Mendelian Genetics: Familial Hemophagocytic Lymphohistiocytosis

| PRJNA173803 | ENA

A single recurrent dominant variant in ITPR3 leads to a syndromic immunodeficiency

Project description:Intracellular calcium levels are finely tuned through intricate actions of a number of channels and transporters, including those at key endocellular stores, e.g. endoplasmic reticulum (ER), lysosomes, and mitochondria. Along with the highly homologous genes Inositol 1,4,5-trisphosphate (IP3) receptor type 1 (ITPR1) and 2 (ITPR2), ITPR3 encodes the IP3 receptor (IP3R), a key player in intracellular calcium release in animals. Here we report the first cases of ITPR3 defects in man leading to a primarily dysimmune phenotype. In four unrelated patients of diverse ethnicity, and suffering from a complex immunodeficiency syndrome, we report the same de novo pathogenic variant - c.7570C>T; p.Arg2524Cys - in ITPR3. Clinically, recurrent severe infectious episodes of viral and bacterial origins, features of ectodermal dysplasia and that of Charcot-Marie-Tooth disease were paramount. The identified variant does not affect gene transcription, yet it was structurally predicted and biologically proven to disrupt proper protein folding and function in vivo. This eventually leads to defective Calcium flux in patient cells, dysregulation of mitochondrial function and a broad dysimmune phenotype characterized primarily by a profound CD4 T cell lymphopenia associated with quasi absence of naïve CD4 and CD8 cells, itself mirrored by an increase in cognate memory cells. The Calcium signaling defect was recapitulated ex vivo through the introduction of this single variant in Jurkat cells. Moreover, site-directed mutagenesis displayed the exquisite sensitivity of Arg2524 to any amino acid change. In conclusion, a single unique recurrent de novo variant in ITPR3 leads to a novel syndromic immunodeficiency.

2023-07-05 | E-MTAB-13124 | biostudies-arrayexpress

CpG short fragments with continuous CG patterns in patients of hemophagocytic lymphohistiocytosis

Project description:mNGS of hemophagocytic lymphohistiocytosis patients' plasma Raw sequence reads

| PRJNA813341 | ENA

human metagenome

Project description:Metagenomics of serum specimen from a patient with hemophagocytic lymphohistiocytosis

| PRJNA576033 | ENA