Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA818525 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18498402_1.fastq.gz | Fastqsanger.gz | |||
| SRR18498402_2.fastq.gz | Fastqsanger.gz | |||
| SRR18498403_1.fastq.gz | Fastqsanger.gz | |||
| SRR18498403_2.fastq.gz | Fastqsanger.gz | |||
| SRR18498404_1.fastq.gz | Fastqsanger.gz |
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Project description:Clinical remission is apparent when laboratory markers of inflammation are normal and clinical symptoms are absent. However, sub-clinical inflammation can still be present. A detailed analysis of the immune status during this inactive state of disease may provide a useful tool to subcategorize patients with subclinical immune activation We performed (un)supervised clustering analysis of IBD-associated genes and applied IngenuityM-BM-. pathway software to identify specific molecular profiles between patients. We analyzed RNA gene expression profiles of peripheral blood leucocytes (PBL) from pediatric IBD patients in clinical remission and age-matched controls.
2013-10-04 | E-GEOD-33943 | biostudies-arrayexpress
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Project description:Deficiency in the X-linked inhibitor of apoptosis protein (XIAP) is the cause for the X-linked lymphoproliferative syndrome 2 (XLP2). About one third of all patients suffers from severe and therapy refractory inflammatory bowel disease (IBD), but the exact pathogenesis remains undefined. We examined the differences in gene expression of pediatric XLP2 patients with IBD to healthy controls and pediatric IBD patients.
2021-09-20 | GSE183069 | GEO
Project description:16S and ITS2 rRNA sequencing analysis of faecal samples from pediatric IBD patients
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Project description:Thalidomide Exerts Distinct Molecular Antileukemic Effects and Combined Thalidomide/Fludarabine Therapy is Clinically Effective in High-Risk Chronic Lymphocytic Leukemia Background: Thalidomide represents a promising immunomodulatory drug that targets both leukemia cells and the tumor microenvironment. Methods: We treated chronic lymphocytic leukemia (CLL) patients with a combined thalidomide/fludarabine regimen and monitored cellular and molecular changes induced by thalidomide in-vivo prior to fludarabine treatment. Thalidomide was given daily (100mg p.o./day) and fludarabine was administered on days 7-11 (25 mg/m² i.v./day) within each 4-week cycle (maximum of 6 cycles). Twenty patients received thalidomide/fludarabine as first line therapy and 20 patients were previously treated. Unmutated IgVH mutation status was found in 36 cases and 13 had high-risk cytogenetic aberrations (deletion of 17p13 or 11q22-q23). Results: The overall response rate was 80% and 25% for untreated and previously treated patients, respectively. While thalidomide effectively reduced the number of CLL cells, the number of CD3 lymphocytes showed no significant change, but the number of CD4+CD25hiFOXP3+ T-regulatory cells was significantly decreased. Gene expression profiling revealed a thalidomide induced signature containing both targets known to play a role in immunomodulatory drug action as well as novel candidate genes. Conclusions: Combined thalidomide/fludarabine therapy demonstrated efficacy in high-risk CLL patients. Furthermore, our study provides novel biological insights into thalidomide effect, which might act by enhancing apoptosis of CLL cells and reducing Tregs, thereby enabling T-cell dependent anti-tumor effect.
2009-08-21 | GSE15913 | GEO
Project description:Objective: Children with very early onset inflammatory bowel disease (VEO IBD) present with more extensive, severe, and refractory disease than older children and adults with IBD. In the current study, we evaluated functional and transcriptomic differences in epithelial cells from patients with VEO and older onset IBD compared to controls. Design: We established enteroids and colonoid lines from patients with VEO and older onset IBD and control patients. We evaluated crypt conversion (initial growth efficiency) compared to histopathological and clinical parameters. We performed RNA-sequencing on colonoids followed by validation via qPCR and flow cytometry in additional patients and in colonoids after multiple passages. Results: Control enteroids and colonoids exhibited consistently high crypt conversion, whereas patients with VEO and older onset IBD exhibited decreased crypt conversion associated with higher inflammation scores. Transcriptomic analysis revealed increased expression of LYZ, reported previously in colonoids from adult patients with ulcerative colitis, as well as antigen presentation genes HLA-DRB1 and HLA-DRA, which persisted after prolonged passaging as verified by flow cytometry. Conclusion: We present the first functional comparison of enteroids and colonoids from patients with VEO and older onset IBD, a subset of which exhibit poor initial growth. Enhanced and persistent expression of epithelial antigen presentation genes in patient colonoids supports the notion that epithelial cell-intrinsic differences may result from or contribute to disease. Analyses of colonoids from pediatric patients with IBD will contribute to a greater understanding of epithelial cell-autonomous defects in patients with VEO and older onset IBD and will be an important tool for understanding novel disease variants in the future.
2021-01-27 | GSE135170 | GEO
Project description:Thalidomide has been shown to be effective in patients with refractory cutaneous lupus erythematosus (CLE). However, its use is still limited by its potential severe side-effects. We conducted an RNA-sequencing study using CLE skin biopsies before and after thalidomide treatment to discover its mechanism of action. Methods: Total mRNA from skin biopsies from 10 CLE patient have been processed by RNA-seq in duplicate using Illumina Hiseq 2000 sequencing platform version 3. Application was stranded mRNA-Seq, paired-end and read length was 75bp. The sequence reads that passed quality filters were analyzed at the transcript isoform level using STAR program, RSEM program and DESeq2. Mapping was done with STAR (version 2.5.2a), quantification by RSEM (1.2.28) and differential analysis by DESeq. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to human genome (hs37d5). Average un-mapped was between 11,40-7,05 %, average unique was 80.48-76,62% and average alignment insert size was 170,00-155,00 in the 20 samples. Conclusions: Plausibles mechanisms of action for thalidomide in lupus cutaneous were discovered using this study; however, in vitro and in vivo experiments would be performed to demostrate them.
2021-12-07 | GSE162424 | GEO
Project description:To unravel the mechanisms of thalidomide developmental toxicity, we used microarrays to study transcriptomic changes induced by thalidomide during mouse embryonic stem cell (mESC) differentiation. C57BL/6 mESCs were allowed to differentiate spontaneously and global gene expression changes were studied using microarrays at at different time points after exposure to 0.25 mM thalidomide (THD).
2015-05-31 | GSE61306 | GEO
Project description:Background: In pediatric inflammatory bowel disease (IBD) up to 30% of patients do not respond to anti-TNF therapy. The aim was to identify pharmacogenomic markers that predict early response to anti-TNF drugs in pediatric patients with IBD. Methods: The study population included 29 responders and 9 non-responders to anti-TNF therapy patients aged <18 years with IBD who started treatment with infliximab or adalimumab. Whole gene expression profiles from total RNA isolated from whole-blood samples of 6 responders and 6 non-responders taken before biologic administration and after 2 weeks were analyzed by RNA next-generation sequencing. The expression of 6 selected genes was measured for validation in all of 38 patients recruited using qPCR; Results: Differentially expressed genes in non-responders versus responders to anti-TNF treatment were identified, 32 prior treatment initiation and 44 after 2 weeks (Log2FC (Fold change)>0.6 o <-0.6 and p value < 0.05). After validation, FCGR1A, FCGR1B and GBP1 were overexpressed in non-responders after 2 weeks of anti-TNF treatment (Log2FC 1.05, 1.21 and 1.08, respectively, p value <0.05,); Conclusion: Expression of the FCGR1A, FCGR1B, and GBP1 genes is a pharmacogenomic biomarker of early response to anti-TNF agents in pediatric IBD.
2021-01-14 | GSE159034 | GEO
Project description:Background & Aims: Most inflammatory bowel diseases (IBDs) are classic polygenic disorders represented by common alleles. However, multiple determinants of very early-onset IBD characterized by a more extensive disease course remain largely unknown. The present study aimed to define the genetic architecture of pediatric and adult-onset IBDs in the Polish population. Results: Of 82 SNPs validated/replicated for association with IBD, a novel BRD2 (rs1049526) association was found in both pediatric (OR= 2.35) and adult (OR= 2.66) patients. Thirty SNPs were shared between pediatric and adult patients; 22 and 30 were unique to adult-onset and pediatric-onset IBD, respectively. WES identified numerous rare/infrequent, potentially deleterious variants in IBD-associated or innate immunity-associated genes. Both groups of variants were over-represented in affected children. Two highly deleterious homozygous variants, HLA-DRB1 c.565_566insC and NCF4 p.Arg8Trp, were found in two affected children, and WAS p.Glu131Lys was found in one child and one adult patient. Conclusions: Our GWAS revealed differences in the polygenic architecture of pediatric- and adult-onset IBD. A significant accumulation of rare/low frequency deleterious variants in affected children suggests a contribution by yet unexplained genetic components.
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