ScRNA sequencing of 2 leukemia patients in remission after T cell therapy
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE128933 | GEO | 2019/05/01
REPOSITORIES: GEO
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Project description:scRNA sequencing of 2 leukemia patients in remission after T cell therapy
| PRJNA529403 | ENA
Project description:Gastric bypass surgery (GBP) emerging as a powerful tool for treatment of obesity has been applied for remission of diabetes. However, the GBP global molecular effects on diabetes remission independent of weight loss remain largely unknown. We profiled plasma metabolites and proteins of 10 normoglycemic obese (NO) and 9 diabetic obese (DO) patients at 1-week, 3-months and 1-year stages after Roux-en-Y gastric bypass (RYGB) as well pre-RYGB stage, by which 146 proteins and 128 metabolites were detected from both NO and DO groups at all four stages. By analyzing a set of bi-molecular associations among the corresponding network of the subjects with our newly developed computational method, we defined the representing physiological states (called the edge-states, in contrast to the traditional node-states) and the related molecular networks of NO and DO patients, respectively. The PCA results and hubnetworks of NO subjects were significantly different from those of DO patients; particularly, the hub-network rearrangement of both groups differentially went through after RYGB. In conclusion, by developing network-based systems signatures rather than relying on individual molecules, we for the first time reveal that RYGB generates a unique recovering-path for diabetes remission independent of weight loss.
2017-12-13 | PXD008071 | Pride
Project description:Identify biomarkers to predict response to therapy in polyarticular juvenile idiopathic arthritis (JIA) using gene expression microarrays. 42 samples from 13 controls, 14 active patients, 9 patients in clinical remission with medication (CRM), and 6 patients in clinical remission without medication (CR). All patients had polyarticular JIA.
2009-04-13 | E-GEOD-15645 | biostudies-arrayexpress
Project description:Remission has become both the gold standard for clinical care and the end point for clinical trials for children with juvenile idiopathic arthritis (JIA). Using gene expression microarrays, we found that when remission induced by methotrexate (MTX) or MTX plus a TNF inhibitor (etanercept, Et) (MTX+Et) was compared with healthy controls, there were notable differences in gene expression patterns, demonstrating that remission is not a restoration of immunologic normalcy. Differences were detected in PBMC as well as in granulocytes. Total RNA was extracted from isolated PBMC and granulocytes from patients with polyarticular JIA and from healthy controls. Patients had achieved remission (clinical remission on medicine as defined by Wallace et al, Arthritis Rheum. 2005;52(11):3354-3562) using either MTX or MTX+Et.
2013-10-24 | E-GEOD-41831 | biostudies-arrayexpress
Project description:Acute lymphoblastic leukemia (ALL) is a type of heterogeneous hematopoietic malignancy that accounts for approximately 20% of adult ALL. Although ALL complete remission (CR) rate has increased to 85%–90% after induction chemotherapy, 40%–50% of patients eventually relapsed. Therefore, it is necessary to improve the outcomes of ALL via accurate diagnosis and individualized treatments,which benefits in part from molecular biomarkers. Here, we identified a new fusion gene,Acyl-CoA Thioesterase 7–Nephrocystin 4 (ACOT7–NPHP4), in a 34-year-old patient with ALL. The fusion gene contributed to chemoresistance to doxorubicin and acted as a new molecular marker.
2022-10-01 | GSE214117 | GEO
Project description:Background: This study addresses whether existing specific transcriptional profiles can improve and support the current status of the definition of ulcerative colitis (UC) remission apart from the existing endoscopic, histologic, and laboratory scoring systems. For that purpose, a well-stratified UC patient population in remission was compared to active UC and control patients and was investigated by applying the next-generation technology RNA-Seq. Methods: Mucosal biopsies from patients in remission (n = 14), patients with active UC (n = 14), and healthy control patients (n = 16) underwent whole-transcriptome RNA-Seq. Principal component analysis, cell deconvolution methods, gene profile enrichment, and pathway enrichment methods were applied to define a specific transcriptional signature of UC in remission. Results: Analyses revealed specific transcriptional signatures for UC in remission with increased expression of genes involved in O-glycosylation (MUC17, MUC3A, MUC5AC, MUC12, SPON1, B3GNT3), ephrin-mediated repulsion of cells (EFNB2E, EFNA3, EPHA10, EPHA1), GAP junction trafficking (TUBA1C, TUBA4A, TUBB4B, GJB3, CLTB), and decreased expression of several toll-like receptors (TLR1, TLR3, TLR5, TLR6). Conclusions: This study reveals specific transcriptional signatures for remission. Partial restoration and improvement of homeostasis in the epithelial mucus layer and revival of immunological functions were observed. A clear role for bacterial gut flora composition can be implied. The results can be useful for the development of treatment strategies for UC in remission and may be useful targets for further investigations aiming to predict the outcome of UC in the future.
2020-01-18 | GSE128682 | GEO
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
Project description:As a prominent feature of gout, monosodium urate (MSU) crystal deposition can induce gout flare, yet its impact on blood immune in gout remission patients still remains unclear. In this study, single-cell RNA sequencing (scRNA-seq) is used to compare the gene expression profiling of peripheral blood mononuclear cells (PBMCs) among intercritical gout remission patients, advanced gout remission patients and healthy volunteers. The increase of HLA-DQA1high classical monocytes, and their important role in immune inflammatory responses and osteoclast differentiation are discovered in advanced gout remission patients. Moreover, the differentiation level of CD8+T cells are found to elevate in advanced gout remission patients, which is further validated via flow cytometry. It is also observed that pathways related to bone metabolism and inflammatory responses are overactive in advanced gout remission patients. By analysis on intercellular communication network, immune-related cell-cell interactions among PBMCs are shown to enhance in both intercritical and advanced gout remission patients. The analyses on gene expression and LC-MS/MS together indicate the increased metabolic level of arachidonic acid in gout remission patients with MSU deposition at the intercritical and advanced stage. The study reveals distinctive blood immune characteristics in gout remission with MSU deposition, which provides more sights into its pathogenesis.
2023-06-01 | GSE217561 | GEO
Project description:To understand the molecular and immunological mechanisms of remission in pemphigus patients. Remission was evaluated 5 years after rituximab onset. PBMC were purified from pemphigus whole blood patients. CD4+ T cells and CD19+ B cells were isolated by flow cytometry. Genes differentially regulated between CR and IR both in CD4+ and CD19+ cells were identified by transcriptomic approach (whole human genome).
2018-11-30 | GSE90152 | GEO
Project description:Sustained remission is now an achievable goal in rheumatoid arthritis (RA) using modern treat-to-target regimens of disease-modifying anti-rheumatic drugs (DMARDs). Recent studies have demonstrated that up to half of patients in remission can discontinue DMARDs and maintain drug-free remission (DFR), with consequent benefits of avoidance of drug toxicity and the need for regular and expensive safety monitoring. However, there are currently no reliable biomarkers that can predict DFR prior to withdrawal of DMARDs. Aim: As part of a wider study of DMARD withdrawal (the BioRRA study), we aimed to identify predictors of time-to-flare following DMARD cessation using whole-genome bulk RNA sequencing data from circulating CD4+ T cells.
2019-07-12 | GSE122612 | GEO