Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Application of next-generation sequencing in infections after allogeneic haematopoietic stem cell transplantation: a retrospective study

ABSTRACT: A retrospective study aimed to determine the characteristics of infection and the diagnostic efficacy of next-generation sequencing (NGS) in patients with fever after allogeneic haematopoietic stem cell transplantation (allo-HSCT).

PROVIDER: PRJEB51878 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Faecal Microbiota Transplantation After Allogeneic Stem Cell Transplantation

Project description:The aim of this study is to assess the Fecal Microbiota Transplantation (FMT) efficacy in the prevention of allogeneic hematopoietic stem cell transplantation (allo-HSCT) complications and particularly Graft versus Host Disease (GvHD). The hypothesis of this study is that allogeneic FMT may improve outcomes of these patients.

| 2381286 | ecrin-mdr-crc

Circulating lymphoid committed progenitors after allogeneic stem cell transplantation in humans

Project description:Lymphoid committed CD34+lin-CD10+CD24- progenitors undergo a rebound at month 3 after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in the absence of acute graft-versus-host disease (aGVHD). Here, we analyzed transcriptional programs of cell-sorted circulating lymphoid committed progenitors and CD34+Lin-CD10- non lymphoid progenitors in 11 allo-HSCT patients having (n=5) or not developed (n=6) grade 2 or 3 aGVHD and in 7 age-matched healthy donors. Major deregulated pathways included protein synthesis, energy production, cell cycle regulation and cytoskeleton organization. Notably, genes from protein biogenesis, translation machinery and cell cycle (CDK6) were over-expressed in progenitors from patients in the absence of aGVHD compared with healthy donors and patients affected by aGVHD. Expression of many genes from the mitochondrial oxidative phosphorylation metabolic pathway leading to ATP production were more specifically increased in lymphoid committed progenitors in absence of aGVHD. This was also the case for genes involved in cell mobilization such as those regulating Rho GTPases activity. In all, we show that circulating lymphoid committed progenitors undergo profound changes in metabolism favoring cell proliferation, energy production and cell mobilization after allo-HSCT in humans. These mechanisms are abolished in case of aGVHD or its treatment, indicating a persistent cell-intrinsic defect after exit from bone marrow.

2018-11-14 | GSE75344 | GEO

Multiomic Single Cell Evaluation Reveals Inflammatory Cytokines Affect Innate Lymphoid Cell Fate After Allogeneic Stem Cell Transplantation [ChIP-Seq]

Project description:Type II innate lymphoid cells (ILC2s) maintain homeostasis and barrier integrity in mucosal tissues. Previous work has shown that in mice and humans, ILC2s fail to reconstitute after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Determining the mechanisms involved in their impaired reconstitution could improve transplant outcomes. By integrating chromatin and transcriptomic analysis of marked, transplanted ILC2s at the single cell level, we identify a previously unreported population of converted ILC1-like cells in the small intestine post-transplant. Exposure of ILC2s to proinflammatory cytokines in vitro results in a mixed ILC1-ILC2 phenotype but was able to convert only an extremely small population of ILC2s to ILC1s as observed in vivo. Whereas ILC2s protected against acute graft-versus-host disease (aGVHD) mediated-morbidity and mortality, infusion of proinflammatory cytokine-exposed ILC2s accelerated aGvHD. Finally, circulating peripheral blood mononuclear cells from patients with aGvHD have an altered ILC2-associated chromatin landscape compared to transplanted controls. These data demonstrate, for the first time, that ILC2s fail to repopulate their protective niche after allo-HSCT in part due to conversion to a pro-pathogenic population marked by an ILC1-like chromatin state, providing novel insights into the contribution of ILC plasticity to aGvHD pathogenesis after allo-HSCT.

2023-09-14 | GSE232000 | GEO

CD70 identifies donor derived alloreactive T cells in severe acute Graft vs Host Disease post allogeneic SCT

Project description:Graft-versus-host disease (GvHD) remains a major challenge post allogeneic hematopoietic stem cell transplantation (allo-HSCT) and understanding its immunopathology is crucial for effective therapeutic intervention. Here we investigated the significance of CD70, a co-stimulatory molecule, in the context of aGvHD. CD70 was found to be transiently expressed on activated T cells during early immune reconstitution post-transplantation but persisted longer in aGvHD. Our findings illustrate that CD70+ T cells are characterized by upregulated activation receptors and enhanced cytokine production, while displaying signs of exhaustion. Remarkably, CD70+ T cells expressed chemokine receptors CCR4 and CCR6 and were actively recruited to inflamed tissues, implicating them in aGvHD pathogenesis. The chromatin at transcription factor MGA and NFAT5 loci was found to be selectively altered upon allo-antigenic stimulation in CD70+ T cells ex-vivo. Gene transcriptions of Toll-like receptors and MAPK signalling pathway were also found to differ in CD70+ and CD70- T cells of aGvHD patients. Insights into the clonality and antigen specificity of CD70+ T cell populations revealed potential novel antigenic targets. Further blocking CD70 in allogeneic T cells from aGvHD patients primed with autologous antigen presenting cells prior to HSCT demonstrated that anti-CD70 antibody reduced T cell proliferation and cytokine production. These findings implicate CD70 as a potential therapeutic target to modulate T cell responses and mitigate aGvHD. Targeting the CD70-CD27 co-stimulation pathway holds promise for prophylactic treatment.

2024-10-02 | GSE247452 | GEO

Comparison of transcriptomic data obtained from stimulated and unstimulated samples for the stratification of patients with a compromised immune system (in the context of sepsis and allogeneic hematopoietic stem cell transplantation)

Project description:Recently, immune function assessment has gained prominence in clinical settings. Immune functional assays (IFAs), involving in vitro stimulation, offer a relevant approach to complement traditional immunomonitoring methods which, while widely used, do not fully capture functional immune capabilities. Despite growing interest in IFAs, their added value remains unclear. To address this gap, our study aimed to determine if insights from IFAs could be replicated with unstimulated immunoprofiling. Using the same analytical pipeline, we compared transcriptomic profiles (Nanostring®) between stimulated (TruCulture®) and unstimulated (PaxGene™) samples from i) patients with an overstimulated immune system 3-4 days post-sepsis onset, and ii) patients undergoing immune reconstitution 6-months post-allogeneic hematopoietic stem cell transplantation (allo-HSCT). In sepsis, post-stimulation transcriptomic profiles revealed immune clusters linked to disease severity and outcomes, surpassing traditional markers like mHLA-DR, while baseline analyses failed to generate clinically relevant stratification. Similarly, allo-HSCT patients’ post-stimulation data revealed immune heterogeneity and treatment-related alterations not detected using baseline transcriptomic or cellular profiles alone. Our findings emphasize the value of IFAs in uncovering functional immune alterations that unstimulated assessments may miss, which could offer deeper insights into immune dysfunction. This study supports IFAs as complementary tools to current clinical practices, enhancing patient management with a functional view of immune system dynamics.

2025-01-15 | GSE285098 | GEO

Longitudinal single-cell dynamics in chronic lymphocytic leukemia mirror disease history

Project description:Longitudinally sampled peripheral blood samples of 9 CLL patients were subjected to single cell RNA sequencing before and at relapse after chemotherapy with fludarabine, cyclophosphamide and rituximab (FCR); allogeneic hematopoietic stem cell transplantation (RIC allo-HSCT); ibrutinib treatment, or before and after transformation to Richter's syndrome.

2021-06-09 | GSE165087 | GEO

Transcriptional analysis of beta-catenin overexpressing T cells

Project description:Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is one of the most widely applied forms of adaptive immunotherapy. Both the detrimental graft-versus-host disease (GVHD) and the beneficial graft-versus-leukemia (GVL) effects occurring after allo-HSCT are largely mediated by alloantigen-reactive donor T cells in the graft. Separating GVHD from GVL effects is a formidable challenge, and a greater understanding of donor T cell biology is required to accomplish the uncoupling of GVHD from GVL. Here, we tested a novel mouse model of transgenic over-expression of human β-catenin (Cat-Tg) in an allo-HSCT model. Our data show that T cells from Cat-Tg mice did not cause GVHD. Surprisingly, Cat-Tg T cells maintained the GVL effect. Donor T cells from Cat-Tg mice exhibited significantly lower inflammatory cytokine production and reduced donor T cell proliferation, while upregulating cytotoxic mediators that resulted in enhanced cytotoxicity. RNA sequencing data revealed changes in the expression of 1169 genes for CD4, and 1006 genes for CD8+T cells involved in essential aspects of immune response and GVHD pathophysiology. Transgenic over-expression of human β-catenin primarily affects CD8+ T cell phenotype. Altogether, our data suggest that β-catenin is a druggable target for developing therapeutic strategies to reduce GVHD while preserving the beneficial GVL effects following allo-HSCT treatment

2021-08-01 | GSE180808 | GEO

Analysis of allogeneic and syngeneic CD8+ T cells reveals novel target genes and related pathway in acute graft-versus host disease

Project description:The goals of the study are to compare differenely expressed genes in allogeneic and syngeneic CD8+ T cells isolated from splenocytes of allogeneic (donor: C57BL/6, host: Balb/c) and syngeneic (donor: Balb/c, host: Balb/c) HSCT mice.

2022-12-16 | GSE212137 | GEO

Analysis of allogeneic and syngeneic CD4+ T cells reveals novel target genes and related pathway in acute graft-versus host disease

Project description:The goals of the study are to compare differently expressed genes in allogeneic and syngeneic CD4+ T cells isolated from splenocytes of allogeneic (donor: C57BL/6, host: Balb/c) and syngeneic (donor: Balb/c, host: Balb/c) HSCT mice.

2022-12-16 | GSE212135 | GEO

Analysis of allogeneic and syngeneic CD3+ T cells reveals novel target genes and related pathway in acute graft-versus host disease

Project description:The goals of the study are to compare differenely expressed genes in allogeneic and syngeneic CD3+ T cells isolated from splenocytes of allogeneic (donor: C57BL/6, host: Balb/c) and syngeneic (donor: Balb/c, host: Balb/c) HSCT mice.

2022-12-16 | GSE212129 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data