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Tracking of donor and recipient immune and leukemia phenotypes after allogeneic stem cell transplantation using mitochondrial DNA mutations. [ASAP-Seq 1]

ABSTRACT: Mitochondrial DNA mutations (mtDNA) enable deconvolution of donor- and recipient-derived single cell profiles. Here, we provide examples for sensitive donor-recipient deconvolution of peripheral blood and bone marrow ASAP-seq profiles in the context of incipient and overt AML relapse following allogeneic hematopoietic stem cell transplantation. Further, using single cell DNA sequencing (Tapestri), we demonstrate co-evolution of mtDNA and somatic nuclear DNA mutations in relapsed CLL post-HSCT.

ORGANISM(S): Homo sapiens

PROVIDER: GSE234551 | GEO | 2024/08/31

REPOSITORIES: GEO

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Tracking of donor and recipient immune and leukemia phenotypes after allogeneic stem cell transplantation using mitochondrial DNA mutations. [ASAP-Seq 4]

Project description:Mitochondrial DNA mutations (mtDNA) enable deconvolution of donor- and recipient-derived single cell profiles. Here, we provide examples for sensitive donor-recipient deconvolution of peripheral blood and bone marrow ASAP-seq profiles in the context of incipient and overt AML relapse following allogeneic hematopoietic stem cell transplantation. Further, using single cell DNA sequencing (Tapestri), we demonstrate co-evolution of mtDNA and somatic nuclear DNA mutations in relapsed CLL post-HSCT.

2024-08-31 | GSE275725 | GEO

Tracking of donor and recipient immune and leukemia phenotypes after allogeneic stem cell transplantation using mitochondrial DNA mutations. [ASAP-Seq 3]

2024-08-31 | GSE234555 | GEO

Tracking of donor and recipient immune and leukemia phenotypes after allogeneic stem cell transplantation using mitochondrial DNA mutations. [ASAP-Seq 2]

2024-08-31 | GSE234552 | GEO

Tracking of donor and recipient immune and leukemia phenotypes after allogeneic stem cell transplantation using mitochondrial DNA mutations. [Tapestri]

2024-08-31 | GSE234556 | GEO

ASAP – Automated Sonication free Acid assisted Proteomes from cells & FFPE tissues

Project description:Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for retrospective studies but protein extraction and subsequent sample processing steps have shown to be challenging for mass spectrometry (MS) analysis. Streamlined high-throughput sample preparation workflows are essential for efficient peptide extraction from complex clinical specimens such as fresh frozen tissues or FFPE. Overall, proteome analysis has gained significant improvements in the instrumentation, acquisition methods, sample preparation workflows and analysis pipelines yet even the most recent FFPE workflows remain complex and are not readily scalable. Here, we present an optimized workflow for Automated Sonication-free Acid-assisted Proteome (ASAP) extraction from FFPE sections. ASAP enables efficient protein extraction from FFPE specimens achieving similar proteome coverage as established methods using time in equipment-heavy sonication-based methods at reduced sample processing time. The broad applicability of ASAP on archived pediatric tumor FFPE specimens resulted in high-quality data with increased proteome coverage and quantitative reproducibility. Our study demonstrates the practicality and superiority of the ASAP workflow as a streamlined, time and cost-effective pipeline for high-throughput FFPE proteomics of clinical specimens.

2024-05-21 | PXD036910 | Pride

Homo sapiens

Project description:Recipient and donor expression differences in children treated with HSCT

| PRJNA348809 | ENA

T cell reperoire sequencing of donor and patient samples after abT/CD19-depleted allogenic HSCT with CD45RA-depleted DLI

Project description:To track for T cell clones from donor memory T cell fraction infused after abT/CD19-depleted allogenic HSCT we performed TCR beta repertoire sequencing. Patient peripheral blood repertoire was sequenced in two timepoints (p3 and p4: d120-180 and d360-500). Reperotoires for bulk and CD4+ or CD8+ cells from CD45RA-depleted donor apheresis were obtained for most donor-recipient pairs. TCR beta cDNA libraries were prepared using previously published protocol (Zvyagin I.V. et al., Leukemia, 2017). Libraries were sequenced on Illumina NextSeq 500/550 and HiSeq2000/2500 in pair-end mode with read length 100-150 bp. MiGEC software were used for demultiplexing and unique molecular identifier sequence extraction software (https://github.com/mikessh/migec).

2020-07-01 | E-MTAB-8874 | biostudies-arrayexpress

BLUEPRINT DNA methylation profiles of graft donors in allogenic hematopoietic stem cell transplantation

Project description:Allogenic hematopoietic stem cell transplantation (HSCT) is a curative treatment for many hematological conditions. Acute graft-versus-host disease (aGVHD) is a prevalent immune-mediated complication following HSCT. Current diagnostic biomarkers that correlate with aGVHD severity, progression, and therapy response in graft recipients are insufficient. We investigated whether epigenetic marks measured in peripheral blood of healthy graft donors stratify aGVHD severity in HLA-matched sibling recipients prior to HSCT. We measured genome-wide DNA methylation levels in peripheral blood of 91 HSCT donors using Illumina Infinium HumanMethylation450 BeadChips. We showed that epigenetic signatures underlying aGVHD severity in recipients correspond to immune pathways relevant to aGVHD etiology. We identified distinct DNA methylation marks in graft donors that are associated with aGVHD severity status in recipients. Together, our findings suggest that ‘epigenetic matching’ of HSCT donor-recipient pairs in a clinical setting may be used in conjunction with genetic matching to inform both donor selection and transplantation strategy, with the ultimate aim of improving patient outcome.

| EGAS00001001287 | EGA

Homo sapiens isolate:HSCT recipient

Project description:Homo sapiens isolate:HSCT recipient Genome sequencing

| PRJNA481029 | ENA

Pressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and Fates

Project description:Generating mammalian cells with desired mtDNA sequences is enabling for studies of mitochondria, disease modeling, and potential regenerative therapies. MitoPunch, a high-throughput mitochondrial transfer device, produces cells with specific mtDNA-nDNA combinations by transferring isolated mitochondria from mouse or human cells into primary or immortal mtDNA-deficient (p0) cells. Stable isolated mitochondrial recipient (SIMR) cells isolated in restrictive media permanently retain donor mtDNA and reacquire respiration. However, SIMR fibroblasts maintain a p0-like cell metabolome and transcriptome despite growth in restrictive media. We reprogram non-immortal SIMR fibroblasts into induced pluripotent stem cells (iPSCs) with subsequent differentiation into diverse functional cell types, including mesenchymal stem cells (MSCs), adipocytes, osteoblasts, and chondrocytes. Remarkably, following reprogramming and differentiation, SIMR fibroblasts molecularly and phenotypically resemble un-manipulated control fibroblasts carried through the same protocol. Thus, our MitoPunch ‘pipeline’ enables the production of SIMR cells with unique mtDNA-nDNA combinations for additional studies and applications in multiple cell types.

2020-12-29 | GSE115871 | GEO

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