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Single-cell transcriptomics during different phases post cardiac ischemia reveals secreted B2M to regulate fibroblast activation

ABSTRACT: Single-cell transcriptomics during different phases post cardiac ischemia reveals secreted B2M to regulate fibroblast activation

PROVIDER: PRJNA609983 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11219602_1.fastq.gz	Fastqsanger.gz
	SRR11219602_2.fastq.gz	Fastqsanger.gz
	SRR11219603_1.fastq.gz	Fastqsanger.gz
	SRR11219603_2.fastq.gz	Fastqsanger.gz
	SRR11219604_1.fastq.gz	Fastqsanger.gz

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Single-cell transcriptomics during different phases post cardiac ischemia reveals secreted B2M to regulate fibroblast activation

Project description:The efficiency of the repair process following ischemic cardiac injury is a crucial determinant for the progression into heart failure and is controlled by both intra- and intercellular signaling within the heart. An enhanced understanding of this complex interplay will enable better exploitation of these mechanisms for therapeutic use. We used single-cell transcriptomics to collect gene expression data of all main cardiac cell types at different time-points after ischemic injury.

2020-03-04 | GSE146285 | GEO

Gene Expression analysis of hESC B2M knock-out

Project description:The clinical use of human pluripotent stem cells and their derivatives is limited by the rejection of transplanted cells due to differences in their HLA genes. This has led to the proposed use of histocompatible, patient-specific stem cells, however the preparation of many different stem cell lines for clinical use is a daunting task. Here we develop two distinct genetic engineering approaches that address this problem. First, we use a combination of gene targeting and mitotic recombination to derive HLA-homozygous embryonic stem cell (ESC) subclones from an HLA-heterozygous parental line. A small bank of HLA-homozygous stem cells with common haplotypes would match a significant proportion of the population. Second, we derive HLA class I-negative cells by targeted disruption of both alleles of the B2M gene in ESCs. Mixed leukocyte reactions and peptide-specific HLA-restricted CD8+ T cell responses were reduced in class I-negative cells that had undergone differentiation in embryoid bodies. These B2M-/- ESCs could act as universal donor cells in applications where the transplanted cells do not express HLA class II genes. Both approaches used adeno-associated virus (AAV) vectors for efficient gene targeting in the absence of potentially genotoxic nucleases, and produced pluripotent, transgene-free cell lines. Total RNA, 4 samples were analyzed as follows: 2 replicates for the hESC H1 wt ( rep1 and rep2) and 2 independent clones of hESC B2M knock-out

2014-01-01 | E-GEOD-42289 | biostudies-arrayexpress

Gene expression changes in HSV-1 infected HeLa cells with knockdown of B2M

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2019-09-24 | GSE137843 | GEO

LC-MS/MS analysis of human brain fibroblast-secreted molecules

Project description:Our study showed that fibroblasts significantly attenuated blood-brain barrier (BBB) disruption in an in vitro intracerebral hemorrhage (ICH) model. Since fibroblasts and brain microvascular endothelial cells were not in direct contact in this model, we reasoned that fibroblasts did so by secreting molecules with BBB-protective function. Here, we further screened fibroblast-secreted molecules in this in vitro ICH model by mass spectrometry.

2022-11-14 | PXD037247 | Pride

CD34+ Cell-derived Fibroblast–Macrophage Crosstalk Drives Limb Ischemia Recovery through the OSM–ANGPTL Signaling Axis

Project description:CD34+ cells improve the perfusion and function of ischemic limbs in humans and mice. However, there is no direct evidence of the differentiation potential and functional role of these cells in the ischemic muscle microenvironment. Here, we combined the single-cell RNA sequencing and genetic lineage tracing technology and then provided exact single-cell atlases of normal and ischemic limb tissues in human and mouse, consequently found that bone marrow-derived macrophages with antigen-presenting function migrated to the ischemic site, while resident macrophages underwent apoptosis. The macrophage oncostatin M (OSM) regulatory pathway was specifically turned on by ischemia. Simultaneously, bone marrow CD34+-derived pro-regenerative fibroblasts were recruited to the ischemia niche, where they received macrophage-released OSM, and promoted angiopoietin-like protein (ANGPTL)-associated angiogenesis. These findings provided novel mechanisms on the cellular events and cell–cell communications during tissue ischemia and regeneration, and provided new evidence that CD34+ cells serve as fibroblast progenitors promoting tissue regeneration.

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Transcriptional profiling of tumor microenvironment in B2M KO CD40-treated B16 tumors implanted in mice

Project description:The immune changes induced by loss of antigen presentation by tumor cells, a common mechanism of acquired resistance to immunotherapy, as well as the mechanisms by which CD40 agonist treatment controls the growth of B2m-null tumors, are unknown. We performed single-cell RNA-seq of total tumor-infiltrating immune cells in control and B2m-null tumors treated with isotype control or CD40 agonist antibodies to identify changes in immune cell states due to tumor cell loss of B2m and agonist CD40 treatment.

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Project description:β2-microglobulin (B2M) is the light chain subunit of type I human leukocyte antigen complexes that play a key role in the immune system. Genetic knockout (KO) of B2M in human pluripotent stem cells (hPSCs) has been used as a major approach together with many other strategies to generate hypo-immunogenic, universal stem cells for allogeneic cell transplantation without triggering immune rejection. However, this approach assumes that B2M is dispensable for stem cell differentiation and therapy, although it lacks evidence from thorough evaluation. Here, we conducted genome-wide analyses of isogenic pairs of wild-type (WT) and B2M-KO hESCs and their derived mesenchymal stem cells (E-MSCs), which revealed proteomic and transcriptomic alternations due to the KO. Over 200 proteins were mistargeted from the plasma membranes of B2M-KO hESCs and E-MSCs, suggesting that B2M is crucial for protein trafficking in the subcellular organelles. The expression of osteo-chondrogenic determinants and inflammation-related cytokines differed dramatically in B2M-KO E-MSCs from WT E-MSCs, consistent with the impaired osteogenic differentiation and wound-healing efficacy of B2M-KO E-MSCs. This study reveals previously unrecognized functions of B2M, which alerts cautions be used when applying B2M-KO cells to therapy.

2025-02-04 | GSE288189 | GEO

Fibroblast histone deacetylase-1 promotes kidney interstitial fibrosis following ischemia-reperfusion injury.

Project description:Fibroblast histone deacetylase-1 promotes kidney interstitial fibrosis following ischemia-reperfusion injury.

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PFKFB3-mediated glycolysis boosts fibroblast activation and subsequent kidney fibrosis

Project description:<p>Renal fibrosis, a hallmark of chronic kidney diseases, is driven by the activation of renal fibroblasts. Recent studies have highlighted the role of glycolysis in this process. Nevertheless, one critical glycolytic activator, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3), remains unexplored in renal fibrosis. Upon reanalyzing the single-cell sequencing data from Dr. Humphreys' lab, we noticed an upregulation of glycolysis, gluconeogenesis, and TGFβ signaling pathway in myofibroblasts from fibrotic kidneys after unilateral ureter obstruction (UUO) or kidney ischemia/reperfusion. Furthermore, our experiments showed significant induction of PFKFB3 in mouse kidneys following UUO or kidney ischemia/reperfusion. To delve deeper into the role of PFKFB3, we generated mice with Pfkfb3 deficiency specifically in myofibroblasts (Pfkfb3f/fPostnMCM). Following UUO or kidney ischemia/reperfusion, a substantial decrease of fibrosis in injured kidneys of Pfkfb3f/fPostnMCM mice was identified compared to their wild-type littermates. Additionally, in cultured renal fibroblast NRK-49F cells, PFKFB3 was elevated upon exposure to TGFβ1, accompanied by the increase of α-SMA and fibronectin. Notably, this upregulation was significantly diminished with PFKFB3 knockdown, correlated with a glycolysis suppression. Mechanistically, the glycolytic metabolite lactate promoted the fibrotic activation of NRK-49F. In conclusion, our study demonstrates the critical role of PFKFB3 in driving fibroblast activation and subsequent renal fibrosis.</p>

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Project description:We have employed microarray expression profiling to identify genes up- and down-regulated after the restitution of beta-2 microglobulin (B2M) gene in lung cancer cell lines.

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