Unknown,Transcriptomics,Genomics,Proteomics

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Characterization of enterotropic CD4 T cells reaching the tdLN after antibiotics

ABSTRACT: 4 groups of mice : Control, antibiotics, antibiotics + 4days of recolonization, antibiotics + 4days of recolonization + Enterocloster clostridioformis. Tumor draining lymph node were harvested after CFSE injection were harvested and CFSE+ cells were sorted and proccessed in order to generate single cell RNA-sequencing using BD Rhapsody mouse immune response targeted panel. Groups were barcoded using BD Rhapsody Multiplexing Kit.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Laurence Zitvogel

PROVIDER: E-MTAB-12784 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We employed CITE-Seq profiling of 62 277 high-quality FACS-enriched human bone marrow hematopoietic stem and progenitor cells (HSPCs) from 15 healthy donors representing young, mid and old age groups, using the BD Rhapsody platform. Our targeted gene panel consisting of 596 genes was supplemented with 46 cell-surface proteins to cover the most relevant markers of early HSPC differentiation and cell cycle status. We demonstrate a molecular map of early human hematopoietic stem cell (HSC) differentiation and provide evidence of early branching points into lineage trajectories across different age groups. Our data shows that the HSC branched into two main lineages, with the first branching point giving rise to megakaryocytic and erythroid progenitors (MKP/ERP), followed by lymphoid and myeloid progenitors (LMP/MDP). As expected, the most immature HSCs were defined by high expression of CD34, CD90, CRHBP, HOPX, HLF, MLLT3. Re-clustering and trajectory analysis of the most immature HSPCs confirmed early lineage commitment, suggesting that an MKP/ERP development does not include myeloid or lymphoid progenitors. A similar pattern was observed for all age groups. Interestingly, we observed increased expression of novel marker genes (HLA-E, DLK1, ADGRG6, and MMRN1) and the surface protein CD273/PD-L2 in the most immature HSCs. Besides a gradual upregulation of CD38 along differentiation, differentiated cells showed lower CD45 levels. tradeSeq analysis defined the continuous single cell expression changes in genes upon early differentiation and lineage commitment, allowing the detection of decision-making gene networks. Our data adds further evidence to a structured hierarchical organization of human hematopoiesis with a sequential loss of lineage potential, with the first branching point into the MEK/ERY lineage, and not an early commitment of uni-lineage restricted precursors. We report on the upregulation of ADGRG6, DLK1, HLA-E, MMRN1 and CD273 in the most immature HSCs. Functional experiments confirmed that CD273+ HSCs displayed the most quiescent profile with a high stemness signature as well as the immune-modulatory function of CD273+ on HSPCs in regulating T cell activation and cytokine release.

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Characterization of enterotropic CD4 T cells reaching the tdLN after antibiotics

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