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| Status |
Public on Oct 01, 2022 |
| Title |
Single-cell transcriptomics in bone marrow delineates CD56dimGranzymeK+ subset as intermediate stage in NK cell differentiation |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In this study we performed single-cell RNA sequencing on 7000 negatively enriched fresh NK and progenitor cells from one healthy bone marrow donor, that were pre-labeled with oligonucleotide-conjugated antibodies against CD34, CD117, CD56 and CXCR6. A new CD56dimGzmK+ subset was identified that shared features with CD56bright and CD56dimGzmK- NK cells based on transcriptome, phenotype (NKG2AhighCD16lowKLRG1highTIGIThigh) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned CD56bright, CD56dimGzmK+ and CD56dimGzmK- cells in one differentiation trajectory, while ltNK cells were separated in a distinct lineage. Integrative analysis with bone marrow cells from the human cell atlas did not demonstrate a developmental connection between CD34+ progenitor and NK cells, implicating that bone marrow is not a site of active NK cell development.
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| Overall design |
Single-cell RNA sequencing on negatively enriched NK and progenitor cells from one healthy bone marrow donor, combined with oligonucleotide-conjugated antibodies against CD34, CD117, CD56 and CXCR6.
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| Contributor(s) |
Melsen JE, van Ostaijen-ten Dam MM, Schoorl DJ, Schol PJ, van den Homberg DA, Lankester AC, Lugthart G, Schilham MW |
| Citation(s) |
36505452 |
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| Submission date |
Mar 25, 2022 |
| Last update date |
Jan 03, 2023 |
| Contact name |
Janine Melsen |
| E-mail(s) |
j.e.melsen@lumc.nl
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| Organization name |
LUMC
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| Department |
Pediatrics
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| Street address |
Albinusdreef 2
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| City |
Leiden |
| ZIP/Postal code |
2333ZA |
| Country |
Netherlands |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA819966 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE199411_RAW.tar |
68.0 Mb |
(http)(custom) |
TAR (of H5, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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