The Human Cell Atlas bone marrow single-cell interactive web portal
Open accessAbstract
The Human Cell Atlas (HCA) is expected to facilitate the creation of reference cell profiles, marker genes, and gene regulatory networks that will provide a deeper understanding of healthy and disease cell types from clinical biospecimens. The hematopoietic system includes dozens of distinct, transcriptionally coherent cell types, including intermediate transitional populations that have not been previously described at a molecular level. Using the first data release from the HCA bone marrow tissue project, we resolved common, rare, and potentially transitional cell populations from over 100,000 hematopoietic cells spanning 35 transcriptionally coherent groups across eight healthy donors using emerging new computational approaches. These data highlight novel mixed-lineage progenitor populations and putative trajectories governing granulocytic, monocytic, lymphoid, erythroid, megakaryocytic, and eosinophil specification. Our analyses suggest significant variation in cell-type composition and gene expression among donors, including biological processes affected by donor age. To enable broad exploration of these findings, we provide an interactive website to probe intra-cell and extra-cell population differences within and between donors and reference markers for cellular classification and cellular trajectories through associated progenitor states.
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Other RFX members such as RFX1 and RFX8 have been demonstrated to regulate MHC class II expression.
“Although RFX2/3 are not well characterized in hematopoiesis, other RFX members such as RFX1 and RFX8 have been demonstrated to regulate MHC class II expression 35-37 .”
From Type 1 interferon perturbates clonal competition by reshaping human blood development (2026) · cites this paper as [36]
The Results passages describe bone marrow cell populations and lineage trajectories, not regulation of MHC class II expression. Searches for RFX1, RFX8, and MHC class II found no passage in our copy addressing the attributed claim. (LLM, conf=0.76)
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- Authors
- Hay, S. B., Ferchen, K., Chetal, K., Grimes, H. L., & Salomonis, N.
- Affiliations
- Cincinnati Children's Hospital Medical Center (US)
- University of Cincinnati (US)
- Corresponding author
- Salomonis, Nathan
- Venue
- Experimental Hematology
- Publisher
- Elsevier BV
- Published
- 2018-12
- Volume
- 68
- Pages
- 51-61
- ISSN
- 0301-472X (ISSN-L)
- PMC
- PMC6296228
- OpenAlex
- W2889628524
- Cited by
- 256
- References
- 28
- Citations by year
- 2026: 29 · 2025: 37 · 2024: 44 · 2023: 34 · 2022: 37 · 2021: 39 · 2020: 20 · 2019: 13 · 2018: 3
- FWCI
- 6.67
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Experimental Hematology (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion, cc-by)
- PubMed Central (acceptedVersion, cc-by)
- Funders
- Evans MDS Foundation (H.L.G.), National Cancer Institute (R01 CA196658, R01 CA226802)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Health Sciences › Medicine › Hematology › Hematopoietic Stem Cell Transplantation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- Human Cell Atlas, bone marrow, single-cell transcriptomics, hematopoietic progenitor cells, cell differentiation trajectories, granulopoiesis, monocyte differentiation, erythroid differentiation, megakaryopoiesis, eosinophil differentiation, lymphoid differentiation, interactive web portal
- MeSH terms
- Atlases as Topic, Base Sequence, Bone Marrow Cells, Female, Hematopoietic Stem Cells, Humans, Male, Reference Standards, RNA, Tissue Donors, User-Computer Interface, Genetic Variation, Bone Marrow Transplantation, Sequence Alignment, Cell Lineage, Computational Biology, Internet, Gene Regulatory Networks, DNA Barcoding, Taxonomic, Transcriptome
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