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Cited by 179Cancer-related molecular mechanisms researchT-cell and B-cell ImmunologyGenomics and Chromatin Dynamics

Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages

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Casero, David, Sandoval, Salemiz, Seet, Christopher S, Scholes, Jessica, Zhu, Yuhua, Ha, Vi Luan, Luong, Annie, Parekh, Chintan +1 more·2015·Nature Immunology
DOI 10.1038/ni.3299PMC PMC4653072
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Abstract

To elucidate the transcriptional 'landscape' that regulates human lymphoid commitment during postnatal life, we used RNA sequencing to assemble the long non-coding transcriptome across human bone marrow and thymic progenitor cells spanning the earliest stages of B lymphoid and T lymphoid specification. Over 3,000 genes encoding previously unknown long non-coding RNAs (lncRNAs) were revealed through the analysis of these rare populations. Lymphoid commitment was characterized by lncRNA expression patterns that were highly stage specific and were more lineage specific than those of protein-coding genes. Protein-coding genes co-expressed with neighboring lncRNA genes showed enrichment for ontologies related to lymphoid differentiation. The exquisite cell-type specificity of global lncRNA expression patterns independently revealed new developmental relationships among the earliest progenitor cells in the human bone marrow and thymus.

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  • PU.1 expression timing relative to other developmentally regulated transcription factors is conserved between human and mouse.

    “This expression timing relative to other developmentally regulated transcription factors is conserved between human and mouse (35, 36)”

    From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [35]

    The Discussion describes a transcriptional map of human lymphoid progenitors but does not compare the timing of PU.1 expression in humans and mice. Searches for PU.1, SPI1, and conserved expression timing found no passage in our copy addressing that comparison. (LLM, conf=0.75)

    Experimental — accuracy not yet measured

  • The developmental expression patterns of these genes and PU.1 (Spi1) in human pro-T cells (Thy1-Thy4) are similar to their patterns in murine pro-T cells.

    “Consistent with an evolutionarily conserved program in regulating these genes, the developmental expression patterns of these genes and PU.1 (Spi1) in human pro-T cells (Thy1—Thy4) are similar to their patterns in murine pro-T cells (35).”

    From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [35]

    The Results section on co-expression modules describes expression across human Thy1–Thy4 populations, but does not compare their developmental patterns with murine pro-T cells. Searches for PU.1/SPI1 and cross-species thymic expression found no passage in our copy establishing the claimed similarity (page unavailable). (LLM, conf=0.74)

    Experimental — accuracy not yet measured

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Authors
Casero, D., Sandoval, S., Seet, C. S., Scholes, J., Zhu, Y., Ha, V. L., Luong, A., Parekh, C., & Crooks, G. M.
Affiliations
  • University of California, Los Angeles (US)
  • Children's Hospital Los Angeles (US)
  • University of Southern California (US)
Corresponding author
  • Parekh, Chintan
  • Crooks, Gay M
ORCID
Venue
Nature Immunology
Publisher
Springer Science and Business Media LLC
Published
2015-12
Volume
16
Issue
12
Pages
1282-1291
ISSN
  • 1529-2908 (ISSN-L)
  • 1529-2916
DOI
10.1038/ni.3299
PMC
PMC4653072
OpenAlex
W2206207244
Cited by
179
References
4
Citations by year
2026: 1 · 2025: 5 · 2024: 6 · 2023: 6 · 2022: 12 · 2021: 29 · 2020: 28 · 2019: 22 · 2018: 24 · 2017: 30 · 2016: 16
FWCI
7.72
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature Immunology (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • National Institutes of Health (4k12hd034610-20)
  • National Heart, Lung, and Blood Institute (T32HL086345, P01HL073104, T32HL066992)
  • National Institute of Allergy and Infectious Diseases (AI-28 697, P30AI028697)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (K12 HD-034610, K12HD052954)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
  • Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
long non-coding RNA, lymphoid progenitor cells, T cell lineage specification, lymphoid differentiation, bone marrow, thymus, lncRNA transcriptome, cell type-specific gene expression, transcriptional regulation
MeSH terms
B-Lymphocytes, Bayes Theorem, Bone Marrow Cells, Humans, T-Lymphocytes, Thymus Gland, Cluster Analysis, Sequence Analysis, RNA, Cell Lineage, Reverse Transcriptase Polymerase Chain Reaction, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Lymphoid Progenitor Cells, Transcriptome, RNA, Long Noncoding, Gene Ontology

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