Evaluation of Ranzoni et al.: Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis

This article shows an example of the peer review process for “Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis Human Developmental Hematopoiesis” (Ranzoni et al., 2021Ranzoni A.M. Tangherloni A. Berest I. Riva S.G. Myers B. Strzelecka P.M. Xu J. Panada E. Mohorianu Zaugg J.B. Cvejic Integrative Hematopoiesis.Cell Stem Cell. 2021; 28 (this issue, 471–487. Published online December 15, 2020)https://doi.org/10.1016/j.stem.2020.11.015Abstract Full Text PDF PubMed Scopus (28) Google Scholar). Editor’s note: These are first-round reviewer comments on by colleagues; these were written Cell during this paper. We chose to feature particular because it provides several constructive suggestions ways develop paper that would increase its impact stem cell community, addressing points significantly strengthened overall. Following first round review, colleagues submitted a revised incorporated Reviewers’ comments, was re-reviewed, accepted publication, published in March 2021 issue Ranzoni al. utilize scRNA-Seq scATAC-Seq assess transcriptional identity chromatin accessibility immunophenotypic blood populations from human fetal liver (FL) bone marrow (FBM). The authors (1) identify three oligopotent progenitor downstream hematopoietic cell/multipotent cells (HSC/MPPs), (2) show profiles alone do not reveal significant lineage priming HSC/MPPs, while is apparent when one examines chromatin, (3) FBM HSC/MPPs more quiescent than time-matched FL HSC/MPPs. have generated compelling bioinformatic data regarding fate tissue. However, further functional validation some authors’ claims (e.g., new markers HSC/MPP enrichment, involvement priming, increased quiescence HSC/MPPs), along with deeper exploration differences between versus populations, greatly study. (1)The state their CD-REF population enriches but based definition. Showing ability produce multipotent colonies vitro proves they proof panel Is there any way can prove compartment comparing previous populations? Furthermore, used enrich FBM. Could same see if tissue? Considering contain higher proportion cells, may be actually (or subset HSC/MPPs).(2)In line concern, could provide evidence HSC/MPPs? analyses compelling, strengthen claim, as note shift seen FBM/postnatal mice.(3)The feels incomplete. only explore cycle. It seems wealth biologically interesting questions put toward explored here bioinformatically. Indeed, findings respect cycle, although interesting, feel particularly surprising also fairly modest (with magnitude cycle shift). There asking unique dataset (to mention few: expression surface receptors likely ligand engagement, appear propensity migrate/home tissues, differentiation pathways, etc.?). (1)Could explicit how many each (both tissue populations) used? Also, unclear performed Figures 1–4 independently processed tissues FBM) or pooled before sorting until Figure 6. needs clearly stated.(2)Could include representative index-sort FACS plots confirm transcriptionally identified falls appropriate gate (Figure 1C S3)? help resolve concerns discrepancies sorted defined due technical issues sorting.(3)Is absence T innate lymphoid (ILCs) didn’t pass QC poorly sorted) included fell different annotation? Again, showing issue.(4)It flow 2B adjacent 2E.(5)Could repeat S4 lineage-specific markers)? subpopulations little no clear lineage-affiliated programs.(6)Could average genes/cell instead average, perhaps supplemental table? stated bit low typical SMART-seq, raising concern seeing capturing too few genes.(7)The claim clusters 1, 2, 4 3B display highest accessibility, quantification presented. at all cluster displays (for example) 7. please quantified cluster, separate marker gene?(8)Is 6C bar graph? current unnecessarily complex. HematopoiesisRanzoni al.Cell CellDecember 21, 2020In BriefRanzoni detailed map (HSCs). Within HSCs, revealed extensive epigenetic priming. They HSCs marrow. Full-Text Open Access