Pitfalls of Applying Mouse Markers to Human Adrenal Medullary Cells

In this letter, we re-analyze human fetal adrenal data generated by Dong et al. to demonstrate the pitfalls of relying on mouse marker genes annotate data. We show that unbiased cell label transfer methods imply neuroblastoma cells resemble sympathoblasts and not chromaffin cells, as had suggested. A key challenge in analyzing single-cell transcriptome is annotation types. their recent analysis (Dong al., 2020Dong R. Yang Zhan Y. Lai H.-D. Ye C.-J. Yao X.-Y. Luo W.-Q. Cheng X.-M. Miao J.-J. Wang J.-F. al.Single-cell characterization malignant phenotypes developmental trajectories neuroblastoma.Cancer Cell. 2020; 38: 716-733Abstract Full Text PDF PubMed Scopus (27) Google Scholar), might have mislabeled medullary leading erroneous conclusion cells. However, sympathoblasts, recently shown us others (De Preter 2006De K. Vandesompele J. Heimann P. Yigit N. Beckman S. Schramm A. Eggert Stallings R.L. Benoit Renard M. al.Human neuroblast confirms origin highlights candidate genes.Genome Biol. 2006; 7: R84Crossref (109) Scholar; Kildisiute 2020Kildisiute G. Kholosy W.M. Young M.D. Roberts Elmentaite van Hooff S.R. Khabirova E. Piapi Thevanesan C. Bugallo Blanco al.Tumor normal single mRNA comparisons reveal a pan-neuroblastoma cancer cell.bioRxiv. https://doi.org/10.1101/2020.06.22.164301v3Crossref Scholar). The trap authors seem fallen into rely small number manually curated murine markers Although many cell-defining are conserved across species, universally case. Therefore, it advisable apply unbiased, quantitative approaches when transferring labels from one species another. Using such methods, here derive correct studied highlight fickle inter-species markers. four principal types developing medulla Schwann precursors (SCPs), bridge (sympathetic neuroblasts). Recent investigations mice (e.g., Furlan 2017Furlan Dyachuk V. Kastriti M.E. Calvo-Enrique L. Abdo H. Hadjab Chontorotzea T. Akkuratova Usoskin D. Kamenev al.Multipotent peripheral glial generate neuroendocrine medulla.Science. 2017; 357: eaal3753Crossref (117) Scholar) provided transcriptomic definitions these types, which used for reference transcriptomes, reanalyzed (Figures S1A S1B). To avoid biases due individual markers, two independent computational widely between datasets based entire transcriptome. an established map our standard (Furlan projected al.’s orthogonal ways. For comparison, restricted both transcriptomes those could be unambiguously mapped (1-to-1 orthologs). trained logistic regression (Young 2018Young Mitchell T.J. Vieira Braga F.A. Tran M.G.B. Stewart B.J. Ferdinand J.R. Collord Botting R.A. Popescu D.-M. Loudon K.W. kidneys cellular identity renal tumors.Science. 2018; 361: 594-599Crossref (215) canonical correlation (Butler 2018Butler Hoffman Smibert Papalexi Satija Integrating different conditions, technologies, species.Nat. Biotechnol. 36: 411-420Crossref (2826) TransferData function Seurat package), predict likelihood each was precursor, cell, or sympathoblast (Figure S1C). agreement with assigned high probability cluster 1 representing indicated highest being lie 2, labeled Likewise, 3, That is, should reversed S1A). Our conclusions were further corroborated highlighting defined readouts directly excised laser capture microscopy This also illustrated some transcripts applicable vice versa Together, analyses interspecies subjective manual curation genes. can avoided leveraging powerful enable through methods. Assuming all downstream study valid, would reached conclusion: most closely sympathoblasts. acknowledge funding Wellcome Trust. Download .pdf (.45 MB) Help pdf files Document S1. Figure S1 Single-Cell Characterization Malignant Phenotypes Developmental Trajectories Adrenal NeuroblastomaDong al.Cancer CellSeptember 17, 2020In BriefDong provide detailed phenotypic landscape (NB) using RNA sequencing proliferation/differentiation status highly associated clinical heterogeneity NB. Full-Text Open ArchiveEvolutionary switch expression leads mis-assignment medullaKameneva CellApril 29, 2021In BriefWe like clarify aspects ongoing discussion (Bedoya-Reina Schlisio, 2021; 2021b; 2021) regarding 2020), performed transcriptomics medulla, followed comparison heterogeneous populations. grateful publishing valuable data, believe communal work will interpretation context embryos pathological tissues. Response Kildsiute Bedoya-Reina SchlisioYang CellDecember 31, appreciate Schlisio attention comments publication 2020). letters response interest neural development communities well bioinformaticians. Chromaffin Cells Sympathoblast Signature: Too Similar Keep Apart?Bedoya-Reina (2020) built atlas crest derivatives humans trace origins neuroblastoma. compared anlagen found clusters designated mouse.