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Reply to: Ptbp1 deletion does not induce astrocyte-to-neuron conversion

Nature volume 618, pages E8–E13 (2023)Cite this article

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The Original Article was published on 07 June 2023

replying to: T. Hoang et al. Nature https://doi.org/10.1038/s41586-023-06066-9 (2023)

In the accompanying Comment1, Hoang et al.1 state that Ptbp1 knockout does not convert astrocytes to neurons in mouse brain, a phenotype that is distinct from the astrocyte-to-neuron conversion induced by Ptbp1 knockdown that we reported2. However, after analysing the same single-cell RNA-sequencing (scRNA-seq) data generated by Hoang et al.1, we reach the opposite conclusion. Unbiased investigators can now independently analyse the same dataset to draw their own conclusions. In this Reply, we also consider two related papers3,4 that report that—although Ptbp1 knockdown results in the appearance of new neurons—these neurons are not genetically traced to astrocytes.

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Fig. 1: Analysis of the scRNA-seq data from the cortex of Ptbp1-knockout mice.
Fig. 2: Re-analysis of the original lineage-tracing data.

Data availability

The scRNA-seq data are from the Gene Expression Omnibus (GSE184933) generated and deposited by Hoang et al.1. All other data supporting the findings of this study are available from the corresponding authors on request.

References

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Author information

Authors and Affiliations

  1. Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA

    Yajing Hao & Steven F. Dowdy

  2. Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China

    Jing Hu & Hao Qian

  3. Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

    Yuanchao Xue

  4. Department of Neurosciences, University of California, San Diego School of Medicine, La Jolla, CA, USA

    William C. Mobley

  5. Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, China

    Xiang-Dong Fu

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  1. Yajing Hao
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Contributions

Y.H. performed analysis of the scRNA-seq data. H.Q., J.H. and X.-D.F. wrote the Reply with input from J.H., Y.X., S.F.D. and W.C.M. Note that the author list is different from that in the original paper2 because we recruited the first author of the Reply, Y.H., to analyse the scRNA-seq data and omitted several collaborators whose work was not related to the subjects raised by Hoang et al.1.

Corresponding authors

Correspondence to Hao Qian or Xiang-Dong Fu.

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The authors declare no competing interests.

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Extended data figures and tables

Extended Data Fig. 1 Quality control in analyzing the scRNA-seq data.

a,b,c, Violin plots of n-count_RNA, n-feature_RNA and Percent_mt (mitochondrial transcripts) distribution in cells from WT, heterozygous or homozygous Ptbp1 KO cortex (a), striatum (b) and substantia nigra (c). Center lines in boxplots are the median and box is the interquartile range (IQR). n = 13198, n = 14732, n = 17071 cells for WT, heterozygous and homozygous Ptbp1 KO cortex; n = 12145, n = 12175, n = 15710 cells for WT, heterozygous and homozygous Ptbp1 KO striatum; n = 5741, n = 4518, n = 2965 cells for WT, heterozygous and homozygous Ptbp1 KO substantia nigra. d,e,f, Expression of cell type-specific marker genes in each cluster defined from cortex (d), striatum (e) and substantia nigra (f) scRNA-seq data.

Extended Data Fig. 2 Reanalyzing the scRNA-seq data from striatum.

a, UMAP of cells from striatum of different genotypes (left). Colored clusters are annotated to different cell types based on an established panel of cell markers. Expression of top 10 marker genes in Cluster 10 was compared with other clusters (right). Red text: neuronal genes. b, Expression of GFP, Ptbp1, and Ptbp2 in individual cell clusters from WT (red); green: heterozygous (green), and homozygous (blue) Ptbp1 KO mice.

Extended Data Fig. 3 Reanalyzing the scRNA data from substantia nigra.

a, UMAP of cells from substantia nigra of different genotypes. b, Relative quantity of cells in different clusters (indicated at top). c, Expression of GFP, Ptbp1, and Ptbp2 in individual cell clusters from WT (red), heterozygous (green), and homozygous (blue) Ptbp1 KO mice. d, Expression of top 10 marker genes in Cluster 5, compared with other clusters (right). Green text: astrocytic genes, Red text: neuronal genes. e, Identification of potential doublets with DoubletFinder, showing that most cells in Cluster 5 are unlikely to be doublets.

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Hao, Y., Hu, J., Xue, Y. et al. Reply to: Ptbp1 deletion does not induce astrocyte-to-neuron conversion. Nature 618, E8–E13 (2023). https://doi.org/10.1038/s41586-023-06067-8

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