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Methodological concerns and lack of evidence for single-synapse RNA-seq

Nature Biotechnology volume 41, pages 1221–1224 (2023)Cite this article

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Matters Arising to this article was published on 27 July 2023

The Original Article was published on 16 January 2023

arising from M. Niu et al. Nature Biotechnology https://doi.org/10.1038/s41587-022-01635-1 (2023)

In a recent issue of Nature Biotechnology, Niu et al.1 develop a new droplet-based RNA sequencing (RNA-seq) method and apply it to particles derived from subcellular fractionation of brain tissue1. The authors first establish that their new method, multiple-annealing-and-tailing-based quantitative single-cell RNA-seq in droplets (MATQ-Drop), is compatible with aldehyde-fixed human and mouse nuclei. The authors apply MATQ-Drop to study the transcriptome of subcellular particles from the mouse hippocampus, identifying numerous transcriptomic clusters. They further employ MATQ-Drop to study subcellular particles from frozen human brain samples of healthy controls and patients with Alzheimer’s disease. The goals of this paper are laudable, and the MATQ-Drop method as applied to fixed nuclei may be widely useful to researchers. However, we have major technical concerns about the methods employed to generate and isolate synaptosomes. Due to a lack of critical control and validation experiments, the authors present little or no evidence that they are analyzing the transcriptomes of single synapses.

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Fig. 1: Conventional synaptosome fractionation and sorting compared to the method of Niu et al.

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Author notes

  1. Benjamin D. Hobson

    Present address: Department of Psychiatry, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA

Authors and Affiliations

  1. Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA

    Benjamin D. Hobson

  2. Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA

    Benjamin D. Hobson

  3. University of Bordeaux, CNRS, IINS, UMR 5297, Bordeaux, France

    Etienne Herzog

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  1. Benjamin D. Hobson
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B.D.H. and E.H. co-wrote and edited the manuscript. B.D.H. generated the figure with input from E.H.

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Correspondence to Benjamin D. Hobson or Etienne Herzog.

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Hobson, B.D., Herzog, E. Methodological concerns and lack of evidence for single-synapse RNA-seq. Nat Biotechnol 41, 1221–1224 (2023). https://doi.org/10.1038/s41587-023-01877-7

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