Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol
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1.
California Institute of Technology
Abstract
Single-cell transcriptomic platforms provide an opportunity to map an organism's response to environmental cues with high resolution. Here, we applied single-nucleus RNA sequencing (snRNA-seq) to establish the tissue and cell type-resolved transcriptome of the adult C. elegans and characterize the inter- and trans-generational transcriptional impact of ethanol. We profiled the transcriptome of 41,749 nuclei resolving into 31 clusters, representing a diverse array of adult cell types including syncytial tissues. Following exposure to human-relevant doses of alcohol, several germline, striated muscle, and neuronal clusters were identified as being the most transcriptionally impacted at the F1 and F3 generations. The effect on germline clusters was confirmed by phenotypic enrichment analysis as well as by functional validation, which revealed a remarkable inter- and trans-generational increase in germline apoptosis, aneuploidy, and embryonic lethality. Together, snRNA-seq represents a valuable approach for the detailed examination of an adult organism's response to environmental exposures.
Copyright and License
© 2023 The Author(s). Under a Creative Commons license CC BY-NC-ND 4.0
Acknowledgement
The authors would like to thank Doug Arneson for input on single-nucleus sequencing parameters; Ingrid Cely, In Sook Ahn, and Graciel Diamante for discussions and troubleshooting advice; Eyal Ben David for advice on single-cell/-nuclei dissociation methods; Jessica Scholes, Jeffrey Calim, Felicia Codrea, and Salem Haile for guidance with single-nucleus cytometry; Michael Mashock and Marco De Simone for their library preparation and sequencing expertise; the CNSI ALMS (RRID: SCR_022789) for their guidance with advanced microscopy; and Matteo Pellegrini for advice and input on data analysis. We thank Judith Kimble, Tina Lynch, and Sarah Crittenden for advice on smFISH and providing the sygl-1 probe. The Caenorhabditis Genetics Center (CGC) (RRID:SCR_007341) provided the strains used in this study. We thank Yuji Kohara for permission to use NEXTDB (RRID:SCR_004480) in situ data. Figure 1A and the graphical abstract were created with BioRender.com. L.T. is supported by the NIH Training Grant in Genomic Analysis and Interpretation T32 HG002536; Y.-W.C. is supported by the UCLA Eureka fellowship and Burroughs Wellcome Fund Inter-school Training Program in Chronic Diseases; P.A. is supported by NIEHS R01 ES027487, NIAAA R21 AA024889, the John Templeton Foundation, and the Burroughs Wellcome Innovation in Regulatory Science Award. E.d.V.B. and P.W.S. are supported by U24HG002223.
Contributions
L.T., R.B.-C., K.S., W.X., M.T.L., B.P., and E.R. performed biological experiments and corresponding analyses; Y.-W.C. performed bioinformatic analyses; P.A. and X.Y. supervised experiments; P.A. and X.Y. supervised analyses; E.d.V.B. devised a visualization approach that assisted cell-type assignment and cluster identification, which P.S. supervised; and L.T., R.B.-C., M.T.L., Y.-W.C., X.Y., and P.A. wrote the manuscript.
Data Availability
The data can be accessed and browsed through the Broad Single Cell Portal: https://singlecell.broadinstitute.org/single_cell/study/SCP922/single-nucleus-resolution-mapping-of-the-adult-c-elegans-and-its-application-to-elucidate-inter-and-trans-generational-response-to-alcohol.
Conflict of Interest
The authors declare no competing interests.
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Additional details
- PMCID
- PMC10592506
- National Institutes of Health
- T32 HG002536
- University of California, Los Angeles
- Burroughs Wellcome Fund
- National Institutes of Health
- R01 ES027487
- National Institutes of Health
- R21 AA024889
- John Templeton Foundation
- National Institutes of Health
- U24HG002223
- Caltech groups
- Division of Biology and Biological Engineering