The Human and Mouse Enteric Nervous System at Single-Cell Resolution

Eugene Drokhlyansky; Christopher S Smillie; Nicholas Van Wittenberghe; Maria Ericsson; Gabriel K Griffin; Gokcen Eraslan; Danielle Dionne; Michael S Cuoco; Max N Goder-Reiser; Tatyana Sharova; Olena Kuksenko; Andrew J Aguirre; Genevieve M Boland; Daniel Graham; Orit Rozenblatt-Rosen; Ramnik J Xavier; Aviv Regev

doi:10.1016/j.cell.2020.08.003

The Human and Mouse Enteric Nervous System at Single-Cell Resolution

Cell. 2020 Sep 17;182(6):1606-1622.e23. doi: 10.1016/j.cell.2020.08.003. Epub 2020 Sep 3.

Authors

Eugene Drokhlyansky¹, Christopher S Smillie¹, Nicholas Van Wittenberghe¹, Maria Ericsson², Gabriel K Griffin³, Gokcen Eraslan¹, Danielle Dionne¹, Michael S Cuoco¹, Max N Goder-Reiser⁴, Tatyana Sharova⁴, Olena Kuksenko¹, Andrew J Aguirre⁵, Genevieve M Boland⁶, Daniel Graham⁷, Orit Rozenblatt-Rosen⁸, Ramnik J Xavier⁹, Aviv Regev¹⁰

Affiliations

¹ Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
² Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
³ Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
⁴ Massachusetts General Hospital, Cambridge, MA, USA.
⁵ Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
⁶ Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
⁷ Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA.
⁸ Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: orit@broadinstitute.org.
⁹ Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA. Electronic address: xavier@molbio.mgh.harvard.edu.
¹⁰ Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address: aregev@broadinstitute.org.

Abstract

The enteric nervous system (ENS) coordinates diverse functions in the intestine but has eluded comprehensive molecular characterization because of the rarity and diversity of cells. Here we develop two methods to profile the ENS of adult mice and humans at single-cell resolution: RAISIN RNA-seq for profiling intact nuclei with ribosome-bound mRNA and MIRACL-seq for label-free enrichment of rare cell types by droplet-based profiling. The 1,187,535 nuclei in our mouse atlas include 5,068 neurons from the ileum and colon, revealing extraordinary neuron diversity. We highlight circadian expression changes in enteric neurons, show that disease-related genes are dysregulated with aging, and identify differences between the ileum and proximal/distal colon. In humans, we profile 436,202 nuclei, recovering 1,445 neurons, and identify conserved and species-specific transcriptional programs and putative neuro-epithelial, neuro-stromal, and neuro-immune interactions. The human ENS expresses risk genes for neuropathic, inflammatory, and extra-intestinal diseases, suggesting neuronal contributions to disease.

Keywords: ENS; GWAS; aging; circadian; colon; enteric nervous system; enteric neuron; ileum; neuro-immune; single cell.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Aging / genetics
Aging / metabolism
Animals
Circadian Clocks / genetics
Colon / cytology
Colon / metabolism
Endoplasmic Reticulum, Rough / genetics
Endoplasmic Reticulum, Rough / metabolism
Endoplasmic Reticulum, Rough / ultrastructure
Enteric Nervous System / cytology*
Enteric Nervous System / metabolism*
Epithelial Cells / metabolism
Female
Gene Expression Regulation, Developmental / genetics*
Genetic Predisposition to Disease / genetics
Humans
Ileum / cytology
Ileum / metabolism
Inflammation / genetics
Inflammation / metabolism
Intestinal Diseases / genetics
Intestinal Diseases / metabolism
Male
Mice
Mice, Inbred C57BL
Mice, Transgenic
Microscopy, Electron, Transmission
Nervous System Diseases / genetics
Nervous System Diseases / metabolism
Neuroglia / cytology
Neuroglia / metabolism
Neurons / cytology
Neurons / metabolism*
Nissl Bodies / genetics
Nissl Bodies / metabolism*
Nissl Bodies / ultrastructure
RNA, Messenger / genetics
RNA, Messenger / metabolism*
RNA-Seq
Ribosomes / metabolism
Ribosomes / ultrastructure
Single-Cell Analysis / methods*
Stromal Cells / metabolism

Substances

RNA, Messenger

Abstract

Publication types

MeSH terms

Substances

Grants and funding