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Related Experiment Video

Updated: Dec 9, 2025

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

Eugene Drokhlyansky1, Christopher S Smillie1, Nicholas Van Wittenberghe1

  • 1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Cell
|September 5, 2020
PubMed
Summary

This study developed novel methods to map the enteric nervous system (ENS) at single-cell resolution in mice and humans. Findings reveal extensive neuron diversity, circadian patterns, and links between aging, disease genes, and ENS function.

Keywords:
ENSGWASagingcircadiancolonenteric nervous systementeric neuronileumneuro-immunesingle cell

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Area of Science:

  • Neuroscience
  • Genomics
  • Gastroenterology

Background:

  • The enteric nervous system (ENS) controls gut functions but is complex due to rare and diverse cell types.
  • Comprehensive molecular profiling of the ENS has been challenging.

Purpose of the Study:

  • To develop and apply novel single-cell resolution techniques for comprehensive molecular characterization of the ENS in mice and humans.
  • To uncover neuron diversity, identify cell-type-specific transcriptional programs, and explore disease associations within the ENS.

Main Methods:

  • Developed RAISIN RNA-seq for profiling intact nuclei with ribosome-bound mRNA.
  • Developed MIRACL-seq for label-free enrichment of rare ENS cell types using droplet-based profiling.
  • Generated large-scale single-nucleus RNA sequencing atlases for mouse and human ENS.

Main Results:

  • Created a mouse ENS atlas with over 1 million nuclei, including 5,068 neurons, revealing significant neuron diversity and circadian expression changes.
  • Identified dysregulation of disease-related genes with aging and distinct molecular profiles between ileum and colon ENS.
  • Generated a human ENS atlas with over 400,000 nuclei, including 1,445 neurons, identifying conserved and species-specific programs and potential cell-cell interactions.
  • Found that the human ENS expresses risk genes for neuropathic, inflammatory, and extra-intestinal diseases.

Conclusions:

  • The developed methods enable unprecedented molecular insights into ENS complexity.
  • The ENS exhibits dynamic circadian regulation and age-related molecular changes.
  • Neuronal contributions to various diseases are suggested by the expression of risk genes in the human ENS.