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Related Experiment Video

Updated: Oct 29, 2025

Automated Quantification of Hematopoietic Cell – Stromal Cell Interactions in Histological Images of Undecalcified Bone

Automated Quantification of Hematopoietic Cell – Stromal Cell Interactions in Histological Images of Undecalcified Bone

Published on: April 8, 2015

An unsupervised method for physical cell interaction profiling of complex tissues.

Nathanael Andrews¹, Jason T Serviss¹, Natalie Geyer²

¹Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden.

|July 13, 2021

Summary

This summary is machine-generated.

We developed cell interaction by multiplet sequencing (CIM-seq), a new high-throughput method to map direct cell-cell interactions within tissues. CIM-seq identifies known and novel cellular connections, revealing new insights into tissue organization.

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Last Updated: Oct 29, 2025

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Area of Science:

Cellular and Molecular Biology
Genomics
Bioinformatics

Background:

Cellular identity and tissue function depend on physical cell-cell interactions.
Analyzing the complex cellular interactome at scale is a significant technical challenge.

Purpose of the Study:

To develop a high-throughput, unsupervised method for analyzing direct physical cell-cell interactions within tissues.
To enable large-scale investigation of the cellular interactome.

Main Methods:

Developed cell interaction by multiplet sequencing (CIM-seq), a method based on RNA sequencing of incompletely dissociated cells.
Employed computational deconvolution to identify cell types and interaction parameters from sequencing data.
Validated CIM-seq on gut epithelium, lung, and spleen tissues.

Main Results:

CIM-seq accurately identifies known cell-type interactions in various tissues.
Discovered a novel goblet cell subtype adjacent to colonic stem cells, expressing the wound-healing marker Plet1.
Demonstrated compatibility with high-throughput droplet-based sequencing methods.

Conclusions:

CIM-seq is a broadly applicable and powerful tool for unsupervised profiling of cell-type interactions.
The method advances our understanding of tissue organization and cellular communication.
Identified a previously unrecognized cell subtype with potential roles in colonic wound healing.