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Cell Specific Gene Expression

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...

Cell Specific Gene Expression

Cell Specific Gene Expression

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Updated: Mar 28, 2026

Transcriptome Analysis of Single Cells

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

Subcellular transcriptome sequencing with single cell APEX-seq identifies regulators of cell-cell interactions.

Andrew Xue^1,2, Bo Cai¹, Qian Xue^1,3

¹Department of Genetics, Stanford University, Stanford, CA, 94305, USA.

Biorxiv : the Preprint Server for Biology

|March 27, 2026

Summary

This summary is machine-generated.

Single-cell APEX-seq (scAPEX-seq) maps RNA locations within cells, revealing new insights into cell interactions and functions. This proximity labeling method enhances understanding of complex biological systems.

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Last Updated: Mar 28, 2026

Transcriptome Analysis of Single Cells

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Area of Science:

Molecular Biology
Genomics
Cell Biology

Background:

Single-cell RNA sequencing (scRNA-seq) offers insights into cell diversity but lacks subcellular resolution.
RNA localization is critical for gene expression regulation, influencing splicing, translation, and protein function.
Understanding transcript distribution is key to deciphering cellular heterogeneity and function.

Purpose of the Study:

To introduce single-cell APEX-seq (scAPEX-seq), a novel method for mapping subcellular transcriptomes at single-cell resolution.
To investigate the role of RNA localization in cell-cell interactions and uncover previously unresolved transcriptomic signatures.
To characterize activated chimeric antigen receptor (CAR) T cell states and their functional impact on tumor cells.

Main Methods:

Developed single-cell APEX-seq (scAPEX-seq) by integrating proximity labeling with droplet-based RNA sequencing.
Optimized probe design and RNA recovery for enhanced sensitivity and efficiency.
Applied scAPEX-seq to co-cultures of tumor cells with macrophages and CAR T cells.

Main Results:

scAPEX-seq successfully mapped endoplasmic reticulum-associated transcripts in thousands of individual cells.
Revealed interaction-dependent cell states and transcriptomic signatures in tumor-macrophage co-cultures, enriching for cell surface and secretory transcripts.
Identified distinct activated CAR T cell states, including populations with upregulated NT5E or CTSW expression.
Demonstrated that CTSW overexpression in CAR T cells promotes stem-like phenotypes, enhanced proliferation, and sustained tumor cell killing.

Conclusions:

scAPEX-seq is a powerful and scalable method for profiling subcellular RNA populations at single-cell resolution.
The technique enables the discovery of cell-cell interaction regulators missed by conventional scRNA-seq approaches.
scAPEX-seq provides critical insights into the functional roles of RNA localization in cellular processes and disease.