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Fluorescence-Activated Cell Sorting for the Isolation of Scleractinian Cell Populations

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Alleviating batch effects in cell type deconvolution with SCCAF-D.

Shuo Feng^1,2, Liangfeng Huang^1,3, Anna Vathrakokoili Pournara⁴

¹GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China.

Nature Communications

|December 31, 2024

Summary

This summary is machine-generated.

Cell type deconvolution methods reveal cell proportion changes. This study introduces SCCAF-D, a computational workflow addressing batch effects for reliable analysis across diverse tissues, including non-alcoholic fatty liver disease.

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Area of Science:

Computational biology
Genomics
Bioinformatics

Background:

Cell type deconvolution methods estimate cell proportions from bulk transcriptomics.
Current benchmarking often uses simulated data from the same source, limiting real-world applicability.
Batch effects can significantly impact deconvolution accuracy.

Purpose of the Study:

To evaluate the impact of batch effects on cell type deconvolution.
To introduce SCCAF-D, a novel computational workflow for robust deconvolution.
To validate SCCAF-D's performance across diverse tissue types and simulated/real data.

Main Methods:

Development of the SCCAF-D computational workflow.
Assessment of batch effects in cell type deconvolution.
Benchmarking using simulated and real bulk transcriptomics data.
Application to non-alcoholic fatty liver disease (NAFLD) datasets.

Main Results:

SCCAF-D ensures a Pearson Correlation Coefficient above 0.75 across simulated and real bulk data.
The workflow demonstrates reliable performance across various tissue types.
Analysis of NAFLD reveals significant changes in cell proportions during disease progression.

Conclusions:

SCCAF-D provides a robust solution for cell type deconvolution, mitigating batch effect issues.
The workflow enhances the reliability of transcriptomics data analysis in biological studies.
SCCAF-D offers valuable insights into cellular dynamics in diseases like NAFLD.