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scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis.

Valentina Nale1, Alice Chiodi1, Noemi Di Nanni1

  • 1Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.

BMC Bioinformatics
|November 28, 2023
PubMed
Summary
This summary is machine-generated.

scMuffin is a new R package for single-cell (SC) gene expression analysis in solid tumors. It helps identify cell identity and link genomic changes to tumor phenotypes, improving cancer treatment development.

Keywords:
CancerCell identitySingle-cell transcriptomicsTumor heterogeneity

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Area of Science:

  • Bioinformatics
  • Genomics
  • Cancer Research

Background:

  • Solid tumors exhibit complex cellular heterogeneity, hindering effective cancer treatment development.
  • Bulk RNA sequencing struggles to identify specific cell subpopulations crucial for cancer progression.
  • Single-cell (SC) gene expression analysis is vital for dissecting tumor cellularity.

Purpose of the Study:

  • To introduce scMuffin, an R package for characterizing cell identity in solid tumors using SC gene expression data.
  • To provide a comprehensive suite of analytical tools for SC data from solid tumors.
  • To facilitate the identification of critical cell subpopulations and their genomic underpinnings.

Main Methods:

  • scMuffin offers functions to calculate scores for marker gene expression, pathway activity, and cell state trajectories.
  • The package enables analysis of Copy Number Variations (CNVs), transcriptional complexity, and proliferation states.
  • It integrates diverse evidence to distinguish cell types and link genomic aberrations to phenotypes.

Main Results:

  • scMuffin was validated using public SC expression datasets of human high-grade gliomas.
  • Analyses revealed potential links between chromosomal amplifications and invasive tumor phenotypes.
  • Findings suggest chromosomal amplifications may be associated with cells possessing tumor-initiating characteristics.

Conclusions:

  • scMuffin effectively addresses key bioinformatics challenges in analyzing SC gene expression data from solid tumors.
  • The tool aids in distinguishing normal and tumor cells and defining cell identities.
  • scMuffin facilitates the identification of subtle differences between cell subtypes and states.