Estimation of immune cell content in tumor using single-cell RNA-seq reference data.

Abstract

BACKGROUND:

The rapid development of single-cell RNA sequencing (scRNA-seq) provides unprecedented opportunities to study the tumor ecosystem that involves a heterogeneous mixture of cell types. However, the majority of previous and current studies related to translational and molecular oncology have only focused on the bulk tumor and there is a wealth of gene expression data accumulated with matched clinical outcomes.

RESULTS:

In this paper, we introduce a scheme for characterizing cell compositions from bulk tumor gene expression by integrating signatures learned from scRNA-seq data. We derived the reference expression matrix to each cell type based on cell subpopulations identified in head and neck cancer dataset. Our results suggest that scRNA-Seq-derived reference matrix outperforms the existing gene panel and reference matrix with respect to distinguishing immune cell subtypes.

CONCLUSIONS:

Findings and resources created from this study enable future and secondary analysis of tumor RNA mixtures in head and neck cancer for a more accurate cellular deconvolution, and can facilitate the profiling of the immune infiltration in other solid tumors due to the expression homogeneity observed in immune cells.

• Authors: Xiaoqing Yu, Y Ann Chen, Jose R Conejo-Garcia, Christine H Chung, Xuefeng Wang
• Journal: BMC cancer (BMC Cancer) Vol. 19 Issue 1 Pg. 715 (Jul 19 2019) ISSN: 1471-2407 [Electronic] England
• PMID: 31324168 (Publication Type: Journal Article)

Chemical References

• RNA, Small Cytoplasmic

Topics

• CD8-Positive T-Lymphocytes (immunology)
• Databases, Genetic
• Datasets as Topic
• Ecosystem
• Genes, Neoplasm
• Genetic Heterogeneity
• Head and Neck Neoplasms (genetics, immunology, pathology)
• Humans
• RNA, Small Cytoplasmic (genetics)
• RNA-Seq (methods)
• Single-Cell Analysis (methods)
• Software
• Squamous Cell Carcinoma of Head and Neck (genetics, immunology, pathology)
• T-Lymphocytes, Regulatory (immunology)
• Transcriptome
• Tumor Microenvironment (genetics, immunology)