Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data

Genome Med. 2021 Dec 16;13(1):187. doi: 10.1186/s13073-021-01001-x.


We present Beyondcell, a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments. Our method calculates an enrichment score in a collection of drug signatures, delineating therapeutic clusters (TCs) within cellular populations. Additionally, Beyondcell determines the therapeutic differences among cell populations and generates a prioritised sensitivity-based ranking in order to guide drug selection. We performed Beyondcell analysis in five single-cell datasets and demonstrated that TCs can be exploited to target malignant cells both in cancer cell lines and tumour patients. Beyondcell is available at: .

Keywords: Drug repositioning; Intratumoural heterogeneity; Personalised therapy; Single-cell RNA-seq; Therapeutic clusters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Profiling / methods
  • Humans
  • Neoplasms* / drug therapy
  • Neoplasms* / genetics
  • RNA-Seq
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis* / methods