Cancer cell lines often used in research had transcriptomic heterogeneity reminiscent of tumors.

  • Major Finding: Cancer cell lines often used in research had transcriptomic heterogeneity reminiscent of tumors.

  • Concept: Single-cell RNA sequencing revealed recurrent heterogeneous gene-expression patterns in vitro.

  • Impact: This work provides a resource showing the overlap between gene expression in vitro and in vivo.

Intratumoral heterogeneity is known to play a role in important aspects of cancer biology, such as treatment resistance and metastasis. Although established cell lines are commonly used in cancer research, it is not clear to what extent, if any, they recapitulate the cellular heterogeneity observed within tumors. To investigate this, Kinker, Greenwald, and colleagues performed single-cell RNA-sequencing analyses on 53,513 cells from 198 cancer cell lines representing 22 cancer types. This revealed substantial variability in the transcriptomes of individual cells within each cell line, and the variability was in some cases discrete (11% of cell lines) but was more often continuous. The most common recurrent heterogeneous programs of gene expression, which were found in multiple cell lines, were related to the cell cycle; another common theme was the epithelial–mesenchymal transition. Strikingly, the most frequent recurrent heterogeneous patterns of gene expression observed in these cell lines overlapped substantially with patterns observed in vivo in tumors of diverse origins. An additional type of heterogeneous gene-expression program detected in the cancer cell lines was related to senescence, and this category could be further split into one set related to classic p53-mediated senescence and another epithelial senescence–specific set. Deeper investigation revealed that regulation of recurrent heterogeneous gene-expression programs occurred at the genetic level in some cases and could also sometimes be regulated by chemical cues often found in the tumor microenvironment, such as the cytokine TGFβ and hypoxia signals. Notably, the transcriptomally defined subpopulations identified in this work exhibited different sensitivity to anticancer drugs. In summary, this study demonstrates that cancer cell lines commonly used in research accurately represent many of the types of cells observed in individual tumors and delineates the overlap of recurrent heterogeneous gene-expression patterns between these cell lines and tumors.

Kinker GS, Greenwald AC, Tal R, Orlova Z, Cuoco MS, McFarland JM, et al. Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity. Nat Genet 2020;52:1208–18.

Note:Research Watch is written by Cancer Discovery editorial staff. Readers are encouraged to consult the original articles for full details. For more Research Watch, visit Cancer Discovery online at