Ephemeral yet consequential: DUX4 activates an early embryonic program in cancer cells

From the Tapscott lab, Human Biology Division

“There have been great advances in cancer treatments over the past decade, but cancer reoccurrence after treatment remains a huge hurdle,” explained Dr. Andrew Smith, a newly minted PhD and current postdoctoral researcher in the Tapscott lab at Fred Hutch. “It is known that most cancers are heterogeneous and that rare subpopulations of cells, or specific cell states, are likely responsible for cancer progression and reoccurrence after treatment.”

Our prior publication with the [Robert] Bradley lab analyzed The Cancer Genome Atlas and other datasets to discover that the early embryonic transcription factor DUX4, is expressed in subsets of many different cancers. This study also showed that DUX4-expressing cancers had lower levels of MHC Class I expression and resistance to checkpoint blockade therapy,” said Dr. Stephen Tapscott, Professor in the Human Biology and Clinical Research Divisions at Fred Hutch. The study indicated that DUX4 mRNA was present at relatively low levels in cancer cells. However, it was unclear “whether this represented a homogeneously low level of expression in the population of cancer cells or high expression in a subpopulation,” Dr. Tapscott said. The effects of DUX4 expression on other transcriptional programs in cancer cells also remained unknown.

In a new study published in Cell Reports led by Dr. Smith, researchers reported that DUX4 is also expressed in some cancer cell lines, but only transiently, resulting in a small percentage of cells expressing DUX4 at any time point. Importantly, the DUX4 expression induces an early embryonic totipotent-like state.

“In the current study, we identify cancer cell lines that, like the cancers identified in the prior analysis of The Cancer Genome Atlas datasets, express low levels of DUX4 mRNA based on bulk RNA sequencing,” explained Dr. Smith. “Single-cell analysis of protein and RNA expression demonstrates that the low DUX4 expression in the population represents very high expression in a relatively rare subpopulation of cells. The findings are consistent with transient bursts of DUX4 mRNA expression that establish small clusters of cells.” The authors also found that DNA damage increased the number of DUX4-expressing cells.

A cartoon of DUX4 being transiently expressed in some cancer cells.
The transcription factor DUX4 is transiently expressed in a small subset of cancer cells. DUX4 expression activates the zygotic gene activation transcriptional program, totipotent 8C-like program, and markers of early embryonic lineages, while suppressing MHC Class I expression. Image from Cell Reports article

“Furthermore, these cells that have expressed DUX4 and their progeny have activated comprehensive programs of early embryonic development and lineage specification, including genes regulating trophectoderm specification and epithelial/mesenchymal specification,” explained Dr. Smith. These include the activation of the zygotic gene activation transcriptional program, totipotent 8C-like program, and markers of early embryonic lineages.

In addition to an increase in early lineage markers, cancer cells with DUX4 expression also had decreased MHC (major histocompatibility complex) Class I mRNA and protein expression. MHC Class I molecules are expressed on the surface of all nucleated cells, and alert the immune system to infection by presenting fragments of foreign proteins on the cell surface. Thus, a reduction in MHC-I expression compromises the cell’s ability to fight off infections. This finding “provides a molecular mechanism for the previously described correlation of DUX4 expression and immune evasion,” said Dr. Smith.

The findings from this study have important clinical implications for cancer therapies. “We suggest that the DUX4-expressing cells establish a transient, embryonic state that might facilitate metastasis and also be resistant to conventional cancer therapies. In this context, targeting DUX4 might be a new approach to cancer therapies,” said Dr. Tapscott. The authors explained that future studies should examine the role of DUX4 in cancer progression, metastasis, and immune evasion. “And most importantly,” said Dr. Tapscott, future studies should “determine the consequences of interventions to suppress DUX4 expression in cancer cells.”

Future studies could also take advantage of surrogate markers for DUX4 expression identified in this study. “Specifically, DUX4-expressing cancers have decreased CpG methylation at the DUX4 locus,” said Dr. Tapscott. “Therefore, retrospective and prospective studies could assess the implications of DUX4 expression in cancers and response to therapies.”

Researchers at Fred Hutch, including the team in the Tapscott lab, are well equipped to tackle these questions as part of the Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium. “We are grateful to have received advice from many members of the Cancer Consortium Collaboration, including our co-authors,” said Dr. Tapscott. “We will rely on the Consortium for the next steps to validate our findings in clinical cohorts and extend our studies to PDX [patient-derived xenograft] models and lineage tracing experiments to define the role of DUX4 in cancer progression. Ultimately, we hope to work with the Consortium to incorporate measurements of DUX4 expression in clinical studies.”

This work was supported by the National Institutes of Health, Friends of SFH Research, and The Chris Carrino Foundation for FSHD.  

The Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium member Drs. Manu Setty and Stephen Tapscott contributed to this work.

Smith AA, Nip Y, Bennett SR, Hamm DC, Lemmers RJLF, van der Vliet PJ, Setty M, van der Maarel SM, Tapscott SJ. 2023. DUX4 expression in cancer induces a metastable early embryonic totipotent program. Cell Rep. 42(9):113114.