Cancer immunotherapies such as immune checkpoint blockade therapies that act on T cell inhibitory receptors have been widely adopted across different types of cancers. However, a majority of patients either do not respond to such therapies or eventually relapse. Therefore, identifying molecular mechanisms that influence therapeutic response and relapse is crucial to unlocking the full potential of checkpoint blockade therapies.
Immune checkpoint blockade in cancer relies on efficient tumor antigen presentation to activate antitumor immunity. Nevertheless, a variety of tumor-immune modulators allow malignant cells to evade cytotoxic T cells. To identify new regulators of tumor-immune interactions, Dr. Robert Bradley (Public Health Sciences and Basic Sciences divisions) and Dr. Stephen Tapscott (Human Biology division) and members of their laboratories teamed up to perform an unbiased pan-cancer analysis of tumor transcriptomes, to identify genes with expression restricted to cancers of immune-privileged sites, that can reveal regulators of antigen presentation and immune modulation. Their work was published in a recent issue of the journal Developmental Cell.
Led by Dr. Guo-Liang Chew (postdoc in the Bradley lab) and Dr. Amy Campbell (staff scientist in the Tapscott lab), the authors searched the transcriptomes of 9,759 samples from 33 different cancer types, and found that DUX4, an early embryonic transcription factor that is typically silenced in normal tissues, is re-expressed in many solid tumors of the bladder, breast, lung, kidney, stomach and other organ sites. DUX4 is usually expressed when an embryo forms and develops, but is later epigenetically repressed and silenced in somatic tissues. DUX4 is best known for causing facioscapulohumeral muscular dystrophy (FSHD), in which changes in the chromosome prevent DUX4 from being turned off in muscle cells. In particular, the authors found that cancers expressed a full-length transcript of the DUX4 mRNA, suggesting a distinct mechanism from the prior identification of DUX4 translocations in other cancer types.
Interestingly, the authors found that DUX4-positive cancers had reduced expression of immune cell-specific genes, decreased estimated infiltration of immune cells (based on gene expression analysis using the Tumor Immune Estimation Resource algorithm) and decreased expression of the cytolytic markers GZMA and PRF1 compared with DUX4-negative cancers. In addition, expression levels of MHC class I genes was reduced in DUX4-positive cancers. Further analysis of published RNA sequencing (RNA-seq) data of cultured myoblasts with ectopic expression of DUX4 or myoblasts spontaneously expressing DUX4 showed that MHC class I gene expression negatively correlated with DUX4 expression, indicating that DUX4 suppresses MHC class I genes in a cell intrinsic manner.
Importantly, Dr. Campbell performed cellular experiments, where she expressed DUX4 in several cancer cells types with intact antigen presenting machinery and showed that DUX4 blocked interferon-gamma-induced up-regulation of MHC class I in all tested cells. This result demonstrated that DUX4 expression in cancer cells had the significant biological consequence of actively shielding the cancer cell from the immune system, rather than being a secondary event tolerated by cells with an already dismantled antigen presenting machinery.
Since checkpoint inhibitors rely on antigen presentation to work, the authors hypothesized that DUX4 might promote resistance to these immune therapies. Indeed, biopsies from patients with metastatic melanoma showed those who did not respond well to drugs that inhibit the immune checkpoint CTLA-4 exhibited significantly higher evidence of DUX4 activity compared to responsive patients. Notably, the authors also reported that clinical data confirmed DUX4 expression was associated with significantly reduced progression-free and overall survival in response to anti-CTLA-4 treatment.
This work highlights a potential pan-cancer role for DUX4 in mediating immune evasion and provides a basis for exploring inhibition of DUX4 as a method to overcome resistance to immune checkpoint blockade. The re-expression of DUX4 in cancer is significant because it provides a functional link between early embryogenesis and cancer. Furthermore, the association of DUX4 activity with failure to respond to immune checkpoint blockade provides a clinical incentive for figuring out the exact molecular underpinnings of DUX4 re-expression in cancer.
“This initial study needs to be validated in additional cancer cohorts undergoing immunotherapies. From there, the next steps will be to do the basic research to determine the mechanisms of dismantling the antigen presenting machinery and the translational research to determine whether interventions that turn off DUX4 in cancers will improve responses to immunotherapies” says Dr. Bradley.
Perhaps DUX4-targeted treatments might one day improve the success of immunotherapies? That is the hope of the authors, and the future looks promising. “Drugs and oligonucleotides that turn off DUX4 have already been developed as candidate treatments for the facioscapulohumeral muscular dystrophy caused by DUX4 expression in skeletal muscle and it is possible that some of these drugs might be repurposed for helping to treat cancers” says Dr. Tapscott.
Chew GL, Campbell AE, De Neef E, Sutliff NA, Shadel SC, Tapscott SJ, Bradley RK. 2019. DUX4 suppresses MHC class I to promote cancer immune evasion and resistance to checkpoint blockade. Dev Cell Jul 19. Pii: S1534-5807(19)30529-5.
This work was supported by the National Institutes of Health, Friends of FSH Research, and the Chris Carrino Foundation for FSHD. Dr. Bradley is a Leukemia and Lymphoma Society Scholar and Dr. Chew is supported by the Mahan Fellowship.