Mitchell Grinwald

Program: Molecular Genetics and Genomics

Current advisor: Ting Wang, PhD

Undergraduate university: Washington University, 2020

Enrollment year: 2021

Research summary
Defining the Role of Polycomb Repressive Complex 2 in Regulating Transposable Element Activation in Malignant Peripheral Nerve Sheath Tumor

Transposable elements (TE) are derepressed in cancer and can give rise to therapeutic vulnerabilities including tumor-specific TE antigens (TS-TEAs). TS-TEAs are primarily repressed by DNA methylation, but emerging evidence suggests that other epigenetic mechanisms including Polycomb Repressive Complex 2 (PRC2) may provide a backup method of TE repression in human cancers. I am collaborating with Dr. Angela Hirbe and Dr. Ben Garcia to investigate TE and TS-TEA regulation in malignant peripheral nerve sheath tumor (MPNST), an incurable cancer in which PRC2-compromising mutations are highly recurrent and prognostically significant. These efforts will provide the first direct investigation of whether PRC2-mediated H3K27me3 directly regulates TEs in human cancer, and may provide a rationale for combinatorial PRC2 inhibitor and DNA methyltransferase inhibitor (DNMTi) therapy in patients with PRC2 WT tumors.
Through DUA and MTA agreements with the Neurofibromatosis Therapy Acceleration Program (NTAP) and the Genomics of MPNST consortium (GeM), I’ve assembled the largest collection of MPNST transcriptomic data to date. Analysis of these data links TE dysregulation with the progression of nerve sheath Neurofibromas towards transformation into MPNST. Within MPNST cohorts, PRC2-LOF is associated with a further increase in TE dysregulation. TE transcript profiles can distinguish plexiform and atypical neurofibromas from one another and from MPNSTs, and distinguish PRC2-LOF from PRC2-WT MPNST tumors. These findings build upon previously published observations that TE dysregulation is progressive with transformation in the in vitro Weinberg Transformation Model and emphasize the potential applications of TE research to better understanding tumorigenesis and identifying tumor type and stage-specific biomarkers and therapeutic targets. Ongoing analysis is focused on identifying tumor-specific and tumor type specific TE transcripts, and on predicting resultant tumor-specific TE proteins and antigens in these tumor types.
Through a collaboration with Ben Garcia’s lab, I used a PRC2-LOF and isogenic, doxycycline-inducible PRC2-rescue cell line to assess the effects of DNMTi and PRC2-LOF on TE regulation in isolation and in combination in MPNST. TEs are progressively dysregulated with increased DNMTi treatment duration and a sizeable proportion of TEs in this experiment appear to be regulated by PRC2-mediated H3K27me3 or coregulated by H3K27me3 and DNA methylation. PRC2-rescue leads to rapid reconstitution of large, H3K27me3-organized chromatin lysine repressive domains (LOCKs), and TE promoters within these LOCK domains tend to be co-regulated by H3K27me3 and DNA methylation. This finding may inform future strategies to manipulate TE promoter activity using epigenetic therapy and the selection of TE-derived immunotherapy targets for the development of new therapies for MPNST.
The Wang lab has predicted thousands of TS-TEAs from a large pan-cancer cohort, and many of these TS-TEAs are widely shared between patients. Other pioneering studies have shown that TS-TEAs can stimulate potent and partially recurrent immune responses across healthy donors and patients with cancer. Together, these groundbreaking findings suggest TS-TEAs are a new class of shared neoantigens with great potential for the development of off-the-shelf, generalizable immunotherapies. In order to efficiently prioritize high-quality TS-TEAs for further research and immunotherapy development, I am developing a high-throughput functional assay to identify immunogenic TS-TEAs. This effort is also progressing, and I have performed limited library-on-library pilot screens simulating screens of ~1,000 TCRs against ~500 antigens per screen. Ongoing efforts will extend these pilots to understand the sensitivity and specificity of this approach across a range of screen complexities. Future applications will seek to utilize this assay to screen libraries of in vitro expanded TCRs against candidate antigens, and to screen tumor inflitrating lymphocyte TCRs against TS-TEA candidates rapidly identify high-priority immune receptors and antigens for the development of future cancer immunotherapies.

Graduate publications