Transposable Element Regulation and Expression During Cancer Progression

George Washington University, Washington DC

Investigators

Abstract

Project Summary The expression of noncoding, repetitive regions of the genome termed Transposable Elements (TEs) have shown strong preclinical potential as immunogenic agents that sensitize tumor cells to immune-modulating therapies. Hypomethylation of the genome, dysregulated heterochromatin silencing, and mutations in regulatory transcription factors results in elevated TE expression. Transcription of retrotransposons, a class of TEs that rely on an RNA intermediate, result in type-I interferon (IFN) signaling and improve immune cell recruitment and cytotoxic removal of tumor cells in cancer models including ovarian, colorectal, breast, and melanoma. However, it remains unclear how durable interferon responses induced by TEs can be harnessed therapeutically. Therefore, characterization of TE regulation and downstream activation of the type-I IFN response is critical to improving the immunogenic potential of tumor cells. In the F99 phase of this proposal, I will investigate how mutations in p53, a known regulator of TEs, derepresses retrotransposon transcription in ovarian cancer. Specifically, I will determine how wildtype and R175H p53 differentially bind and recruit cofactors at TE loci. I will examine the viral signaling cascade activated by TE RNA, known as MAVS/MDA-5, in both wildtype and R175H p53 settings to assess blunted signaling activation in response to high TE transcription. Overall, this work will determine how mutations in p53 alter its chromatin binding to derepress retrotransposons and identify how the ovarian tumor cells circumvent downstream IFN activation. In the K00 phase of this proposal, I will utilize my experience studying TEs to profile how disruptions in nuclear architecture during tumor cell migration contribute to TE expression and type-I IFN signaling. I will compare publicly available matched primary and metastatic RNA-sequencing data to assess TE derepression and type I IFN signaling across metastatic events. I will validate the re-expression of TEs across metastasis using both in vitro microfluidic micron-sized constrictions and in vivo mouse metastatic models. These models will determine the impact of tumor cell migration on TE expression, implicate the disruption of nuclear lamina architecture to TE derepression, and profile the activation of type I IFN. The proposed research will inform the mechanisms of TE regulation and the downstream IFN response during tumor evolution, and this will identify critical targets that mediate TE sensing needed to promote the immunogenic potential of TEs as therapeutic targets in immunologically “cold” tumor types. These mechanisms will inform how TE re-expression can further sensitize tumors to immune-modulating therapies to improve cancer patient outcomes.