Re-Programming the Tumor Microenvironment Via Self-Amplified RNA (Safer) Circuits

Data from patients in diverse cancer types show that increased immune cell infiltration of tumors correlates with improved patient prognosis. It is also clear that a host of immunosuppressive signals are produced by tumors in order to block immune attack, and thus the endogenous immune response is in most cases unable to eliminate established tumors. Recently, efforts to alter the suppressive signaling in tumors through "checkpoint blockade" drugs that block individual suppressive signaling receptors on T-cells have shown promising clinical results, demonstrating tumor regression through shifting of the tumor microenvironment toward a pro-immunity state. However, it is likely that blocking individual signaling pathways will be insufficient for cancer immunotherapy to reach its full potential, because tumors create a complex network of suppressive signals.

Here we propose an approach based on integration of synthetic biology and systems biology to reprogram the suppressive microenvironment in tumors through delivery of sophisticated multi-step genetic circuits to cells in the tumor microenvironment. This strategy will be enabled by the development of self-replicating RNA-based circuits that can (i) identify cell types specifically in the tumor through miRNA expression profiles, (ii) utilize small molecule-regulated induction of new gene expression programs that act in trans on surrounding cells in the tumor, and (iii) alter the function of identified cells in a coordinated fashion to tip the balance within the tumor from immune suppression to immune-mediated tumor destruction.

Specific aims are: (1) We will design a platform for in vivo RNA-based synthetic biology comprising RNA-binding regulatory proteins and small molecule induced protein degradation domains; (2) We will profile the miRNA signatures of 4T1 breast cancer cells and B16F10 melanoma cancer cells and create RNA-encoded multi-input classifier circuits that permit replicon expression only in target cell types, and (3) We will build a series f increasingly sophisticated programmed cancer therapies where cytokine secretion and necroptotic gene expression is restricted to tumor cells and can be precisely regulated by FDA approved small molecules, along with safety switch mechanisms to eliminate replicon-encoded circuits in healthy cells. We will deliver our therapeutic circuits into mouse tumors in vivo and monitor anticancer immune responses, using systems biology principles to analyze the resulting response of multi-cell networks in the tumor.

A key goal of these studies will be to design RNA circuits which drive transfected tumor/immune cells to act in trans on surrounding cells in the microenvironment, to achieve a tumor-wide change in the tumor milieu without the need for successful circuit delivery to every cell in the tumor. Results from this project will provide a ne RNA-based toolkit for engineering mammalian cell function, demonstrate the utility of these approaches in vivo, and provide a framework for reprogramming tumors that overcomes limitations of traditional chemotherapy and targeted drug treatments.