Daniel Rios1, Nafeeza Hafeez1, Brian Desrosiers1, Shradha Rao1, Jess Floro1, Joelle Baddour1, Nisha Perez2, Greg Bisacchi2, Oliver Saunders2, Donna Romero1, Menachem Fromer2, Enrique Garcia-Rivera2, Wilson McKerrow2, Julie Behr2, Bryan Thornlow2, Dennis Zaller2, David Proia2 and Wenyan Miao2, 1Rome Therapeutics, Cambridge, MA, 2Rome Tx, Cambridge, MA
Background/Purpose: Transposable elements (TEs) are mobile DNA elements that can replicate and move from one position to another within the host genome. Through co-evolution, TEs in the human genome have developed complex relationships with the host to regulate a variety of cellular functions. TEs are largely silent in healthy adult cells but are reactivated and transcribed in certain disease states, such as cancer, autoimmunity, and neurodegeneration. Class I TEs are retrotransposons that have mobilized throughout the genome via reverse transcription of RNA intermediates. In humans, there are two Class I TEs that encode functional endogenous reverse transcriptase (RTs), LINE-1 and HERV-K. The DNA and RNA products from TE reactivation and reverse transcription are a potential source of nucleic acids that are recognized by pattern recognition receptors, such as cGAS, which trigger sterile proinflammatory responses. To understand the contribution of LINE-1 (L1) in the production of inflammatory products, we assessed the impact of genetic and chemical L1 perturbation in relevant disease models.
Methods: A rational and structure-guided campaign was initiated to identify nucleoside reverse transcriptase inhibitors (NRTI) for the reverse transcriptase function of L1. Compounds with nanomolar potency were screened for activity in blocking both L1 retrotransposition and a Type 1 interferon response in a cellular model of Aicardi-Goutières syndrome and a UV-keratinocyte model. Compounds with favorable pharmacology were profiled in an in vivo model of hypomethylation-induced Type 1 interferon production.
Results: RPT-A was identified as a potent and selective inhibitor of L1 RT. In enzymatic assays, its tri-phosphorylated form has an IC50 of 0.03 µM and 16 µM against L1 RT and HERV-K RT, respectively. RPT- A blocked 100% of LINE1 retrotransposition in a cell-based assay with an IC50 of 0.002 µM. To characterize the impact of RPT-A on Type 1 immune response, decitabine was used to induce L1 in TREX-1 knock out THP-1 cells carrying an IRF3-inducible luciferase reporter. L1 upregulation after decitabine challenge was confirmed and quantified using the L1EM algorithm. RPT-A effectively inhibited this response (IC50 = 0.55 µM). These observations were recapitulated in THP-1 reporter cells challenged with LPS. RPT-A was further interrogated in an in vitro UV challenge model. Immortalized human keratinocytes (HaCaT) were pre-treated with RPT-A for 72 hr and then exposed to sham or 0.1 mJ/cm2 UVB light. RPT-A blocked the UV-mediated Type 1 interferon response as measured by reduction in pTBK1 in whole cell lysate (IC50 = 327nM pTBK1). To translate these findings in vivo, mice were administered vehicle or RPT-A (1, 10, 100 mg/kg, PO) on days 1-5 and decitabine (10 mg/kg, PO) on days 2-5. RPT-A demonstrated a robust, dose-dependent inhibition of Type 1 IFN signaling in the kidney.
Conclusion: We identified a selective inhibitor of the L1 reverse transcriptase that potently inhibited a Type 1 interferon response in multiple in vitro and in vivo models. These results suggest that chemical inhibition of L1 RT may be a new therapeutic modality for Type 1 interferonopathies.
Disclosures: D. Rios, Rome Therapeutics, Pandion Therapeutics, Obsidian Therapeutics, Abata Therapeutics; N. Hafeez, None; B. Desrosiers, None; S. Rao, None; J. Floro, None; J. Baddour, None; N. Perez, None; G. Bisacchi, None; O. Saunders, None; D. Romero, ROME Therapeutics, Vincere Therapeutics, Centaurus Therapeutics; M. Fromer, ROME Therapeutics; E. Garcia-Rivera, None; W. McKerrow, None; J. Behr, None; B. Thornlow, None; D. Zaller, ROME Therapeutics, Ventus, Anokion, Merck/MSD, Bristol-Myers Squibb(BMS); D. Proia, None; W. Miao, None.