Mouse genome-wide association studies and systems genetics uncover the genetic architecture associated with hepatic pharmacokinetic and pharmacodynamic properties of a constrained ethyl antisense oligonucleotide targeting Malat1.

Elaine Pirie,Aldons J Lusis,Edward N Harris,Richard G Lee,Rosanne M Crooke,Calvin Pan,Katrina M Kudrna,Andrew F Powers,Danielle Polikoff,Colton M Miller,Shayoni Ray,Wuxia Fu

doi:10.1371/journal.pgen.1007732

Abstract

Antisense oligonucleotides (ASOs) have demonstrated variation of efficacy in patient populations. This has prompted our investigation into the contribution of genetic architecture to ASO pharmacokinetics (PK) and pharmacodynamics (PD). Genome wide association (GWA) and transcriptomic analysis in a hybrid mouse diversity panel (HMDP) were used to identify and validate novel genes involved in the uptake and efficacy of a single dose of a Malat1 constrained ethyl (cEt) modified ASO. The GWA of the HMDP identified two significant associations on chromosomes 4 and 10 with hepatic Malat1 ASO concentrations. Stabilin 2 (Stab2) and vesicle associated membrane protein 3 (Vamp3) were identified by cis-eQTL analysis. HMDP strains with lower Stab2 expression and Stab2 KO mice displayed significantly lower PK than strains with higher Stab2 expression and the wild type (WT) animals respectively, confirming the role of Stab2 in regulating hepatic Malat1 ASO uptake. GWA examining ASO efficacy uncovered three loci associated with Malat1 potency: Small Subunit Processome Component (Utp11l) on chromosome 4, Rho associated coiled-coil containing protein kinase 2 (Rock2) and Aci-reductone dioxygenase (Adi1) on chromosome 12. Our results demonstrate the utility of mouse GWAS using the HMDP in detecting genes capable of impacting the uptake of ASOs, and identifies genes critical for the activity of ASOs in vivo.

Highlights

Antisense oligonucleotides (ASOs) are highly selective and potent therapeutic agents which has proven effective in treating a variety of disease states including cancer, viral infection and cardio-metabolic, inflammatory and neurological diseases [1,2,3,4,5,6,7]
We utilized an advanced genetic methodology in mice to identify genes involved with the heterogeneity in both accumulation and potency of an ASO targeting metastasis associated lung adenocarcinoma transcript 1 (Malat1) in liver
Detailed analysis of ASO functionality in livers from 100 genetically distinct strains of inbred mice treated with either Malat1 or control ASO led to the selection of specific genetic regions associated with variation in ASO uptake and potency

Summary

Introduction

Antisense oligonucleotides (ASOs) are highly selective and potent therapeutic agents which has proven effective in treating a variety of disease states including cancer, viral infection and cardio-metabolic, inflammatory and neurological diseases [1,2,3,4,5,6,7]. The most widely exploited mechanism of ASO functionality is the degradation of complementary mRNA utilizing ribonuclease H1 (RNase H1), thereby preventing the translation of the associated protein(s) [8] The evolution of this technology over the past 30 years has led to the development of a variety of ASO modifications resulting in greater stability, potency, affinity, and reduced toxicity [9, 10]. While these therapeutic agents have proven to be effective against disease in the clinic, significant variability in ASO response has been reported in several of the drugs [11, 12]. No in vivo systematic interrogation of the role of genetic architecture on ASO accumulation and potency has been performed

Results

Discussion

Conclusion