SomaLogic proteomics reveals new biomarkers and provides mechanistic, clinical insights into Acetyl coA Carboxylase (ACC) inhibition in Non-alcoholic Steatohepatitis (NASH)

Abstract

Non-alcoholic Fatty Liver Disease (NAFLD) and Non-alcoholic Steatohepatitis (NASH) are major metabolic diseases with increasing global prevalence and no approved therapies. There is a mounting need to develop biomarkers of diagnosis, prognosis and treatment response that can effectively replace current requirements for liver biopsies, which are invasive, error-prone and expensive. We performed SomaLogic serum proteome profiling with baseline (n = 231) and on-treatment (n = 72, Weeks 12 and 16, Placebo and 25 mg PF-05221304) samples from a Phase 2a trial (NCT03248882) with Clesacostat (PF-05221304), an acetyl coA carboxylase inhibitor (ACCi) in patients with NAFLD/NASH. SomaSignal NASH probability scores and expression data for 7000+ analytes were analyzed to identify potential biomarkers associated with baseline clinical measures of NAFLD/NASH [Magnetic Resonance Imaging-Proton Density Fat Fraction (MRI-PDFF), alanine aminotransferase (ALT) and aspartate aminotransferase (AST)] as well as biomarkers of treatment response to ACCi. SomaSignal NASH probability scores identified biopsy-proven/clinically defined NIT-based (Presumed) NASH classification of the cohort with > 70% agreement. Clesacostat-induced reduction in steatosis probability scores aligned with observed clinical reduction in hepatic steatosis based on MRI-PDFF. We identify a set of 69 analytes that robustly correlate with clinical measures of hepatic inflammation and steatosis (MRI-PDFF, ALT and AST), 27 of which were significantly reversed with ACC inhibition. Clesacostat treatment dramatically upregulated Wnt5a protein and Apolipoproteins C3 and E, with drug-induced changes significantly correlating to changes on MRI-PDFF. Our data demonstrate the utility of SomaLogic- analyte panel for diagnosis and treatment response in NAFLD/NASH and provide potential new mechanistic insights into liver steatosis reduction, inflammation and serum triglyceride elevation with ACC inhibition. (Clinical Trial Identifier: NCT03248882).

Keywords: Acetyl CoA Carboxylase; Biomarkers; Liver fibrosis; NAFLD/NASH; SomaLogic proteomics.

Figure 1

Description of cohort used for SomaScan biomarker assay.

Figure 2

Contingency table of alignment between SomaSignal-derived versus clinically defined NASH and NAFLD classification in entire analyses cohort (a), patients with SomaSignal fibrosis score ≤ 0.5 (b) and ≥ 0.5 (c). Supplemental Table 1 contains details on algorithm for SomaSignal NASH classification, and clinical NASH classification of study cohort is described in Calle et al..

Figure 3

Comparison of clinical end point of liver fat reduction, (a) % change from baseline in MRI-PDFF; (b) SomaSignal panel derived end point of liver fat reduction, % change from baseline in steatosis probability score (n = 72, Wilcoxon signed-rank test).

Figure 4

Identification of SomaScan analytes (serum proteins) significantly correlated to baseline clinical measures. (a) Venn diagram showing common analytes correlated to liver fat assessed using MRI-PDFF, ALT and AST; (b) KEGG pathway analyses of common analytes from (a); (c) Venn diagram comparing baseline correlated analytes with those changing with clesacostat treatment; (d) KEGG pathway analyses of analytes correlated at baseline as well as changing with clesacostat treatment. (Spearman's correlation with adjusted p-value cutoff of < 0.05 for baseline correlation and unadjusted p-value cutoff of < 0.05 for treatment response).

Figure 5

Volcano plot of placebo adjusted changes in SomaScan analytes with Clesacostat treatment.

Figure 6

Change in expression from baseline for key analytes (serum proteins) significantly impacted by clesacostat compared to placebo (adjusted p value < 0.05).

Figure 7

Correlation of change from baseline in Wnt5a, ApoC3, ApoE to change from baseline in liver fat assessed using MRI-PDFF.

Figure 8

Hallmark pathway analyses of analytes significantly modulated with Clesacostat compared to placebo (placebo-adjusted changes are used for analyses).

Figure 9

Proposed mechanism by which ACC inhibition modulates steatosis, TG homeostasis and inflammation. ACC Inhibition is well known to reduce steatosis primarily through inhibition of “de novo lipogenesis". This is also known to be accompanied by elevated SREBP-1c that increases ApoC3 and elevates serum TG. It is possible that compartmental activation of LRP1 could drive the Wnt5a increase and impact lipid homeostasis in liver, while possibly modulating inflammatory endpoints through its activity in macrophages. Increased SREBP-1c activity may also potentiate the modulation of macrophage maturation and expression of CHI3L1. impacting some aspects of systemic inflammation. APOE increase may also potentially contribute to liver steatosis reduction.