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Hepatic expression profiling identifies steatosis-independent and steatosis-driven advanced fibrosis genes
Divya Ramnath, Katharine M. Irvine, Samuel W. Lukowski, Leigh U. Horsfall, Zhixuan Loh, Andrew D. Clouston, Preya J. Patel, Kevin J. Fagan, Abishek Iyer, Guy Lampe, Jennifer L. Stow, Kate Schroder, David P. Fairlie, Joseph E. Powell, Elizabeth E. Powell, Matthew J. Sweet
Divya Ramnath, Katharine M. Irvine, Samuel W. Lukowski, Leigh U. Horsfall, Zhixuan Loh, Andrew D. Clouston, Preya J. Patel, Kevin J. Fagan, Abishek Iyer, Guy Lampe, Jennifer L. Stow, Kate Schroder, David P. Fairlie, Joseph E. Powell, Elizabeth E. Powell, Matthew J. Sweet
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Research Article Hepatology Inflammation

Hepatic expression profiling identifies steatosis-independent and steatosis-driven advanced fibrosis genes

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Abstract

Chronic liver disease (CLD) is associated with tissue-destructive fibrosis. Considering that common mechanisms drive fibrosis across etiologies, and that steatosis is an important cofactor for pathology, we performed RNA sequencing on liver biopsies of patients with different fibrosis stages, resulting from infection with hepatitis C virus (HCV) (with or without steatosis) or fatty liver disease. In combination with enhanced liver fibrosis score correlation analysis, we reveal a common set of genes associated with advanced fibrosis, as exemplified by those encoding the transcription factor ETS-homologous factor (EHF) and the extracellular matrix protein versican (VCAN). We identified 17 fibrosis-associated genes as candidate EHF targets and demonstrated that EHF regulates multiple fibrosis-associated genes, including VCAN, in hepatic stellate cells. Serum VCAN levels were also elevated in advanced fibrosis patients. Comparing biopsies from patients with HCV with or without steatosis, we identified a steatosis-enriched gene set associated with advanced fibrosis, validating follistatin-like protein 1 (FSTL1) as an exemplar of this profile. In patients with advanced fibrosis, serum FSTL1 levels were elevated in those with steatosis (versus those without). Liver Fstl1 mRNA levels were also elevated in murine CLD models. We thus reveal a common gene signature for CLD-associated liver fibrosis and potential biomarkers and/or targets for steatosis-associated liver fibrosis.

Authors

Divya Ramnath, Katharine M. Irvine, Samuel W. Lukowski, Leigh U. Horsfall, Zhixuan Loh, Andrew D. Clouston, Preya J. Patel, Kevin J. Fagan, Abishek Iyer, Guy Lampe, Jennifer L. Stow, Kate Schroder, David P. Fairlie, Joseph E. Powell, Elizabeth E. Powell, Matthew J. Sweet

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Figure 7

FSTL1 is elevated in patients with steatosis-associated late-stage fibrosis.

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FSTL1 is elevated in patients with steatosis-associated late-stage fibro...
(A) A scatter plot showing the log2-corrected counts of FSTL1 for all patients from the RNA-sequencing analysis (n = 69 patients; horizontal bars indicate mean ± SEM; circles, early stages; triangles, advanced stages). (B) Correlation analysis showing FSTL1 expression as the independent variable and ELF score as the dependent variable in HCV (blue), HCV with steatosis (red), NAFLD (orange), and alcoholic FLD (brown) patients (n = 69 patients). (C) FSTL1 corrected counts were plotted in early (E) versus advanced (A) stages of fibrosis from patients with HCV alone or HCV and steatosis (n = 55 patients; horizontal bars indicate mean ± SEM; circles, early stages; triangles, advanced stages). (D and E) Circulating levels of FSTL1 in sera from (D) patients with chronic HCV or NAFLD (see Supplemental Table 1 for details of the cohort; n = 35 patients; detectable levels in 29 patients; circles, early stages; triangles, advanced stages) and (E) patients with NAFLD (see Supplemental Table 2 for details of the cohort; n = 25 patients; detectable levels in 18 patients; circles, early stages; triangles, advanced stages) were determined by ELISA (data represented as mean ± SEM). (F and G) mRNA levels of Fstl1 were measured, relative to the housekeeping gene Hprt, in (F) 6- and 12-week-old TAA- or sham-treated mice (n = 5 mice per group) and (G) 1- and 3-week-old CDE- or sham-treated mice (n = 4 mice per group) (data represented as mean ± SEM). For A and C, FWER values were calculated using Bonferroni multiple-testing corrections; for D and G, FDR values were calculated using nonparametric ANOVA (Kruskal-Wallis test) followed by Benjamini-Hochberg multiple-testing corrections; and for E and F, P values were calculated using the Mann-Whitney test. P or FDR ≤ 0.05 was considered statistically significant.

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