Single-cell and bulk transcriptomics of the liver reveals potential targets of NASH with fibrosis

Zhong-Yi Wang,Adrian Keogh,Rachel Cuttat,Christophe Crochemore,Deborah Stroka,Marilisa Neri,Annick Waldt,Florian Nigsch,Judith Knehr,Hui Ge,Alexandra Ruchti,Jing Wu,Iwona Ksiazek,Shanshan Zhu,Guglielmo Roma,Sven Schuierer,Julie Bastien,Stephen B Helliwell,Daniel Sánchez-Taltavull

doi:10.1038/s41598-021-98806-y

Abstract

Fibrosis is characterized by the excessive production of collagen and other extracellular matrix (ECM) components and represents a leading cause of morbidity and mortality worldwide. Previous studies of nonalcoholic steatohepatitis (NASH) with fibrosis were largely restricted to bulk transcriptome profiles. Thus, our understanding of this disease is limited by an incomplete characterization of liver cell types in general and hepatic stellate cells (HSCs) in particular, given that activated HSCs are the major hepatic fibrogenic cell population. To help fill this gap, we profiled 17,810 non-parenchymal cells derived from six healthy human livers. In conjunction with public single-cell data of fibrotic/cirrhotic human livers, these profiles enable the identification of potential intercellular signaling axes (e.g., ITGAV–LAMC1, TNFRSF11B–VWF and NOTCH2–DLL4) and master regulators (e.g., RUNX1 and CREB3L1) responsible for the activation of HSCs during fibrogenesis. Bulk RNA-seq data of NASH patient livers and rodent models for liver fibrosis of diverse etiologies allowed us to evaluate the translatability of candidate therapeutic targets for NASH-related fibrosis. We identified 61 liver fibrosis-associated genes (e.g., AEBP1, PRRX1 and LARP6) that may serve as a repertoire of translatable drug target candidates. Consistent with the above regulon results, gene regulatory network analysis allowed the identification of CREB3L1 as a master regulator of many of the 61 genes. Together, this study highlights potential cell–cell interactions and master regulators that underlie HSC activation and reveals genes that may represent prospective hallmark signatures for liver fibrosis.

Highlights

Fibrosis is characterized by the excessive production of collagen and other extracellular matrix (ECM) components and represents a leading cause of morbidity and mortality worldwide
non-parenchymal cells (NPCs) were represented by a total of 13 distinct cell lineages (Fig. 1b), which correspond to hepatic stellate cells (HSCs; COL1A1+DCN+), liver sinusoidal endothelial cells (LSECs 1: zone 1, SPARCL1+CLEC14A+; LSECs 2: zone 2 and 3, STAB1+FCN2+), vascular ECs (VWF+ACKR1+), cholangiocytes (SOX9+EPCAM+), T cells (CD3D+TRAC+), natural killer (NK) cells (NKG7+GNLY+), B cells (MS4A1+CD79A+), plasma cells (IGLC2+IGHG1+), dendritic cells (IRF8+LILRA4+), monocyte-derived macrophages (MDMs; CD68+MNDA+), Kupffer cells (CD68+MARCO+) and cycling cells (TOP2A+UBE2C+) (Fig. 1c,d)
Activated HSCs represent an attractive target for antifibrotic therapy, the molecular mechanisms underlying the activation of HSCs remain poorly characterized

Summary

Introduction

Fibrosis is characterized by the excessive production of collagen and other extracellular matrix (ECM) components and represents a leading cause of morbidity and mortality worldwide. Our understanding of this disease is limited by an incomplete characterization of liver cell types in general and hepatic stellate cells (HSCs) in particular, given that activated HSCs are the major hepatic fibrogenic cell population. To help fill this gap, we profiled 17,810 non-parenchymal cells derived from six healthy human livers. Multiple factors may have contributed to this failure to clinically translate the overall positive preclinical results[11] Another approach to promote stellate cell apoptosis through a siRNA targeting heat shock protein 47 (HSP47), a collagen 1 chaperone, was tested in phase 1 in patients with moderate to extensive fibrosis (clinicaltrials.gov— NCT02227459). No therapy that accelerates fibrolysis has reached clinical trials

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Conclusion