Epigenetic and metabolic reprogramming of fibroblasts in Crohn's disease strictures reveals histone deacetylases as therapeutic targets

Amy Lewis; David T Humphreys; Belen Pan-Castillo; Giulio Berti; Carla Felice; Hannah Gordon; Radha Gadhok; Anke Nijhuis; Shameer Mehta S; Liliane Eleid; Sidra Iqbal; Alessandro Armuzzi; Annamaria Minicozzi; Eleni Giannoulatou; Joanne ChinAleong; Roger Feakins; Virag Sagi-Kiss; Dora Barisic; Margarita-Ioanna Koufaki; Jacob G Bundy; James O Lindsay; Andrew Silver

doi:10.1093/ecco-jcc/jjad209

Epigenetic and metabolic reprogramming of fibroblasts in Crohn's disease strictures reveals histone deacetylases as therapeutic targets

J Crohns Colitis. 2023 Dec 9:jjad209. doi: 10.1093/ecco-jcc/jjad209. Online ahead of print.

Authors

Amy Lewis¹, David T Humphreys^{2

3}, Belen Pan-Castillo¹, Giulio Berti¹, Carla Felice^{1

4}, Hannah Gordon⁵, Radha Gadhok⁵, Anke Nijhuis¹, Shameer Mehta S¹, Liliane Eleid¹, Sidra Iqbal¹, Alessandro Armuzzi⁶, Annamaria Minicozzi⁷, Eleni Giannoulatou^{2

3}, Joanne ChinAleong⁸, Roger Feakins⁹, Virag Sagi-Kiss¹⁰, Dora Barisic¹⁰, Margarita-Ioanna Koufaki¹⁰, Jacob G Bundy¹⁰, James O Lindsay⁵, Andrew Silver¹

Affiliations

¹ Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine & Dentistry, London E1 2AT UK.
² Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia.
³ St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia.
⁴ Department of Internal Medicine University of Padua, Internal Medicine 1 Unit, Ca' Foncello Hospital, Treviso, Italy.
⁵ Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine & Dentistry, London E1 2AT UK.
⁶ IBD centre, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.
⁷ Department of Colorectal Surgery, Division of Surgery & Perioperative Care, The Royal London Hospital, Whitechapel, London.
⁸ Department of Histopathology, The Royal London Hospital E1 1BB UK.
⁹ Department of Cellular Pathology, Royal Free London NHS Foundation Trust, London NW3 2QG, UK.
¹⁰ Department of Metabolism, Digestion and Reproduction, Imperial College London, Burlington Danes Building, Du Cane Road, London W12 0NN, UK.

PMID: 38069679
DOI: 10.1093/ecco-jcc/jjad209

Abstract

Background & aims: No effective therapeutic intervention exists for intestinal fibrosis in Crohn's disease [CD]. We characterised fibroblast subtypes, epigenetic and metabolic changes, and signalling pathways in CD fibrosis to inform future therapeutic strategies.

Methods: We undertook immunohistochemistry, metabolic, signalling pathway and Epigenetic [Transposase-Accessible Chromatin using sequencing] analyses associated with collagen production in CCD-18Co intestinal fibroblasts and primary fibroblasts isolated from stricturing [SCD] and non-stricturing [NSCD] CD small intestine. SCD/ NSCD fibroblasts were cultured with TGFβ and valproic acid [VPA].

Results: Stricturing CD was characterised by distinct histone deacetylase [HDAC] expression profiles, particularly HDAC1, HDAC2, and HDAC7. As a proxy for HDAC activity, reduced numbers of H3K27ac+ cells were found in SCD compared to NSCD sections. Primary fibroblasts had increased extracellular lactate [increased glycolytic activity] and intracellular hydroxyproline [increased collagen production] in SCD compared to NSCD cultures. The metabolic effect of TGFβ-stimulation was reversed by the HDAC inhibitor VPA. SCD fibroblasts appear "metabolically primed" and responded more strongly to both TGFβ and VPA. Treatment with VPA revealed TGFβ-dependent and independent Collagen-I production in CCD-18Co cells and primary fibroblasts. VPA altered the epigenetic landscape with reduced chromatin accessibility at the COL1A1 and COL1A2 promoters.

Conclusions: Increased HDAC expression profiles, H3K27ac hypoacetylation, a significant glycolytic phenotype, and metabolic priming, characterise SCD-derived as compared to NSCD fibroblasts. Our results reveal a novel epigenetic component to Collagen-I regulation and TGFβ-mediated CD fibrosis. HDAC inhibitor therapy may 'reset' the epigenetic changes associated with fibrosis.

Keywords: Collagen-I; Crohn’s disease; Histone deacetylase; fibrosis; valproic acid.