Bulk RNA sequencing of liver biopsy-derived organoids from patients with alcohol-associated liver disease and paired tissues

RNA sequencing was performed on liver organoids obtained from biopsies (b-Orgs) and paired tissues collected at different stages of alcohol-associated liver disease (ALD) using biliary (BEC) and hepatocyte (HEP) culture conditions. Different "generations" and passages of b-Orgs cultured with HEP medium were also sequenced. Besides, sequencing was also performed on vehicle and b-Orgs treated with Alcohol-associated hepatitis (AH)-medium. Finally, standard cholangiocyte organoids (Chol-Orgs) generated by dissociation of end-stage liver resections from ALD patients were sequenced. b-Orgs generated using BEC (n=6) and HEP (n=30) culture conditions from patients with ALD were compared to standard Chol-Orgs obtained by dissociation of ALD end-stage liver resections (n=3). Transcritomic stability on b-Orgs generated with HEP medium was assessed by comparing consecutive b-Org "generations" (T0, n=3; T0B, n=3; T0C, n=3) and passages (P1, n=3; P3, n=3). Moreover, b-Org resemblance to their parental tissue was investigated by comparing whole liver biopsy tissue from patients at advanced (n=3) and early (n=3) stages to paired b-Orgs generated with HEP medium. Finally, vehicle (n=4) and b-Orgs treated with AH-medium (n=4) were compared to assess how b-Orgs could model ALD progression.