# Reconstructing Liver Fibrosis: 3D Human Models, Microbiome Interfaces, and Therapeutic Innovation

**Authors:** Dileep G. Nair, Divya B. Nair, Ralf Weiskirchen

PMC · DOI: 10.3390/cimb48020165 · 2026-02-01

## TL;DR

This paper reviews 3D human liver models and microbiome interfaces to better understand and treat liver fibrosis, a major global health issue.

## Contribution

The paper provides a comprehensive review of 3D models and microbiome integration for liver fibrosis research and drug development.

## Key findings

- 3D models like organoids and bioprinted constructs better mimic human liver fibrosis than traditional models.
- Multi-organ models incorporating microbiome cues improve predictive screening for anti-fibrotic therapies.
- These models align with new regulatory frameworks for drug development and testing.

## Abstract

Liver fibrosis is a significant consequence of severe liver injury resulting from viral hepatitis, alcohol, and metabolic dysfunction. Progressive fibrosis and ultimate cirrhosis are leading causes of morbidity and mortality worldwide, generally irreversible and poorly targeted by current therapies. Traditional in vitro models and animal models mostly fail to fully recapitulate human multicellular crosstalk, extracellular matrix (ECM) remodeling, and the chronic, immune modulated nature of the disease. Recent advances in three-dimensional (3D) cell culture models including organoids, spheroids, bioprinted constructs, and organ-on-a-chip systems are advantageous for reconstructing cellular diversity and mechanical microenvironments to understand pathophysiology and aid in drug discovery. Emerging multi-organ models are capable of incorporating microbiome derived cues and using multi-omics readouts and imaging-enabled mechanistic dissection for more predictive anti-fibrotic screening. These technologies align well with the recent Modernization 3.0 regulation and New Approach Methodologies by the Food and Drug Administration (FDA) and recent EU Pharmaceutical Reform. This review summarizes the pathophysiology of liver fibrosis, the current landscape of 3D human liver models, and examines how microbiome interfaces modulate fibrogenesis.

## Linked entities

- **Diseases:** cirrhosis (MONDO:0005155), viral hepatitis (MONDO:0006011)

## Full-text entities

- **Genes:** TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, IL10 (interleukin 10) [NCBI Gene 3586] {aka CSIF, GVHDS, IL-10, IL10A, TGIF}, PIEZO1 (piezo type mechanosensitive ion channel component 1 (Er blood group)) [NCBI Gene 9780] {aka DHS, ER, FAM38A, LMPH3, LMPHM6, Mib}, PNPLA3 (patatin like domain 3, 1-acylglycerol-3-phosphate O-acyltransferase) [NCBI Gene 80339] {aka ADPN, C22orf20, iPLA(2)epsilon}, FGB (fibrinogen beta chain) [NCBI Gene 2244] {aka HEL-S-78p}, TNFSF10 (TNF superfamily member 10) [NCBI Gene 8743] {aka APO2L, Apo-2L, CD253, TANCR, TL2, TNLG6A}, CYP4F3 (cytochrome P450 family 4 subfamily F member 3) [NCBI Gene 4051] {aka CPF3, CYP4F, CYPIVF3, LTB4H}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, GCG (glucagon) [NCBI Gene 2641] {aka GLP-1, GLP1, GLP2, GRPP}, GLP1R (glucagon like peptide 1 receptor) [NCBI Gene 2740] {aka GLP-1, GLP-1-R, GLP-1R}, INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, LOXL2 (lysyl oxidase like 2) [NCBI Gene 4017] {aka LOR, LOR2, WS9-14}, ACTA2 (actin alpha 2, smooth muscle) [NCBI Gene 59] {aka ACTSA, SMDYS}, CXADRP1 (CXADR pseudogene 1) [NCBI Gene 653108] {aka CAR, CXADRP}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}, KLRK1 (killer cell lectin like receptor K1) [NCBI Gene 22914] {aka CD314, D12S2489E, KLR, NKG2-D, NKG2D}, FN1 (fibronectin 1) [NCBI Gene 2335] {aka CIG, ED-B, FINC, FN, FNZ, GFND}, TGFB3 (transforming growth factor beta 3) [NCBI Gene 7043] {aka ARVD, ARVD1, LDS5, RNHF, TGF-beta3}, TIMP1 (TIMP metallopeptidase inhibitor 1) [NCBI Gene 7076] {aka CLGI, EPA, EPO, HCI, TIMP, TIMP-1}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, IL17A (interleukin 17A) [NCBI Gene 3605] {aka CTLA-8, CTLA8, IL-17, IL-17A, IL17, ILA17}, THRB (thyroid hormone receptor beta) [NCBI Gene 7068] {aka C-ERBA-2, C-ERBA-BETA, ERBA2, GRTH, NR1A2, PRTH}, TGFB2 (transforming growth factor beta 2) [NCBI Gene 7042] {aka CAEND2, G-TSF, LDS4, TGF-beta2}, COL1A1 (collagen type I alpha 1 chain) [NCBI Gene 1277] {aka CAFYD, EDSARTH1, EDSC, OI1, OI2, OI3}, ALB (albumin) [NCBI Gene 213] {aka FDAHT, HSA, PRO0883, PRO0903, PRO1341}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, FUT1 (fucosyltransferase 1 (H blood group)) [NCBI Gene 2523] {aka H, HH, HSC}, F2 (coagulation factor II, thrombin) [NCBI Gene 2147] {aka PT, RPRGL2, THPH1}, CYP3A4 (cytochrome P450 family 3 subfamily A member 4) [NCBI Gene 1576] {aka CP33, CP34, CYP3A, CYP3A3, CYPIIIA3, CYPIIIA4}, LOXL3 (lysyl oxidase like 3) [NCBI Gene 84695] {aka LOXL, MYP28}, TM6SF2 (transmembrane 6 superfamily member 2) [NCBI Gene 53345], CYP2C9 (cytochrome P450 family 2 subfamily C member 9) [NCBI Gene 1559] {aka CPC9, CYP2C, CYP2C10, CYPIIC9, P450-2C9, P450IIC9}, LOX (lysyl oxidase) [NCBI Gene 4015] {aka AAT10}, IL4 (interleukin 4) [NCBI Gene 3565] {aka BCGF-1, BCGF1, BSF-1, BSF1, IL-4}
- **Diseases:** cholestatic liver diseases (MESH:D008107), Inflammation (MESH:D007249), injury (MESH:D014947), Cirrhosis (MESH:D005355), Liver Fibrosis (MESH:D008103), hepatitis B and C (MESH:D006509), tumor (MESH:D009369), ischemic (MESH:D002545), endothelial dysfunction (MESH:D014652), scarring (MESH:D002921), biliary disease (MESH:D001660), MASH (MESH:D005234), fibrotic lesions (MESH:D009059), chronic injury (MESH:D020208), metabolic dysfunction (MESH:D008659), viral hepatitis (MESH:D014777), end-stage liver disease (MESH:D058625), toxicity (MESH:D064420), weight loss (MESH:D015431), teratoma (MESH:D013724), infections (MESH:D007239), cholestasis (MESH:D002779), hepatic (MESH:D056486), Liver fibrogenesis (MESH:D017093), HE (MESH:D006501), ALD (MESH:D008108), MPS (MESH:D009084), inflammatory cytokines (MESH:D000080424), autoimmune hepatitis (MESH:D019693), PSC (MESH:D015209), sepsis (MESH:D018805), HCC (MESH:D006528), primary biliary cholangitis (MESH:D008105)
- **Chemicals:** oxygen (MESH:D010100), alginate (MESH:D000464), methionine (MESH:D008715), CCl4 (MESH:D002251), choline (MESH:D002794), indoles (MESH:D007211), vitamin A (MESH:D014801), methylcellulose (MESH:D008747), hyaluronic acid (MESH:D006820), PHH (-), bile acid (MESH:D001647), TAA (MESH:D013853), propionate (MESH:D011422), urea (MESH:D014508), lipid (MESH:D008055), LPS (MESH:D008070), palmitic acid (MESH:D019308), Nintedanib (MESH:C530716), SCFA (MESH:D005232), alcohol (MESH:D000438)
- **Species:** hepatitis C virus [taxon 11103], Mus musculus (house mouse, species) [taxon 10090], Hepatitis B virus (no rank) [taxon 10407], Akkermansia muciniphila (species) [taxon 239935], Homo sapiens (human, species) [taxon 9606], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395]
- **Cell lines:** HepG2 — Homo sapiens (Human), Hepatoblastoma, Cancer cell line (CVCL_0027), LSEC — Homo sapiens (Human), Undefined cell line type (CVCL_QY34), HepaRG — Homo sapiens (Human), Hepatitis C infection, Cancer cell line (CVCL_9720)

## Figures

2 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12939559/full.md

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Source: https://tomesphere.com/paper/PMC12939559