Titles and legends to Supplemental Figures

Suppl. Figure 1. Liver cell production of Indian Hh ligands (Ihh) increases during chronic viral hepatitis. A) Liver section from a representative control liver without viral hepatitis (NRL). Final magnification ´200. B) qRT-PCR analysis of RNA isolated from normal liver, and HBV- or HCV-infected livers with F0/1, F2, or F3/4 fibrosis (n = 3/group). Results were normalized to Ihh expression in normal control livers; mean ± SEM data are displayed. **P < 0.001 vs. controls. C) Immunohistochemical staining for Ihh in representative sections from patients with HBV (top) and HCV (bottom). Left panels display findings in livers with F0 fibrosis; right panels display findings in livers with F3-4 fibrosis. Final magnification ´200.

Suppl. Figure 2. Liver cell production of Sonic Hh ligands (Shh) increases with fibrosis stage. A) Liver section from a second representative control liver without viral hepatitis (NRL). Final magnification ´200. B) Representative immunostaining without anti-Shh antibody (negative control). Final magnification ´200. C) %Shh(+) cells in HBV-infected livers with F0, F1, F2, or F3/4 fibrosis (n = 3/group), and D) %Shh(+) cells in HCV-infected livers with F0, F1, F2, or F3/4 fibrosis (n = 3/group). Results were normalized to Shh expression in normal control livers; means ± SEM are displayed. *P < 0.05 vs. controls

Suppl Figure 3. Hedgehog ligand expression in chronic viral hepatitis. A-B) Representative high-powered magnification (400x) of Shh staining in hepatocytes from HBV (A) and HCV (B) stage 3-4 fibrosis. C-D) Shh staining in ductular cells, sinusoidal endothelial cells and small epithelial cells in HBV (C) and HCV (D) stage 3-4 fibrosis. E-F) Ihh staining in stromal cells in HBV (E) and HCV (F) fibrotic septa.

Suppl Figure 4. Liver cells that express the Hh-target gene, Ptc, accumulate during chronic viral hepatitis A) Liver section from a representative control liver without viral hepatitis (NRL). Final magnification ´200. B) qRT-PCR analysis of RNA isolated from normal liver, and HBV- or HCV-infected livers with F0/1, F2, or F3/4 fibrosis (n = 3/group). Results were normalized to Ptc expression in normal control livers; means ± SEM data are displayed. **P < 0.005 vs. controls. C-D) Immunohistochemical staining for Ptc in representative sections from patients with HBV (C) and HCV (D). Left panels display findings in livers with F0 fibrosis; middle panels display findings in livers with F3-4 fibrosis and right panels display quantification of the immunostaining by morphometric analysis. Final magnification ´200.

Suppl Figure 5. Liver fibrosis and hepatic accumulation of myofibroblasts in chronic viral hepatitis B and C. A) Sirus red staining in HBV (top) and HCV (bottom). B) αSMA staining in HBV (top) and HCV (bottom). C) S100A4 staining, a marker for epithelial derived fibroblastic cells, in HBV (top) and HCV (bottom). Final Magnification x100. Small inserts in each large photomicrographs demonstrate staining in respective non-fibrotic livers. D) qRT-PCR analysis of S100A4 mRNA isolated from normal liver, and HBV- or HCV-infected livers with F0/1, F2, or F3/4 fibrosis (n = 3/group). Results were normalized to S100A4 expression in normal control livers; mean ± SEM data are displayed. **P < 0.005 vs. controls.

Suppl Figure 6. Expression of Hh target genes and a marker of activated sinusoidal endothelial cells (SEC) in fibrotic septae in livers with advanced hepatitis C fibrosis. A) Patched (400x); B) Gli2 (400x); C) CD31 (x400).

Suppl Figure 7. Peri-tumoral tissue adjacent to HCC is enriched with Hh-responsive stromal cells and ductular cells that express tumor stem/initiating cells. A) Representative H&E staining. Ductular proliferation (black arrows) adjacent to tumor infiltrate (white arrow) (100x). Insert shows a

high-powered view of the tumor. Final magnification x400. B) Patched staining in peri-tumoral tissue of a patient with HCV cirrhosis and HCC. C) KRT7 (+) (blue) ductular progenitor cells express Gli2 (brown), a Hh-target gene. Insert displays a high-powered view of KRT7 (blue) /Gli2 (brown) double (+) cells. D) Survivin staining in the same peri-tumoral tissue and adjacent HCC of a patient with HCV cirrhosis and HCC. Final magnification x600.