
Materials and Methods
Approval and Case Selection
Histologic Analysis
Immunolabeling
- Lennerz J.K.
- Kim S.H.
- Oates E.L.
- Huh W.J.
- Doherty J.M.
- Tian X.
- Bredemeyer A.J.
- Goldenring J.R.
- Lauwers G.Y.
- Shin Y.K.
- Mills J.C.
- Lennerz J.K.
- Kim S.H.
- Oates E.L.
- Huh W.J.
- Doherty J.M.
- Tian X.
- Bredemeyer A.J.
- Goldenring J.R.
- Lauwers G.Y.
- Shin Y.K.
- Mills J.C.
- Lennerz J.K.
- Ruhle V.
- Ceppa E.P.
- Neuhuber W.L.
- Bunnett N.W.
- Grady E.F.
- Messlinger K.
Name | Host | Antigen characteristics | Source catalog or order no. | Dilution | Pattern | Reference |
---|---|---|---|---|---|---|
Activated caspase 3 | Rabbit (p) | Synthetic peptide corresponding to Ser29+ of human caspase 3 (N terminus of p17 subunit) | Abcam, Inc. ab-32042 | 1:50 | C | |
E-cadherin (ECAD/CDH1) | Mouse (m) | Human transmembrane protein 36 | Ventana Medical Systems, Inc. 790-4497 | Prediluted by manufacturer | M/C | 85 |
K7 (CK7/K2C7) | Mouse (m) | Clone OV-TL 12/30 | Cell Marque, Corp. CMA538 | Prediluted by manufacturer | C | 13 |
K19 (CK19/K1CS) | Mouse (m) | Clone RCK108 (Immunogen: Human Cell line T24) | Dako Corp. M0888 | 1:100 | C | |
K19 (CK19/K1CS) | Mouse (m) | Clone A53-B/A2.26 | Ventana Medical Systems, Inc. 760-4281 | Prediluted by manufacturer | C | |
pSMAD3 (Figure 5, A and B) | Rabbit (p) | Synthetic phosphopeptide corresponding to residues surrounding Ser 423/425 of SMAD3 | Cell Signaling Technology, Inc. 9520S | 1:100 | N | |
pSMAD2/3 (Figure 5, C–H) | Goat (p) | Short amino acid sequence containing phosphorylated Ser423/425 of human SMAD3 | Santa Cruz Biotechnology, Inc. sc11769 (peptide sc-11769P) | 1:50 | N | 4 |
S100 (Figure S4B) | Rabbit (p) | Purified, full-length, native bovine S100 protein | Ventana Medical Systems, Inc. 760-2523 | Prediluted by manufacturer | C | 88 |
SMAD3 (Figure 5, D, E, G, H) | Rabbit (p) | Synthetic peptide corresponding to AA100-150 of human SMAD3 | Thermo Fisher Scientific, Inc. PA1-38613 | 1:100 | C | 89
A SNAIL1-SMAD3/4 transcriptional repressor complex promotes TGF-beta mediated epithelial-mesenchymal transition. Nat Cell Biol. 2009; 11: 943-950 |
SMAD3 (Figure S6A) | Rabbit (p) | Synthetic peptide corresponding to residues at the AA terminus of human SMAD3 | Cell Signaling Technology, Inc. 9523S | 1:100 | C | 90 |
SMAD4 (Figure S6B) | Rabbit (p) | Recombinant protein epitope signature tag (PrEST) corresponding to AA118-240 of human SMAD4 | Sigma-Aldrich Corp. HPA019154 | 1:150 | C | |
SMAD4 | Rabbit (p) | Synthetic peptide corresponding to residues surrounding Pro278 of human SMAD4 | Cell Signaling Technology, Inc. 9515 | 1:100 | C | |
pSMAD2 (Figure S6C) | Rabbit (p) | Synthetic phosphopeptide corresponding to residues surrounding Ser 465/467 of human SMAD2 | Cell Signaling Technology, Inc. 3101S | 1:100 | N | 95 |
pSMAD2 (Figure S6D) | Rabbit (p) | Synthetic phosphopeptide corresponding to residues surrounding Ser 245/250/255 of human SMAD2 | Cell Signaling Technology, Inc. 3104S | 1:100 | N | 96 |
SNAIL (SNAI1/SLUGH2) | Rabbit (p) | Synthetic KLH-conjugated peptide AA1-100 of human Snail | Abcam, Inc. ab-17732 (peptide ab19126) |
| N | 97 |
TGFβ1R (ALK-5) | Rabbit (p) | Synthetic peptide corresponding to AA158-179 of human TGFb1R | Abcam, Inc. ab-31013 | 1:50 | M/C | 98 |
FSP-1 (S100-A4) | Rabbit (p) | Recombinant protein encoding full-length human FSP-1/S100-A4 | Abcam, Inc. ab-27427 | Prediluted by manufacturer | C/N | |
Vimentin | Mouse (m) | Clone V9 | Ventana Medical Systems, Inc. 790-2917 | Prediluted by manufacturer | C | 99 |
Controls
- Berglund L.
- Bjorling E.
- Oksvold P.
- Fagerberg L.
- Asplund A.
- Szigyarto C.A.
- Persson A.
- Ottosson J.
- Wernerus H.
- Nilsson P.
- Lundberg E.
- Sivertsson A.
- Navani S.
- Wester K.
- Kampf C.
- Hober S.
- Ponten F.
- Uhlen M.
TUNEL Staining
Microscopy
- Lennerz J.K.
- Kim S.H.
- Oates E.L.
- Huh W.J.
- Doherty J.M.
- Tian X.
- Bredemeyer A.J.
- Goldenring J.R.
- Lauwers G.Y.
- Shin Y.K.
- Mills J.C.
- Lennerz J.K.
- Kim S.H.
- Oates E.L.
- Huh W.J.
- Doherty J.M.
- Tian X.
- Bredemeyer A.J.
- Goldenring J.R.
- Lauwers G.Y.
- Shin Y.K.
- Mills J.C.
Density Modeling
Statistical Analysis
Results
- Lennerz J.K.
- Ruhle V.
- Ceppa E.P.
- Neuhuber W.L.
- Bunnett N.W.
- Grady E.F.
- Messlinger K.

Perinodular Structure of K19 Patterns Are Complex, Attenuated, and Absent
Perinodular K19 Pattern as a Valid Surrogate for Intranodular Disease
Variable | Hepatocellular Nodules | |
---|---|---|
Without atypical features (n = 170) | With atypical features (n = 176) | |
True positive | 47 | 47 |
False positive | 15 | 20 |
True negative | 101 | 102 |
False negative | 7 | 7 |
Sensitivity (95% CI) | 87.04 (75.1–94.6) | 87.04 (75.1–94.6) |
Specificity (95% CI) | 87.07 (79.6–92.6) | 83.61 (75.8–89.7) |
Positive predictive value (95% CI) | 75.80 (63.3–85.8) | 70.15 (57.7–80.7) |
Negative predictive value | 93.5 (87.1–97.4) | 93.6 (87.2–97.4) |
Accuracy | 87.06 | 84.7 |
Likelihood ratio | 6.731 | 5.309 |
Pretest odds positive | 0.47 | 0.44 |
Posttest odds positive | 3.13 | 2.35 |
Quantification of Perinodular K19 Pattern
Variable | CN (N = 71) | DN (N = 45) | HCC (N = 54) | ||||||
---|---|---|---|---|---|---|---|---|---|
DR H&E | +++ | + | – | ||||||
Pattern | Complex | Attenuated | Absent | ||||||
K19 | n+ | PCD | % | n+ | PDH | %CN | n+ | PCH | %CN |
Profiles (sectors) | 408.9 ± 23 (36) | 1.5e−14 | Set 100 | 106.3 ± 14 (27) | 4.1e−10 | 26 | 1.52 ± 0.2 (30) | 1.7e−23 | 0.4 |
Cells (sectors) | 2088 ± 262 (27) | 2.9e−9 | Set 100 | 300 ± 44 (30) | 1.3e−5 | 14 | 2.4 ± 0.3 (27) | 1.4e−7 | 0.1 |
Density, cells/mm2 (sectors) | 16925 ± 2191 (27) | 1.6e−9 | Set 100 | 1610 ± 429 (30) | 5.8e−4 | 5.8 | 9.6 ± 3.3 (27) | 6.8e−10 | 0.02 |
Marker (HPF) | Σ+/Σt | x+/xt | %t | Σ+/Σ | x+/xt | %t | % | ||
FSP-1 | 140 | 5.19 ± 0.4 | 10 | 106 | 3.9 ± 0.3 | 65 | NA | ||
(27) | 1344 | 49.8 ± 4.3 | 175 | 6 ± 0.6 | |||||
ECADH | 2777 | 51.4 ± 4 | 80 | 377 | 7 ± 0.6 | 77 | NA | ||
(54) | 3412 | 63.2 ± 5 | 487 | 9 ± 0.7 | |||||
SNAIL | 696 | 25.8 ± 2.3 | 34 | 161 | 5.96 ± 0.6 | 52 | NA | ||
(27) | 2068 | 76.6 ± 7.7 | 312 | 11.6 ± 1.2 | |||||
TGFßR1 | 1095 | 40.6 ± 3.6 | 48 | 39 | 1.4 ± 0.2 | 15 | NA | ||
(27) | 2293 | 84.9 ± 7.6 | 248 | 9.2 ± 0.8 | |||||
SMAD3 | 1573 | 58.3 ± 5 | 68 | 184 | 6.8 ± 0.5 | 74 | NA | ||
(27) | 2293 | 84.9 ± 7.6 | 248 | 9.2 ± 0.8 | |||||
pSMAD2/3 | 619 | 22.9 ± 2 | 27 | 148 | 5.5 ± 0.5 | 60 | NA | ||
(27) | 2293 | 84.9 ± 7.6 | 248 | 9.2 ± 0.8 |
Necrosis and Apoptosis Are Not the Principal Morphologic Mechanisms for Perinodular K19 Loss

Cytomorphology and Immunolabeling in the Perinodular Compartment Are Indicative of Substantial Variability in Cellular Phenotypes
- Roskams T.A.
- Theise N.D.
- Balabaud C.
- Bhagat G.
- Bhathal P.S.
- Bioulac-Sage P.
- Brunt E.M.
- Crawford J.M.
- Crosby H.A.
- Desmet V.
- Finegold M.J.
- Geller S.A.
- Gouw A.S.
- Hytiroglou P.
- Knisely A.S.
- Kojiro M.
- Lefkowitch J.H.
- Nakanuma Y.
- Olynyk J.K.
- Park Y.N.
- Portmann B.
- Saxena R.
- Scheuer P.J.
- Strain A.J.
- Thung S.N.
- Wanless I.R.
- West A.B.

Perinodular Epithelial Alterations Are Associated with Quantitative Differences in TGF-β Signaling Components

Discussion
- Omenetti A.
- Porrello A.
- Jung Y.
- Yang L.
- Popov Y.
- Choi S.S.
- Witek R.P.
- Alpini G.
- Venter J.
- Vandongen H.M.
- Syn W.K.
- Baroni G.S.
- Benedetti A.
- Schuppan D.
- Diehl A.M.
- Choi S.S.
- Omenetti A.
- Witek R.P.
- Moylan C.A.
- Syn W.K.
- Jung Y.
- Yang L.
- Sudan D.L.
- Sicklick J.K.
- Michelotti G.A.
- Rojkind M.
- Diehl A.M.
- Stopa M.
- Anhuf D.
- Terstegen L.
- Gatsios P.
- Gressner A.M.
- Dooley S.
- Omenetti A.
- Porrello A.
- Jung Y.
- Yang L.
- Popov Y.
- Choi S.S.
- Witek R.P.
- Alpini G.
- Venter J.
- Vandongen H.M.
- Syn W.K.
- Baroni G.S.
- Benedetti A.
- Schuppan D.
- Diehl A.M.
- Choi S.S.
- Omenetti A.
- Witek R.P.
- Moylan C.A.
- Syn W.K.
- Jung Y.
- Yang L.
- Sudan D.L.
- Sicklick J.K.
- Michelotti G.A.
- Rojkind M.
- Diehl A.M.
- Omenetti A.
- Porrello A.
- Jung Y.
- Yang L.
- Popov Y.
- Choi S.S.
- Witek R.P.
- Alpini G.
- Venter J.
- Vandongen H.M.
- Syn W.K.
- Baroni G.S.
- Benedetti A.
- Schuppan D.
- Diehl A.M.
- Di Tommaso L.
- Destro A.
- Seok J.Y.
- Balladore E.
- Terracciano L.
- Sangiovanni A.
- Iavarone M.
- Colombo M.
- Jang J.J.
- Yu E.
- Jin S.Y.
- Morenghi E.
- Park Y.N.
- Roncalli M.
- Roskams T.A.
- Theise N.D.
- Balabaud C.
- Bhagat G.
- Bhathal P.S.
- Bioulac-Sage P.
- Brunt E.M.
- Crawford J.M.
- Crosby H.A.
- Desmet V.
- Finegold M.J.
- Geller S.A.
- Gouw A.S.
- Hytiroglou P.
- Knisely A.S.
- Kojiro M.
- Lefkowitch J.H.
- Nakanuma Y.
- Olynyk J.K.
- Park Y.N.
- Portmann B.
- Saxena R.
- Scheuer P.J.
- Strain A.J.
- Thung S.N.
- Wanless I.R.
- West A.B.
- Di Tommaso L.
- Destro A.
- Seok J.Y.
- Balladore E.
- Terracciano L.
- Sangiovanni A.
- Iavarone M.
- Colombo M.
- Jang J.J.
- Yu E.
- Jin S.Y.
- Morenghi E.
- Park Y.N.
- Roncalli M.
Acknowledgments
Supplementary data
- Supplemental Figure S1
Schematic figure illustrating the epithelial-stromal compartment in cirrhosis. A: Representative image of the complex pattern of perinodular reaction (K19 immunohistochemistry; inset, B). B: Higher magnification of the inset in A demonstrates the complex pattern of K19-positive biliary epithelium at the hepatic interface zone extending between hepatic chords (cf. Figure 1A). C: Overlay of selected outlines and original image (background). D: Outlines of a representative region including the interface between hepatocytes and the perinodular compartment. Scheme was generated by extraction and color coding to illustrate key components and epithelial stromal nature of the nonhepatocellular compartment (cf. Figure 1B).
- Supplemental Figure S2
K19 review and assessment of perinodular sectors. A: Overview of an H&E-stained whole mount generated using virtual microscopy (Materials and Methods). A representative dominant nodule is highlighted (orange), illustrating mapping of selected nodules (cf. Figure 2). B: A subsequent section was K19-stained to assess the perionodular pattern around the mapped nodule (orange). C: For correlation, H&E- and K19-stained sections were synchronized. Slide synchronization enables simultaneous review of the same field of view of multiple slides (including x and y orientation and magnification), symbolized here via a horizontal split (dotted line). One perinodular sector is shown (yellow) covering approximately 25% of the nodular circumference, starting at a random point (here, 225 degrees) with an inner margin (hepatocellular nodule interface) and an outer margin (half of the septal thickness). D: Intersection of three hepatocellular nodules including the projected outer limits of the perinodular sectors (dotted lines) illustrates that depending on the perimeter and intersection of the sectors, some of the internodular ductules were not included in the sector-based quantification; K19 and FSP-1 double-labeling. Scale bars: 5 mm (A–C); 200 μm (D).
- Supplemental Figure S3
Screening for cellular phenotypes using K19 and vimentin (VIM) immunohistochemistry in perinodular sectors around cirrhotic nodules (CN) and dysplastic nodules (DN). A: Perinodular sectors around CN demonstrated elongated fibroblast-like cells (arrow) that stained with the epithelial marker K19 (image from Figure 3C, provided for direct comparison with B). B: The attenuated DR around DN demonstrated several weakly K19-positive cells with an elongated fibroblast-like shape, typically located adjacent to or in contact with small clusters of strongly K19-positive ductules (arrow). C: Vimentin-positive epithelioid cells (arrow) within the confines of the basement membrane (outline) were observed rarely in the perinodular sectors around CN. D: Perinodular sectors around DN also demonstrated epithelioid cells within the confines of the basement membrane (outline) that exhibited strong immunoreactivity with the mesenchymal marker vimentin (arrow) (image from Figure 3H, provided for direct comparison with C). These findings, namely fibroblast-like cells with an epithelial immunophenotype (A and B) and epithelioid cells with a mesenchymal phenotype (C and D) are compatible with cellular identity alterations (Materials and Methods) and triggered further examinations. Scale bars: 20 μm (A and B); 10 μm (C and D).
- Supplemental Figure S4
Comparison of FSP-1 and S100 distribution in co-localization with K19 staining in cirrhotic liver. A: Triple labeling of FSP-1 (red), K19 (green), and Hoechst (nuclei, blue). Note the punctate cellular FSP-1 staining pattern. B: Triple labeling of S100 (red), K19 (green), and Hoechst (nuclei, blue) on directly subsequent section. Note the stringlike S100 staining pattern. C: Merge of A and B was achieved by modification of B (shown in D). Specifically, colors in B were switched, resulting in S100 in green and K19 in red. Thereby, the merge in C demonstrates significant overlap of the subsequent sections of the ductular reaction, resulting in the merged color yellow. E: Subtraction of the nuclei (blue) and the merged elements (yellow) demonstrates that there is almost no overlap between FSP-1 (red) and S100 (green) elements. F: Addition of the merged K19 elements (now pseudo-colored in blue) demonstrates triple staining, enabling assessment of the distinct distributions of immunolabeling with rabbit anti–FSP-1 (red) and rabbit anti-S100 (green). Scale bars = 100 μm.
- Supplemental Figure S5
A–C: Single channels of Figure 4H (arrow indicates FSP-1–positive ECADH-negative cell). D–F: Single channels of Figure 4I (arrow indicates SNAIL-positive ECADH-negative cell). G–I. Additional examples of immunophenotypic variability using SNAIL (red) and ECADH (green) in perinodular sectors around cirrhotic nodules (CN) and dysplastic nodules (DN). G: The brisk ductular reaction (DR) around CN demonstrated epithelial (ECADH, green) nuclei (blue) with SNAIL immunoreactivity (red), resulting in the merged color magenta (arrows). SNAIL-negative epithelial cells were also readily identified (arrowheads). In addition, several cells were observed with epithelioid nuclei, faint ECADH-staining, but nuclear SNAIL immunoreactivity, located as elongated fibroblast-like cells adjacent to or within ductules (open arrows). H: The DR around DN was attenuated; however, the few remaining ductules frequently demonstrated epithelial cells (ECADH, green) with SNAIL immunoreactivity (red) in the nucleus (blue), resulting in the merged color magenta (arrows). Note that despite the reduced overall number of SNAIL-immunopositive nuclei, the fraction of SNAIL-immunonegative epithelial cells (arrowheads) is smaller around DN when compared with CN, resulting in a significantly increased percentage of SNAIL-positive cells (cf. Table 2). Also frequently observed were SNAIL-positive ECADH-negative stromal cells around DN (open arrowhead). I: A peculiar staining pattern with alternating SNAIL-positive (red/magenta, arrows) and SNAIL-negative nuclei (blue, arrowhead) was observed in well-oriented internodular ductules. Small clusters of SNAIL-positive (red/magenta, open arrow) and SNAIL-negative (blue, open arrowhead) cells complemented this pattern. Scale bars = 20 μm.
- Supplemental Figure S6
SMAD and pSMAD antibody comparisons at optimized concentrations (cf. Table 1). A: SMAD3 antibodies demonstrated diffuse cytoplasmic reactivity with patchy perinuclear and focal nuclear accentuation. Comparison of labeling patterns of SMAD3 and pSMAD3 is provided in Figure S7. B: SMAD4 staining was strong and homogeneous in the perinodular ductular epithelium (cytoplasmic and patchy nuclear labeling). C: pSMAD2 antibodies (Ser465/467) demonstrated spotty nuclear reactivity in most nuclei. D: pSMAD2 antibodies (Ser 245/250/255) demonstrated irregular multifocal dotlike reactivity (red), here shown in co-labeling with K19 staining (green). Scale bars = 20 μm.
- Supplemental Figure S7
- Supplemental Figure S8
Alternating pSMAD2/3 pattern in internodular ductules. A: Example of internodular ductule between CN and DN labeled using triple color immunofluorescence. Immunoreactivity was observed for pSMAD2/3 (green) in nuclei (blue), resulting in the merged color turquoise (arrows). The pattern was similar to that observed using K19 and FSP-1 and SNAIL and ECADH labeling (Figure 4G, Figure 5G, and Figure S5I). Here, the pSMAD2/3-positive nuclei were typically interspersed by pSMAD2/3-negative nuclei (arrowheads), resulting in a peculiar alternating pattern of staining. Small clusters of pSMAD2/3 (open arrow) complemented the alternating pattern. Cytoplasmic immunoreactivity for SMAD3 was present in most cells (red), with rare perinuclear co-localization of pSMAD2/3 resulting in the merged color yellow, typically observed in pSMAD2/3-positive cells. B: Internodular ductules around DN demonstrated the same alternating pattern of pSMAD2/3-positive nuclei (arrows) and pSMAD2/3-negative nuclei (arrowhead). However, the overall amount of nuclear pSMAD2/3 was significantly higher (notable as an increase in the merged color turquoise). In addition, more frequent clustering was observed consisting of larger numbers of pSMAD2/3-positive nuclei (open arrows). Cytoplasmic SMAD3 positivity was present in most cells. However, the amount of perinuclear co-localization with pSMAD2/3 was increased, and the resulting merged color yellow is not restricted to pSMAD2/3-positive nuclei. These findings were interpreted as indicative of increased pSMAD2/3 activation in perinodular sectors surrounding DN when compared with CN, at least at immunolabeling (cf. Table 2). Scale bars = 20 μm.
- Supplemental Table S1
- Supplemental Table S2
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