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Original Article

Integrative multi-omics profiling identifies infiltrative hepatocellular carcinoma as an immunotherapy-resistant subtype with distinct molecular features

Clinical and Molecular Hepatology 2026;32(1):258-275.
Published online: October 27, 2025

1Medical Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea

2Department of Life Science, CHA University, Seongnam, Korea

3Department of Surgery, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea

4Division of Oncology, Department of Internal Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea

5Department of Internal Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea

6Department of Radiology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea

7Department of Pathology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea

8Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

9Department of Medical Science, CHA University School of Medicine, Seongnam, Korea

10Advanced Omics Center, CHA Bundang Medical Center, Seongnam, Korea

Corresponding author : Hong Jae Chon Medical Oncology, CHA Bundang Medical Center, CHA University School of Medicine, 59 Yatap-ro, Bundang-gu, Seongnam 13496, Korea Tel: +82-31-780-7590, Fax: +82-31-780-3929, E-mail: minidoctor@cha.ac.kr
Chan Kim Medical Oncology, CHA Bundang Medical Center, CHA University School of Medicine, 59 Yatap-ro, Bundang-gu, Seongnam 13496, Korea Tel: +82-31-780-7590, Fax: +82-31-780-3929, E-mail: chan@cha.ac.kr
Sohyun Hwang Department of Pathology, CHA Bundang Medical Center, CHA University School of Medicine, 59 Yatap-ro, Bundang-gu, Seongnam 13496, Korea Tel: +82-31-780-4859, Fax: +82-31-780-5179, E-mail: blissfulwin@cha.ac.kr

These authors equally contributed to this study.


Editor: Julien Calderaro, INSERM & Hopital Henri Mondor, France

• Received: July 17, 2025   • Revised: October 4, 2025   • Accepted: October 26, 2025

Copyright © 2026 by The Korean Association for the Study of the Liver

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Integrative multi-omics profiling identifies infiltrative hepatocellular carcinoma as an immunotherapy-resistant subtype with distinct molecular features
Clin Mol Hepatol. 2026;32(1):258-275.   Published online October 27, 2025
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Integrative multi-omics profiling identifies infiltrative hepatocellular carcinoma as an immunotherapy-resistant subtype with distinct molecular features
Clin Mol Hepatol. 2026;32(1):258-275.   Published online October 27, 2025
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Integrative multi-omics profiling identifies infiltrative hepatocellular carcinoma as an immunotherapy-resistant subtype with distinct molecular features
Image Image Image Image Image Image Image
Figure 1. Workflow of the study with gross type in advanced HCC. Representative radiologic imaging and corresponding schematic diagrams showing the distinct gross types observed in patients with advanced HCC. The red arrow shows portal vein thrombosis. Sunburst plot illustrating the classification of gross types of HCC. The outer ring represents the major gross types, while the inner ring shows more detailed types, including both pure and mixed forms. Some icons were created using BioRender.com. Ate/Bev, atezolizumab plus bevacizumab; DEG, differentially expressed gene; DEP, differentially expressed protein; GO, Gene Ontology; HCC, hepatocellular carcinoma; TCGA, The Cancer Genome Atlas; VAF, variant allele frequency.
Figure 2. Survival analysis of gross type with PFS and OS in patients with advanced HCC treated with atezolizumab and bevacizumab combination therapy. (A, B) Kaplan–Meier curves comparing 307 patients with the gross type of HCC based on tumor extent: <25%, 25–50%, 50–75%, and ≥75%. (C) Results of the multivariable Cox regression analysis with PFS and OS of the gross type and clinical factors in 306 patients with advanced HCC. A patient without α-fetoprotein was excluded from the Cox regression analysis. Clinical factors with a P-value <0.05 in the univariable analysis were included. AFP, alpha-fetoprotein; BCLC, Barcelona Clinic Liver Cancer; ECOG PS, Eastern Cooperative Oncology Group performance status; OS, overall survival; PFS, progression-free survival; PVTT, portal vein tumor thrombosis.
Figure 3. Genomic landscape according to gross types. (A) Frequency of genomic alterations of 20 key genes in patients with advanced HCC, including non-synonymous mutations and copy number variations, ranked by their prevalence. (B) Pathway-level representation of genomic alterations across different gross types. The diagram illustrates the proportion of samples harboring alterations in key oncogenic pathways: p53–RB, RTK–RAS–PI3K, telomerase, WNT, and chromatin modifiers. Each gene is annotated with four percentages corresponding to the frequency of activation (red) or inactivation (blue) across the gross types of advanced HCC. HCC, hepatocellular carcinoma.
Figure 4. Transcriptomic characteristics according to gross types. (A) Volcano plot showing differentially expressed genes between infiltrative (type IV) and non-infiltrative (types I, II, and III) types in patients with advanced HCC. (B) Heatmap illustrating distinct hallmark gene sets and cell cycle-related Reactome pathways identified by gene set variation analysis (GSVA), with colors representing scaled mean enrichment scores for each gross type. (C) Box plots showing immune scores of effector T cells (Teffs) and regulatory T cells (Tregs) across gross types. Statistical significance in panel B was calculated using the Student’s t-test comparing each type to all others, whereas panel C was analyzed using limma; *P<0.05. (D) Box plots comparing representative genes associated with tumor proliferation, pro-tumor cytokines, T cell/Tregs/M2-like, immune checkpoints and metabolism across gross types. (E) Immunohistochemical analysis of tumor tissues across gross types. Representative images and comparisons of CD8 and FOXP3 within tumor tissues. P-values were calculated using the Student’s t-test in infiltrative (type IV) vs. non-infiltrative (types I–III) types; *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001. Scale bars=60 μm.
Figure 5. Validation of the type IV infiltrative signature of HCC in public datasets using the Bayesian compound covariate predictor model. (A) Kaplan–Meier curves for PFS and OS comparing patients having HCC with predicted infiltrative versus non-infiltrative types in the IMbrave150 cohort (n=261) treated with Ate/Bev. (B) Box plots showing immune scores of Teffs and Tregs in predicted infiltrative versus non-infiltrative types in the IMbrave150 cohort. (C) Kaplan–Meier curves for OS comparing infiltrative and non-infiltrative subtypes in four public HCC datasets (n=795): the TCGA cohort, Villa et al.,S6 2016, Kim et al.,S7 2014, and Gao et al.,S8 2019. Hazard ratios (HRs) were estimated with univariable Cox proportional-hazards regression, and P-values were obtained from two-sided log-rank tests. Ate/Bev, atezolizumab plus bevacizumab; HCC, hepatocellular carcinoma; OS, overall survival; PFS, progression-free survival; Teffs, effector T cells; Tregs, regulatory T cells; TCGA, The Cancer Genome Atlas.
Figure 6. Proteomic characteristics of gross type with advanced HCC. (A) Volcano plot showing differentially expressed proteins (DEPs) between infiltrative (gross type IV) and non-infiltrative (gross types I, II, and III) types in patients with advanced HCC. (B) Bar chart of Gene Ontology (GO) enrichment for DEPs from (A); bars colored by adjusted P-value. (C) Heatmap of GSVA scores for hallmark, KEGG and Reactome gene sets that differ significantly between infiltrative and non-infiltrative HCC. (D) Graphical abstract of the characteristics according to gross classification. Some icons were created using BioRender.com. P-values in panels A and C were calculated using the limma package with a significance threshold of P<0.05. DEPs, differentially expressed proteins; EMT, epithelial-mesenchymal transition; HCC, hepatocellular carcinoma; GSVA, gene set variation analysis; ORR, objective response rate; OS, overall survival; PFS, progression-free survival; TGF-β, transforming growth factor beta; Tregs, regulatory T cells.
Graphical abstract
Integrative multi-omics profiling identifies infiltrative hepatocellular carcinoma as an immunotherapy-resistant subtype with distinct molecular features
Characteristics Overall (n=307) Type I (n=38) Type II (n=72) Type III (n=66) Type IV (n=131) P-value
Median age 62 (55–69) 62 (55–69) 63 (59–70) 65 (55–72) 60 (51–66) 0.01
Sex 0.30
 Female 46 (15.0) 3 (7.9) 11 (15.3) 14 (21.2) 18 (13.7)
 Male 261 (85.0) 35 (92.1) 61 (84.7) 52 (78.8) 113 (86.3)
ECOG PS 3.0×10-9
 0 99 (32.2) 24 (63.2) 36 (50.0) 17 (25.8) 22 (16.8)
 1 208 (67.8) 14 (36.8) 36 (50.0) 49 (74.2) 109 (83.2)
Etiology 0.07
 Hepatitis B 199 (64.8) 22 (57.9) 44 (61.1) 36 (54.5) 97 (74.1)
 Hepatitis C 23 (7.5) 5 (13.2) 7 (9.7) 4 (6.1) 7 (5.3)
 Alcohol 46 (15.0) 7 (18.4) 9 (12.5) 12 (18.2) 18 (13.7)
 MASLD 39 (12.7) 4 (10.5) 12 (16.7) 14 (21.2) 9 (6.9)
Child–Pugh 1.3×10-6
 A 235 (76.5) 37 (97.4) 66 (91.7) 48 (72.7) 84 (64.1)
 B7 72 (23.5) 1 (2.6) 6 (8.3) 18 (27.3) 47 (35.9)
BCLC stage 1.8×10-5
 B 47 (15.3) 15 (39.5) 13 (18.1) 10 (15.2) 9 (6.9)
 C 260 (84.7) 23 (60.5) 59 (81.9) 56 (84.8) 122 (93.1)
PVTT 119 (38.8) 2 (5.3) 8 (11.1) 17 (25.8) 92 (70.2) <2.2×10-16
Extrahepatic spread 0.28
 Absent 121 (39.4) 19 (50.0) 24 (33.3) 23 (34.8) 55 (42.0)
 Present 186 (60.6) 19 (50.0) 48 (66.7) 43 (65.2) 76 (58.0)
AFP ≥400 ng/mL 127 (41.5) 9 (23.7) 16 (22.2) 35 (53.0) 67 (51.1) 1.1×10-5
Intrahepatic tumor extent <2.2×10-16
 <25% 137 (44.6) 34 (89.5) 54 (75.0) 11 (16.7) 38 (29.0)
 25–50% 95 (31.0) 4 (10.5) 11 (15.3) 32 (48.5) 48 (36.6)
 50–75% 60 (19.5) 0 (0.0) 7 (9.7) 16 (24.2) 37 (28.3)
 ≥75% 15 (4.9) 0 (0.0) 0 (0.0) 7 (10.6) 8 (6.1)
Prior local treatment
 Surgery 56 (18.2) 17 (44.7) 12 (16.7) 7 (10.6) 20 (15.3) 8.8×10-5
 Radiotherapy 84 (27.4) 12 (31.6) 24 (33.3) 15 (22.7) 33 (25.2) 0.45
 TACE 154 (50.2) 31 (81.6) 48 (66.7) 28 (42.4) 47 (35.9) 1.1×10-7
 RFA 26 (8.5) 8 (21.1) 11 (15.3) 2 (3.0) 5 (3.8) 3.9×10-4
Response Overall (n=307) Type I (n=38) Type II (n=72) Type III (n=66) Type IV (n=131)
Complete response 9 (2.9) 3 (7.9) 4 (5.6) 1 (1.5) 1 (0.8)
Partial response 87 (28.3) 20 (52.6) 33 (45.8) 17 (25.8) 17 (13.0)
Stable disease 131 (42.7) 14 (36.9) 28 (38.9) 28 (42.4) 61 (46.5)
Progressive disease 67 (21.8) 1 (2.6) 5 (6.9) 17 (25.8) 44 (33.6)
Not evaluable 13 (4.2) 0 (0.0) 2 (2.8) 3 (4.5) 8 (6.1)
ORR 96 (32.7) (27.5–38.2) 23 (60.5) (44.7–74.4) 37 (52.9) (41.3–64.1) 18 (28.6) (18.9–40.7) 18 (14.6) (9.5–21.9)
DCR 227 (77.2) (72.1–81.6) 37 (97.4) (86.5–99.5) 65 (92.9) (84.3–96.9) 46 (73.0) (61.0–82.4) 79 (64.2) (55.4–72.1)
Table 1. Baseline characteristics of patients with advanced hepatocellular carcinoma who received atezolizumab plus bevacizumab, categorized by gross type

Values are presented as median (interquartile range) or number (%).

AFP levels were unavailable in one patient with type IV infiltrative HCC. Among type I, II, III, and IV HCC, continuous variables were compared using one-way ANOVA, while categorical variables were analyzed using the chi-squared test.

AFP, alpha-fetoprotein; BCLC, Barcelona Clinic Liver Cancer; ECOG PS, Eastern Cooperative Oncology Group performance status; MASLD, metabolic dysfunction-associated steatotic liver disease; PVTT, portal vein tumor thrombosis; RFA, radiofrequency ablation; TACE, transarterial chemoembolization.

Table 2. Best overall response to atezolizumab plus bevacizumab

Values are presented as number (%) or 95% confidence interval.

ORR and DCR were calculated excluding non-evaluable patients.

DCR, disease control rate; ORR, overall response rate.