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Supplementary Data from Hepatocellular Carcinoma in Mongolia Delineates Unique Molecular Traits and a Mutational Signature Associated with Environmental Agents

Purpose:Mongolia has the world's highest incidence of hepatocellular carcinoma (HCC), with ∼100 cases/100,000 inhabitants, although the reasons for this have not been thoroughly delineated.Experimental Design:We performed a molecular characterization of Mongolian (n = 192) compared with Western (n = 187) HCCs by RNA sequencing and whole-exome sequencing to unveil distinct genomic and transcriptomic features associated with environmental factors in this population.Results:Mongolian patients were younger, with higher female prevalence, and with predominantly HBV–HDV coinfection etiology. Mongolian HCCs presented significantly higher rates of protein-coding mutations (121 vs. 70 mutations per tumor in Western), and in specific driver HCC genes (i.e., APOB and TSC2). Four mutational signatures characterized Mongolian samples, one of which was novel (SBS Mongolia) and present in 25% of Mongolian HCC cases. This signature showed a distinct substitution profile with a high proportion of T>G substitutions and was significantly associated with a signature of exposure to the environmental agent dimethyl sulfate (71%), a 2A carcinogenic associated with coal combustion. Transcriptomic-based analysis delineated three molecular clusters, two not present in Western HCC; one with a highly inflamed profile and the other significantly associated with younger female patients.Conclusions:Mongolian HCC has unique molecular traits with a high mutational burden and a novel mutational signature associated with genotoxic environmental factors present in this country.

Supplementary Figure from Hepatocellular Carcinoma in Mongolia Delineates Unique Molecular Traits and a Mutational Signature Associated with Environmental Agents

Supplementary Figure from Cabozantinib Enhances Anti-PD1 Activity and Elicits a Neutrophil-Based Immune Response in Hepatocellular Carcinoma

Supplementary Materials and Methods, Supplementary Figures and Supplementary Tables

Supplementary Data from Cabozantinib Enhances Anti-PD1 Activity and Elicits a Neutrophil-Based Immune Response in Hepatocellular Carcinoma

Purpose:Immune checkpoint inhibitors combined with antiangiogenic agents produce benefits in the treatment of advanced hepatocellular carcinoma (HCC). We investigated the efficacy and immunomodulatory activity of cabozantinib alone and combined with anti-PD1 in experimental models of HCC, and explored the potential target population that might benefit from this combination.Experimental Design:C57BL/6J mice bearing subcutaneous Hepa1-6 or Hep53.4 tumors received cabozantinib, anti-PD1, their combination, or placebo. Tumor and blood samples were analyzed by flow cytometry, IHC, transcriptome, and cytokine profiling. Cabozantinib-related effects were validated in a colorectal cancer patient-derived xenograft model. Transcriptomic data from three human HCC cohorts (cohort 1: n = 167, cohort 2: n = 57, The Cancer Genome Atlas: n = 319) were used to cluster patients according to neutrophil features, and assess their impact on survival.Results:The combination of cabozantinib and anti-PD1 showed increased antitumor efficacy compared with monotherapy and placebo (P < 0.05). Cabozantinib alone significantly increased neutrophil infiltration and reduced intratumor CD8+PD1+ T-cell proportions, while the combination with anti-PD1 further stimulated both effects and significantly decreased regulatory T cell (Treg) infiltration (all P < 0.05). In blood, cabozantinib and especially combination increased the proportions of overall T cells (P < 0.01) and memory/effector T cells (P < 0.05), while lowering the neutrophil-to-lymphocyte ratio (P < 0.001 for combination). Unsupervised clustering of human HCCs revealed that high tumor enrichment in neutrophil features observed with the treatment combination was linked to less aggressive tumors with more differentiated and less proliferative phenotypes.Conclusions:Cabozantinib in combination with anti-PD1 enhanced antitumor immunity by bringing together innate neutrophil-driven and adaptive immune responses, a mechanism of action which favors this approach for HCC treatment.

Purpose:Chromosomal instability is a hallmark of cancer that results in broad and focal copy-number alterations (CNAs), two events associated with distinct molecular, immunologic, and clinical features. In hepatocellular carcinoma (HCC), the role of CNAs has not been thoroughly assessed. Thus, we dissected the impact of CNA burdens on HCC molecular and immune features.Experimental Design:We analyzed SNP array data from 452 paired tumor/adjacent resected HCCs and 25 dysplastic nodules. For each sample, broad and focal CNA burdens were quantified using CNApp, and the resulting broad scores (BS) and focal scores (FS) were correlated with transcriptomic, mutational, and methylation profiles, tumor immune composition, and clinicopathologic data.Results:HCCs with low broad CNA burdens (defined as BS ≤ 4; 17%) presented high inflammation, active infiltrate signaling, high cytolytic activity, and enrichment of the “HCC immune class” and gene signatures related to antigen presentation. Conversely, tumors with chromosomal instability (high broad CNA loads, BS ≥ 11; 40%), displayed immune-excluded traits and were linked to proliferation, TP53 dysfunction, and DNA repair. Candidate determinants of the low cytotoxicity and immune exclusion features of high-BS tumors included alterations in antigen-presenting machinery (i.e., HLA), widespread hypomethylation, and decreased rates of observed/expected neoantigenic mutations. High FSs were independent of tumor immune features, but were related to proliferation, TP53 dysfunction, and progenitor cell traits.Conclusions:HCCs with high chromosomal instability exhibit features of immune exclusion, whereas tumors displaying low burdens of broad CNAs present an immune active profile. These CNA scores can be tested to predict response to immunotherapies.

Purpose: Immune checkpoint inhibitors combined with antiangiogenic agents produce benefits in the treatment of advanced hepatocellular carcinoma (HCC). We investigated the efficacy and immunomodulatory activity of cabozantinib alone and combined with anti-PD1 in experimental models of HCC, and explored the potential target population that might benefit from this combination. Experimental Design: C57BL/6J mice bearing subcutaneous Hepa1-6 or Hep53.4 tumors received cabozantinib, anti-PD1, their combination, or placebo. Tumor and blood samples were analyzed by flow cytometry, IHC, transcriptome, and cytokine profiling. Cabozantinib-related effects were validated in a colorectal cancer patient-derived xenograft model. Transcriptomic data from three human HCC cohorts (cohort 1: n = 167, cohort 2: n = 57, The Cancer Genome Atlas: n = 319) were used to cluster patients according to neutrophil features, and assess their impact on survival. Results: The combination of cabozantinib and anti-PD1 showed increased antitumor efficacy compared with monotherapy and placebo (P < 0.05). Cabozantinib alone significantly increased neutrophil infiltration and reduced intratumor CD8+PD1+ T-cell proportions, while the combination with anti-PD1 further stimulated both effects and significantly decreased regulatory T cell (Treg) infiltration (all P < 0.05). In blood, cabozantinib and especially combination increased the proportions of overall T cells (P < 0.01) and memory/effector T cells (P < 0.05), while lowering the neutrophil-to-lymphocyte ratio (P < 0.001 for combination). Unsupervised clustering of human HCCs revealed that high tumor enrichment in neutrophil features observed with the treatment combination was linked to less aggressive tumors with more differentiated and less proliferative phenotypes. Conclusions: Cabozantinib in combination with anti-PD1 enhanced antitumor immunity by bringing together innate neutrophil-driven and adaptive immune responses, a mechanism of action which favors this approach for HCC treatment.

BACKGROUND AND AIMS: Cholangiocarcinoma (CCA), a deadly malignancy of the bile ducts, can be classified on the basis of its anatomical location into either intrahepatic (iCCA) or extrahepatic (eCCA), each with different pathogenesis and clinical management. There is marginal understanding of the molecular landscape of eCCA and no targeted therapy with clinical efficacy has been approved. We aimed to provide a molecular classification of eCCA and identify potential targets for molecular therapies. METHODS: An integrative genomic analysis of an international multi-center cohort of 189 eCCA cases was conducted. Genomic analysis included whole-genome expression, targeted DNA-sequencing and immunohistochemistry. Molecular findings were validated in an external set of 181 biliary tract tumors from ICGC. RESULTS: KRAS (36.7%), TP53 (34.7%), ARID1A (14%) and SMAD4 (10.7%) were the most prevalent mutations, with ~25% of tumors having a putative actionable genomic alteration according to OncoKB. Transcriptome-based unsupervised clustering helped us define four molecular classes of eCCA. Tumors classified within the Metabolic class (19%) showed a hepatocyte-like phenotype with activation of the transcription factor HNF4A and enrichment in gene signatures related to bile acid metabolism. The Proliferation class (23%), more common in patients with distal CCA, was characterized by enrichment of MYC targets, ERBB2 mutations / amplifications and mTOR signaling activation. The Mesenchymal class (47%) was defined by signatures of epithelial-mesenchymal transition, aberrant TGF-β signaling and poor overall survival. Finally, tumors in the Immune class (11%) had a higher lymphocyte infiltration, overexpression of PD-1/PD-L1 and molecular features associated with a better response to immune checkpoint inhibitors. CONCLUSION: An integrative molecular characterization identified distinct subclasses of eCCA. Genomic traits of each class provide the rationale for exploring patient stratification and novel therapeutic approaches. LAY SUMMARY: Targeted therapies have not been approved for the treatment of extrahepatic cholangiocarcinoma. We performed a multi-platform molecular characterization of this tumor in a cohort of 189 patients. These analyses revealed four novel transcriptome-based molecular classes of extrahepatic cholangiocarcinoma and identified ~25% of tumors with actionable genomic alterations, which has potential prognostic and therapeutic implications.

Objective: Hepatocellular carcinoma (HCC) is increasingly associated with non-alcoholic steatohepatitis (NASH). HCC immunotherapy offers great promise; however, recent data suggests NASH-HCC may be less sensitive to conventional immune checkpoint inhibition (ICI). We hypothesised that targeting neutrophils using a CXCR2 small molecule inhibitor may sensitise NASH-HCC to ICI therapy. Design Neutrophil infiltration was characterised in human HCC and mouse models of HCC. Late-stage intervention with anti-PD1 and/or a CXCR2 inhibitor was performed in murine models of NASH-HCC. The tumour immune microenvironment was characterised by imaging mass cytometry, RNA-seq and flow cytometry. Results: neutrophils expressing CXCR2, a receptor crucial to neutrophil recruitment in acute-injury, are highly represented in human NASH-HCC. In models of NASH-HCC lacking response to ICI, the combination of a CXCR2 antagonist with anti-PD1 suppressed tumour burden and extended survival. Combination therapy increased intratumoural XCR1(+) dendritic cell activation and CD8(+) T cell numbers which are associated with anti-tumoural immunity, this was confirmed by loss of therapeutic effect on genetic impairment of myeloid cell recruitment, neutralisation of the XCR1-ligand XCL1 or depletion of CD8(+) T cells. Therapeutic benefit was accompanied by an unexpected increase in tumour-associated neutrophils (TANs) which switched from a protumour to anti-tumour progenitor-like neutrophil phenotype. Reprogrammed TANs were found in direct contact with CD8(+) T cells in clusters that were enriched for the cytotoxic anti-tumoural protease granzyme B. Neutrophil reprogramming was not observed in the circulation indicative of the combination therapy selectively influencing TANs. Conclusion: CXCR2-inhibition induces reprogramming of the tumour immune microenvironment that promotes ICI in NASH-HCC., Cancer Research UK (CRUK); Newcastle Experimental Cancer Medicine Centre; Accelerator Award; Fondazione AIRC; MRC program; AstraZeneca; Wellcome Trust; Newcatle University Faculty of Medical Sciences; WE Harker Foundation; Ministry of Economy and Competitiveness (MINECO) (MICINN); Fundació Universitària Agustí Pedro i Pons; Instituto de Salud Carlos III (ISCIII); European Union (EU); European Social Fund; German Research Foundation (DFG); Fulbright España; National Institutes of Health (NIH); Samuel Waxman Cancer Research Foundation; Spanish National Health Institute; Fundación Científica de la Asociación Española Contra el Cáncer; Generalitat de Catalunya; Sara Borrell Fellowship

Background: Transforming growth factor β (TGFβ) has a dual role in cancer, including hepatocellular carcinoma (HCC). It acts as a tumor suppressor in early stages of hepatocarcinogenesis, but promotes epithelial-to-mesenchymal transition, angiogenesis and immunosuppression in advanced stages. PMEPA1 (prostate transmembrane protein androgen induced 1), a direct target gene of the TGFβ pathway that negatively regulates TGFβ signaling by interacting with SMAD proteins, has been shown to promote TGFβ oncogenic effects in other cancers and we decided to explore its role in HCC pathogenesis. Methods: We analyzed transcriptomic, genomic, epigenomic and clinicopathological data of a discovery cohort of 228 HCCs and a validation cohort of 361 HCCs. PMEPA1 levels were quantified by qPCR in the discovery cohort. PMEPA1 overexpression was validated in 6 independent cohorts (n = 916) using microarray and RNAseq data. Genetically engineered mouse models were generated through hydrodynamic tail-vein injection. Equal amounts of plasmids overexpressing PMEPA1, TGFB1 and MYC were injected in mice to evaluate survival. Molecular and histopathological analyses of the murine tumors are currently ongoing. Results: PMEPA1 was overexpressed in 18% of human HCCs [FC > 2; n = 203/1144], a feature associated with TGFβ signaling (p < 0.05). Overexpression of PMEPA1 was associated with gene body hypermethylation (p < 0.0001). HCCs displaying both TGFβ signaling and high PMEPA1 levels (11% of cases) were significantly enriched in signatures of immune exhaustion, late TGFβ activation, TME response to TGFβ and active stroma (p < 0.05) compared to HCCs with TGFβ signalling alone (8% of cases) or PMEPA1 high levels alone (11% of cases). In vivo, overexpression of MYC+PMEPA1 led to HCC development in 9/16 mice and showed a lower survival when compared to the control arm, overexpression of MYC alone (p = 0.014). On the contrary, only 1/12 mice in the MYC+PMEPA1+TGFβ1 condition developed HCC and none of the MYC+TGFβ1 mice. Conclusion: PMEPA1 upregulation is linked to TGF-β activation and an aggressive phenotype in human HCC. Overexpression PMEPA1 in combination with MYC in vivo led to HCC development, showing for the first time the oncogenic role of PMEPA1 in this cancer. Citation Format: Marta Piqué-Gili, Carmen Andreu-Oller, Roser Pinyol, Marina Bárcena-Varela, Roger Esteban-Fabró, Judit Peix, Jordi Abril-Fornaguera, Katherine E. Lindblad, Miguel Torres-Martin, Daniela Sia, Amaia Lujambio, Josep M. Llovet. PMEPA1 is an oncogene linked to TGF-β signaling in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 840.

Somatic copy number alterations (CNAs) are a hallmark of cancer, but their role in tumorigenesis and clinical relevance remain largely unclear. Here, we developed CNApp, a web-based tool that allows a comprehensive exploration of CNAs by using purity-corrected segmented data from multiple genomic platforms. CNApp generates genome-wide profiles, computes CNA scores for broad, focal and global CNA burdens, and uses machine learning-based predictions to classify samples. We applied CNApp to the TCGA pan-cancer dataset of 10,635 genomes showing that CNAs classify cancer types according to their tissue-of-origin, and that each cancer type shows specific ranges of broad and focal CNA scores. Moreover, CNApp reproduces recurrent CNAs in hepatocellular carcinoma and predicts colon cancer molecular subtypes and microsatellite instability based on broad CNA scores and discrete genomic imbalances. In summary, CNApp facilitates CNA-driven research by providing a unique framework to identify relevant clinical implications. CNApp is hosted at https://tools.idibaps.org/CNApp/., eLife digest In most cases, human cells contain two copies of each of their genes, yet sometimes this can change, an effect called copy number alteration (CNA). Cancer is a genetic disease and thus, studying the DNA from tumor samples is crucial to improving diagnosis and choosing the right treatment. Most tumors contain cells with CNAs; however, the impact of CNAs in cancer progression is poorly understood. CNAs can be studied by examining the genome of tumor cells and finding which regions display an unusual number of copies. It may also be possible to gather information about different cancer types by analyzing the CNAs in a tumor, but this approach requires the analysis of large amounts of data. To aid the analysis of CNAs in cancer cells, Franch-Expósito, Bassaganyas et al. have created an online tool called CNApp, which is able to identify and count CNAs in genomic data and link them to features associated with different cancers. The hope is that a better understanding of the effect of CNAs in cancer could help better diagnose cancers, and improve outcomes for patients. Potentially, this could also predict what type of treatment would work better for a specific tumor. Besides, by using a machine-learning approach, the tool can also make predictions about specific cancer subtypes in order to facilitate clinical decisions. Franch-Expósito, Bassaganyas et al. tested CNApp using previously existing cancer data from 33 different cancer types to show how CNApp can help the interpretation of CNAs in cancer. Moreover, CNApp can also use CNAs to identify different types of bowel (colorectal) cancer in a way that could help doctors to make decisions about treatment. Together these findings show that CNApp provides an adaptable and accessible research tool for the study of cancer genomics, which could provide opportunities to inform medical procedures.

Somatic copy number alterations (CNAs) are a hallmark of cancer. Although CNA profiles have been established for most human tumor types, their precise role in tumorigenesis as well as their clinical and therapeutic relevance remain largely unclear. Thus, computational and statistical approaches are required to thoroughly define the interplay between CNAs and tumor phenotypes. Here we developed CNApp, a user-friendly web tool that offers sample- and cohort-level computational analyses, allowing a comprehensive and integrative exploration of CNAs with clinical and molecular variables. By using purity-corrected segmented data from multiple genomic platforms, CNApp generates genome-wide profiles, computes CNA scores for broad, focal and global CNA burdens, and uses machine learning-based predictions to classify samples. We applied CNApp to a pan-cancer dataset of 10,635 genomes from TCGA showing that CNA patterns classify cancer types according to their tissue-of-origin, and that broad and focal CNA scores positively correlate in samples with low amounts of whole-chromosome and chromosomal arm-level imbalances. Moreover, using the hepatocellular carcinoma cohort from the TCGA repository, we demonstrate the reliability of the tool in identifying recurrent CNAs, confirming previous results. Finally, we establish machine learning-based models to predict colon cancer molecular subtypes and microsatellite instability based on broad CNA scores and specific genomic imbalances. In summary, CNApp facilitates data-driven research and provides a unique framework for the first time to comprehensively assess CNAs and perform integrative analyses that enable the identification of relevant clinical implications. CNApp is hosted at http://cnapp.bsc.es.

Introduction: Aneuploidy is a cancer hallmark that includes broad somatic copy-number alterations (SCNAs), being whole chromosome- or arm-level events, or smaller focal SCNAs. Pan-cancer studies suggest that tumor broad and focal SCNAs are linked to distinctive molecular/clinical traits, and broad SCNAs may potentially interfere with tumor immune infiltrates. However, the impact of SCNA genomic loads in hepatocellular carcinoma (HCC) is still unresolved. Here we have assessed broad and focal SCNA burdens in HCC to unveil associations with clinic-molecular characteristics and immune cell profiles. Method: The study includes 520 paired tumor/adjacent surgically resected HCC samples: 150 of a training cohort (HEPTROMIC) and 370 of a validation cohort (TCGA). Tumor ploidy and SCNA segments were extracted from SNP array data using ASCAT and SAASCNV. We applied the CNApp tool (bioinfo.ciberehd.org/CNApp) to extract a Broad SCNA Score (BCS) and Focal SCNA Score (FCS) to assess broad and focal SCNA loads of each sample. Broad and focal alterations were defined as those spanning ≥50% and Results: HCC tumors characterized by a low BCS (25% of Heptromic, 15% of TCGA) were associated with the HCC Immune class and up-regulation of genes related to inflammation, active infiltrate signaling, antigen presentation and cytolytic activity (FDR Conclusions: Broad are more informative than focal SCNA burdens in terms of molecular features and immune status of HCC tumors. Those tumors characterized by chromosomal stability (low broad SCNAs loads) are enriched in antitumor immune response and antigenicity traits and therefore might correspond to those tumors responding to checkpoint inhibitors. Citation Format: Roger Esteban-Fabró, Laia Bassaganyas, Sara Torrecilla, Agrin Moeini, Sebastià Franch-Expósito, Maria Vila-Casadesús, Ferran Nadeu, Daniela Sia, Itziar Salaverria, Laia Cabellos, Roser Pinyol, Jordi Camps, Vicenzo Mazzaferro, Vicenzo Mazzaferro, Josep M Llovet. Aneuploidy profiles in hepatocellular carcinoma and their impact on tumor progression and immune features [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3095.