Genomics of Pediatric Liver Tumors

Team Leader

Projects

Our research explores the genomic and molecular basis of pediatric liver tumors to advance knowledge and improve treatment.

In the Genomics of Pediatric Liver Tumors group, we study tumor evolution using data from patient clinical features, whole-genome and exome sequencing, bulk RNAseq, single-cell, and spatial transcriptomics. We focus primarily on hepatoblastoma (HB), the most common pediatric liver cancer, as well as pediatric hepatocellular carcinoma (HCC), fibrolamellar carcinoma (FLC), and hepatocellular adenoma (HCA).

We partner with clinicians across France to gather samples and address key research questions, and work with Japanese teams to validate findings. We develop computational tools to integrate multi-scale data, exploring tumor evolution and chemotherapy resistance (Figure 1).

Axis 1: Identifying Germline, Mosaic, and Somatic Driver Alterations in Pediatric Liver Cancers

Context:
Tumor cells carry molecular changes (mutations, chromosome alterations) that affect gene function. We use computational methods to find recurring altered genes driving cancer, which can be somatic (tumor-specific) or germline/mosaic (predisposing), especially in early childhood cancers.

Published results:

By analyzing 122 tumor samples from 84 patients using whole-genome or whole-exome sequencing, we pinpointed key driver alterations in pediatric liver cancers (Hirsch et al, Cancer Discov 2021) (Figure 2).

HB and HCC converge on pathways like Wnt/β-catenin and IGF2 but differ in alteration types: HB often have mutations (e.g., CTNNB1), while HCC show deletions (e.g., AXIN1). Some HB patients have germline APC mutations linked to familial adenomatous polyposis, and a somatic second hit (Morcrette et al, Oncoimmunology 2019). Rare driver alterations predict poor chemotherapy response and survival (Pire et al, Eur J Cancer 2024). Alterations at the 11p15.5 locus, causing IGF2 overexpression, are a major driver. We found mosaic 11p15.5 changes in ~20% of HB patients’ non-tumor liver, marking preneoplastic cells and affecting liver function (Pilet et al, Nat Commun 2023).

Ongoing projects:

We aim to identify new driver alterations of pediatric liver cancers by expanding our cohort analyzed by whole-genome sequencing and bulk RNAseq. We have specific projects to further explore mosaic alterations at the single-cell and spatial level.

Axis 2: Linking Phenotypic Diversity, Subclonal Evolution, and Spatial Expansion in Hepatoblastoma

Context:

Tumor evolution is a multi-step process driven by mutations under immune and treatment pressures, leading to diverse phenotypes. We study how clonal changes and phenotypes connect to tumor evolution and resistance.

Published results: 

Using RNAseq on 100 HB samples, we defined three transcriptomic groups tied to differentiation, proliferation, and immune response (Hirsch et al, Cancer Discov 2021) (Figure 3a). Multiple samples from the same tumor showed varied phenotypes despite shared drivers, indicating plasticity. Chemotherapy boosts immune infiltration in ‘Hepatocytic’ tumors but not ‘Liver Progenitor’ ones. Single-cell analysis confirmed these groups, revealing a continuum of cell states and subclonal diversity (Roehrig et al, Nat Commun 2024) (Figure 3b).

Ongoing projects:

We currently explore the intra-tumor heterogeneity of hepatoblastoma at the spatially-resolved single-cell level, by combining high-plex immunofluorescence, single-nucleus RNAseq and spatial transcriptomics.

Axis 3: Leveraging Cisplatin Mutational Signatures to Understand Chemoresistance and Relapses in Hepatoblastoma

Context:

Hepatoblastoma is treated with cisplatin-based chemotherapy, but some cases resist treatment, with few therapeutic alternatives.

Published results:

Whole-genome sequencing revealed cisplatin’s SBS35 mutational signature (Figure 4a) in a subset of primary hepatoblastomas post-chemotherapy, associated with poor treatment response (Hirsch et al, Cancer Discov 2021 ; Pire et al, Eur J Cancer 2024). In primary tumors, SBS35 mutations were subclonal, meaning they appeared in only a fraction of tumor cells, specifically within ‘Liver Progenitor’ sectors, while ‘Hepatocytic’ and ‘Mesenchymal’ areas lacked them. In contrast, relapse samples showed thousands of clonal SBS35 mutations, present in all tumor cells, indicating relapses arise from a single resistant cell that accumulated cisplatin-induced mutations during treatment (Figure 4b). Overall, the longitudinal analysis of cisplatin-induced mutations, integrated with the transcriptomic classification, pinpoints the ‘Liver Progenitor’ cells as being chemoresistant and at the origin of relapses.

Targeting PLK1, a ‘Liver Progenitor’ marker, reduced tumor growth in proof-of-concept experiments developed with Sandra Rebouissou’s group (Hirsch et al, Cancer Discov 2021).

Ongoing projects:

We’re refining detection of cisplatin mutations with machine learning and, with Sandra Rebouissou’s group, seeking drugs to reverse chemoresistance.

Team

Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma. 

Roehrig A, Hirsch TZ, Pire A, Morcrette G, Gupta B, Marcaillou C, Imbeaud S, Chardot C, Gonzales E, Jacquemin E, Sekiguchi M, Takita J, Nagae G, Hiyama E, Guérin F, Fabre M, Aerts I, Taque S, Laithier V, Branchereau S, Guettier C, Brugières L, Fresneau B, Zucman-Rossi J, Letouzé E. Nat Commun. 2024 Apr 8;15(1):3031. doi: 10.1038/s41467-024-47280-x. PMID: 38589411

Mutational signature, cancer driver genes mutations and transcriptomic subgroups predict hepatoblastoma survival. 

Pire A, Hirsch TZ, Morcrette G, Imbeaud S, Gupta B, Pilet J, Cornet M, Fabre M, Guettier C, Branchereau S, Brugières L, Guerin F, Laithier V, Coze C, Nagae G, Hiyama E, Laurent-Puig P, Rebouissou S, Sarnacki S, Chardot C, Capito C, Faure-Conter C, Aerts I, Taque S, Fresneau B, Zucman-Rossi J. Eur J Cancer. 2024 Mar;200:113583. doi: 10.1016/j.ejca.2024.113583. Epub 2024 Feb 1. PMID: 38330765

Preneoplastic liver colonization by 11p15.5 altered mosaic cells in young children with hepatoblastoma. 

Pilet J, Hirsch TZ, Gupta B, Roehrig A, Morcrette G, Pire A, Letouzé E, Fresneau B, Taque S, Brugières L, Branchereau S, Chardot C, Aerts I, Sarnacki S, Fabre M, Guettier C, Rebouissou S, Zucman-Rossi J. Nat Commun. 2023 Nov 6;14(1):7122. doi: 10.1038/s41467-023-42418-9. PMID: 37932266

Integrated Genomic Analysis Identifies Driver Genes and Cisplatin-Resistant Progenitor Phenotype in Pediatric Liver Cancer. 

Hirsch TZ, Pilet J, Morcrette G, Roehrig A, Monteiro BJE, Molina L, Bayard Q, Trépo E, Meunier L, Caruso S, Renault V, Deleuze JF, Fresneau B, Chardot C, Gonzales E, Jacquemin E, Guerin F, Fabre M, Aerts I, Taque S, Laithier V, Branchereau S, Guettier C, Brugières L, Rebouissou S, Letouzé E, Zucman-Rossi J. Cancer Discov. 2021 Oct;11(10):2524-2543. doi: 10.1158/2159-8290.CD-20-1809. Epub 2021 Apr 23. PMID: 33893148

BAP1 mutations define a homogeneous subgroup of hepatocellular carcinoma with fibrolamellar-like features and activated PKA. 

Hirsch TZ, Negulescu A, Gupta B, Caruso S, Noblet B, Couchy G, Bayard Q, Meunier L, Morcrette G, Scoazec JY, Blanc JF, Amaddeo G, Nault JC, Bioulac-Sage P, Ziol M, Beaufrère A, Paradis V, Calderaro J, Imbeaud S, Zucman-Rossi J. J Hepatol. 2020 May;72(5):924-936. doi: 10.1016/j.jhep.2019.12.006. Epub 2019 Dec 18. PMID: 31862487

APC germline hepatoblastomas demonstrate cisplatin-induced intratumor tertiary lymphoid structures. 

Morcrette G, Hirsch TZ, Badour E, Pilet J, Caruso S, Calderaro J, Martin Y, Imbeaud S, Letouzé E, Rebouissou S, Branchereau S, Taque S, Chardot C, Guettier C, Scoazec JY, Fabre M, Brugières L, Zucman-Rossi J. Oncoimmunology. 2019 Mar 28;8(6):e1583547. doi: 10.1080/2162402X.2019.1583547. eCollection 2019. PMID: 31069152

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