Single-cell analysis of hepatoblastoma identifies tumor signatures that predict chemotherapy susceptibility using patient-specific tumor spheroids

Gas1-Mediated Suppression of Hepatoblastoma Tumorigenesis

Hepatoblastoma (HB), the most common pediatric liver cancer, is associated with dysregulated Wnt/β-catenin, Hippo, and/or nuclear factor erythroid 2 ligand 2/nuclear respiratory factor 2 (NFE2L2/NRF2) pathways. In mice, pairwise combinations of oncogenically active forms of the terminal transcription factors of these pathways, namely, β-catenin (B), Yes-associated protein (YAP; Y), and Nrf2 (N), generate HBs, with the triple combination (B + Y + N) being particularly potent. Each tumor group alters the expression of thousands of B-, Y-, and N-driven unique and common target genes. The identification of those most involved in transformation might reveal mechanisms and opportunities for therapy. Herein, transcription profiling of >60 murine HBs revealed a common set of 22 "BYN" genes similarly deregulated in all cases. Most were associated with multiple cancer hallmarks, and their expression often correlated with survival in HBs, hepatocellular carcinomas, and other cancers. Among the most down-regulated of these genes was Gas1, which encodes a glycosylphosphatidylinositol-linked outer membrane protein. The restoration of Gas1 expression impaired B + Y + N-driven HB tumor growth in vivo and in HB-derived immortalized BY and BYN cell lines in vitro in a manner that requires membrane anchoring of the protein via its glycosylphosphatidylinositol moiety, implicating Gas1 as a proximal mediator of HB pathogenesis and validating the BYN gene set as deserving of additional scrutiny in future studies.

Single-Cell Transcriptional Analysis Reveals the Mechanism of AZD6738 in HCC Immunotherapy via EZH2 Targeting

Objective

This study aims to identify specific molecular targets sensitive to AZD6738 through the integration of network pharmacology and transcriptomic methods, and to assess their potential role in the treatment of hepatocellular carcinoma (HCC). Additionally, we explore the specific effects of AZD6738 on the tumor microenvironment and its ability to regulate immune responses.

Methods

We employed a combination of network pharmacology and transcriptomic analysis to identify specific molecules associated with HCC, including EZH2, CCNB1, PRKDC, CTSL, PSEN1, SLC6A3, and FKBP1A. Using these molecules and clinical features, we constructed a robust prognostic model for HCC. We further used single-cell transcriptomic technology to screen for core targets and performed spatial transcriptomic analysis to determine their spatial distribution. To validate the efficacy of AZD6738 in vivo, we established a subcutaneous tumor model, with the experimental group receiving oral administration of AZD6738 (75 mg/kg). Finally, we assessed the changes in the immune cell expression profile in tumor tissues post-AZD6738 treatment using flow cytometry.

Results

Our study indicates that the high expression of genes such as EZH2, CCNB1, PRKDC, and PSEN1 is associated with poor prognosis in HCC patients. Molecular docking and RT-PCR validation demonstrated that AZD6738 exhibits high affinity for these targets and significantly reduces the mRNA levels of EZH2, PRKDC, and CCNB1 in HCC cell lines, with EZH2 showing the most pronounced decrease. Animal experiments revealed that AZD6738 can enhance the immune microenvironment in liver cancer; specifically, AZD6738 not only promotes the proliferation of CD8+ T cells but also enhances their differentiation into effector memory T cells, indicating that the drug can potentiate anti-tumor immune responses.

Conclusion

This study reveals that AZD6738 demonstrates significant therapeutic efficacy by targeting the key molecule EZH2, thereby modulating the tumor microenvironment and enhancing anti-tumor immunity.

Numerical modeling of oxygen diffusion in tissue spheroids undergoing fusion using function representation and finite volumes

A three-dimensional cell culture called a spheroid serves as a foundational entity in a wide variety of modern tissue engineering applications, including 3D-bioprinting and preclinical drug testing. Lack of oxygen within tissue spheroids hinders metabolism of cells and eventually leads to cell death. Prevention of necrosis is crucial to success of tissue engineering methods and such prevention requires estimation of cell viability in the spheroid. We propose a novel approach for numerical modeling of diffusion in tissue spheroids during their fusion. The approach is based on numerical solutions of partial differential equations and the application of Function Representation (FRep) framework for geometric modeling. We present modeling of oxygen diffusion based on meshes derived from the geometry of fusing spheroids, a method for selecting optimal spheroid size, and several statistics for estimating cellular viability. Our findings provide insights into oxygen diffusion in three-dimensional cell cultures thus improving the robustness of biotechnological methods that employ tissue spheroids.

Neutrophil-induced pyroptosis promotes survival in patients with hepatoblastoma

BACKGROUND

Hepatoblastoma (HB) is the predominant hepatic malignancy among children. Despite therapeutic options for HB were gradually refined in recent years, patients with metastasis suffer from an unsatisfactory prognosis. Pyroptosis is a type of programmed and inflammatory necrosis. Neutrophils are crucial in innate immunity, which were shown to be associated with tumor progression. Our study strived to unravel the relationship between neutrophil-induced pyroptosis (NIP) and HB.

METHODS

The clinical and bulk RNA sequencing data of 38 patients with HB were obtained from Shanghai Children's Medical Center. We established NIP score based on the LASSO regression. The single-cell RNA sequencing data (GSE186975) were used for for key genes identification, cellular communication, and differentiation trajectories of neutrophils. KEGG, GO, GSVA, and ssGSEA enrichment were used to analyze biological functions, including neutrophil extracellular traps (NETs), NOD-like receptors pathway, neutrophil activation, neutrophil-mediated cytotoxicity, and others.

RESULTS

We constructed a NIP score based on the expression of three genes related to neutrophil and pyroptosis, namely ELANE, CASP1, and NOD2, which was positively correlated with a favorable prognosis of HB. Moreover, we clarified the function of ELANE in HB microenvironmwnt. Immunohistochemistry and transcriptome analysis unraveled a significant correlation between NETs and pyroptosis in HB, suggesting the key role of NETs-related neutrophils in inducing pyroptosis and prolonging survival. We also found upregulated tumor-promoting and immunosuppression-related pathways in the HB microenvironment. In addition, we clarified the growth trajectories and phenotypic changes of neutrophils in the immune microenvironment of HB, which can serve as potential targets for immunotherapy.

CONCLUSIONS

The novel NIP score for patients with HB shows high predictive value for survival. Moreover, we identified biological function, cellular communication, and growth trajectories of neutrophils in HB. Our findings broaden insights into the treatment of HB.

ACSL4 promotes the formation of the proliferative subtype in hepatoblastoma

Hepatoblastoma (HB) is the most common pediatric liver malignancy, with its significant heterogeneity complicating the identification of the most aggressive subtypes and the development of targeted therapies. In this study, we performed transcriptomic analysis of HB samples from the GEO database and identified three distinct molecular subtypes with varying prognostic outcomes. Among them, the proliferative subtype, characterized by enhanced proliferative capacity, poor prognosis, and an immunosuppressive tumor microenvironment, was particularly notable. ACSL4 emerged as a critical biomarker of this proliferative subtype, driving HB cell proliferation both in vitro and in vivo. Furthermore, pharmacological inhibition of ACSL4 using abemaciclib significantly suppressed tumor growth in xenograft models. Mechanistically, ACSL4 was found to promote cell proliferation by downregulating the interferon response signaling pathway which may implicate contribution to immunosuppression in the tumor. These findings underscore the pivotal role of ACSL4 in HB progression and highlight its potential as a therapeutic target for aggressive HB subtypes.

Multiomic analysis uncovers a continuous spectrum of differentiation and Wnt-MDK-driven immune evasion in hepatoblastoma

BACKGROUND & AIMS

Hepatoblastoma is the most common pediatric cancer of the liver, with the majority of cases displaying activating mutations in the Wnt/β-catenin pathway. Understanding the complex milieu of the tumor microenvironment has resulted in promising new therapies for adult cancers, but similar approaches in pediatric cancers are still lacking. We aimed to provide a comprehensive analysis of the tumor microenvironment of hepatoblastoma, unveiling its spatial architecture and key signaling mechanisms.

METHODS

Single-cell/-nucleus RNA-sequencing (RNA-seq) (n = 15), spatial transcriptomics (n = 22), and multiplex immunofluorescence stainings (n = 7) of treated, untreated, and metastasized pediatric hepatoblastomas were performed. An RNA-seq validation cohort (n = 110) including hepatoblastoma, non-tumor and fetal liver samples and single-cell RNA-seq data of healthy immune cells were used for further analysis. Western blotting and RNA-seq of hepatoblastoma and macrophage cell lines were conducted for experimental validation.

RESULTS

Of four identified transcriptional tumor programs, "Developmental" and "Metabolic" reflected different hepatic differentiation stages, while "Cycling" was enriched in undifferentiated cells and relapsed samples, and "Intermediate" displayed high activity in samples from patients with poor outcomes. We discovered an increased ratio of anti-to pro-inflammatory immune cells and evidence of immune exclusion from tumor areas. Wnt-responsive upregulation of the immunomodulator midkine in hepatoblastoma cells was associated with a change in macrophage phenotype, which could be partially reversed through midkine inhibition.

CONCLUSIONS

Hepatoblastoma cells exist along a continuous spectrum of hepatic differentiation and inhabit an altered immune environment. Wnt signaling augments midkine expression, which appears to be involved in shaping the immune environment by modifying macrophages to enable immune evasion, thereby providing a potential therapeutic target.

IMPACT AND IMPLICATIONS

Despite hepatoblastoma being the most common pediatric liver cancer, there has been a critical knowledge gap in understanding how the tumor microenvironment and immune landscape contribute to disease progression. Our novel findings, revealing a continuous spectrum of tumor differentiation states and Wnt-MDK-driven immune evasion, are significant for pediatric oncology clinicians and researchers, improving our functional understanding of the immune environment of hepatoblastoma. The identification of midkine as a tumor-specific immunomodulator suggests a potential for developing new targeted therapies, though further mechanistic and practical validation would be needed to realize clinical translation of these findings.

A patient-derived HCC spheroid system to model the tumor microenvironment and treatment response

Background & Aims

Hepatocellular carcinoma (HCC) is the third-leading and fastest rising cause of cancer-related death worldwide. The discovery and preclinical development of compounds targeting HCC are hampered by the absence of authentic tractable systems recapitulating the heterogeneity of HCC tumors in patients and the tumor microenvironment (TME).

Methods

We established a novel and simple patient-derived multicellular tumor spheroid model based on clinical HCC tumor tissues, processed using enzymatic and mechanical dissociation. After quality controls, 22 HCC tissues and 17 HCC sera were selected for tumor spheroid generation and perturbation studies. Cells were grown in 3D in optimized medium in the presence of patient serum. Characterization of the tumor spheroid cell populations was performed by flow cytometry, immunohistochemistry (IHC), and functional assays. As a proof of concept, we treated patient-derived spheroids with FDA-approved anti-HCC compounds.

Results

The model was successfully established independently from cancer etiology and grade from 22 HCC tissues. The use of serum from patients with HCC was essential for tumor spheroid generation, TME function, and maintenance of cell viability. The tumor spheroids comprised the main cell compartments, including epithelial cancer cells, as well as all major cell populations of the TME [i.e. cancer-associated fibroblasts (CAFs), macrophages, T cells, and endothelial cells]. Tumor spheroids reflected HCC heterogeneity, including variability in cell type proportions and TME, and mimicked the original tumor features. Moreover, differential responses to FDA-approved anti-HCC drugs were observed between the donors, as observed in patients.

Conclusions

This patient HCC serum-tumor spheroid model provides novel opportunities for drug discovery and development as well as mechanism-of-action studies including compounds targeting the TME. This model will likely contribute to improve the therapeutic outcomes for patients with HCC.

Impact and implications

HCC is a leading and fast-rising cause of cancer-related death worldwide. Despite approval of novel therapies, the outcome of advanced HCC remains unsatisfactory. By developing a novel patient-derived tumor spheroid model recapitulating tumor heterogeneity and microenvironment, we provide new opportunities for HCC drug development and analysis of mechanism of action in authentic patient tissues. The application of the patient-derived tumor spheroids combined with other HCC models will likely contribute to drug development and to improve the outcome of patients with HCC.

AAV capsid prioritization in normal and steatotic human livers maintained by machine perfusion

Therapeutic efficacy and safety of adeno-associated virus (AAV) liver gene therapy depend on capsid choice. To predict AAV capsid performance under near-clinical conditions, we established side-by-side comparison at single-cell resolution in human livers maintained by normothermic machine perfusion. AAV-LK03 transduced hepatocytes much more efficiently and specifically than AAV5, AAV8 and AAV6, which are most commonly used clinically, and AAV-NP59, which is better at transducing human hepatocytes engrafted in immune-deficient mice. AAV-LK03 preferentially transduced periportal hepatocytes in normal liver, whereas AAV5 targeted pericentral hepatocytes in steatotic liver. AAV5 and AAV8 transduced liver sinusoidal endothelial cells as efficiently as hepatocytes. AAV capsid and steatosis influenced vector episome formation, which determines gene therapy durability, with AAV5 delaying concatemerization. Our findings inform capsid choice in clinical AAV liver gene therapy, including consideration of disease-relevant hepatocyte zonation and effects of steatosis, and facilitate the development of AAV capsids that transduce hepatocytes or other therapeutically relevant cell types in the human liver with maximum efficiency and specificity.

Asynchronous Transitions from Hepatoblastoma to Carcinoma in High-Risk Pediatric Tumors

Most malignant hepatocellular tumors in children are classified as either hepatoblastoma (HB) or hepatocellular carcinoma (HCC), but some tumors demonstrate features of both HB and HCC1-3. These tumors have been recognized under a provisional diagnostic category by the World Health Organization and are distinguished from HB and HCC by a combination of histological, immunohistochemical, and molecular features4-6. Their outcomes and cellular composition remain an open question7-9. The heterogeneous histological and molecular profiles of hepatoblastomas with carcinoma features (HBCs)4 may result from cells with combined HB and HCC characteristics (HBC cells) or from mixtures of cells displaying either HB or HCC signatures. We used multiomics profiling to show that HBCs are mixtures of HB, HBC, and HCC cell types. HBC cells are more chemoresistant than HB cells, and their chemoresistance-a driver of poor outcomes10-12-is determined by their cell types, genetic alterations, and embryonic differentiation stages. We showed that the prognosis of HBCs is significantly worse than that of HBs. We also showed that HBC cells are derived from HB cells at early hepatoblast differentiation stages, that aberrant activation of WNT-signaling initiates HBC transformation, and that WNT inhibition promotes differentiation and increases sensitivity to chemotherapy. Furthermore, our analysis revealed that each HBC is the product of multiple HB-to-HBC and HBC-to-HCC transitions. Thus, multiomics profiling of HBCs provided key insights into their biology and resolved major questions regarding the etiology of these childhood liver tumors.

A developmental biliary lineage program cooperates with Wnt activation to promote cell proliferation in hepatoblastoma

Cancers evolve not only through the acquisition and clonal transmission of somatic mutations but also by epigenetic mechanisms that modify cell phenotype. Here, we use histology-guided and spatial transcriptomics to characterize hepatoblastoma, a childhood liver cancer that exhibits significant histologic and proliferative heterogeneity despite clonal activating mutations in the Wnt/β-catenin pathway. Highly proliferative regions with embryonal histology show high expression of Wnt target genes, the embryonic biliary transcription factor SOX4, and striking focal expression of the growth factor FGF19. In patient-derived tumoroids with constitutive Wnt activation, FGF19 is a required growth signal for FGF19-negative cells. Indeed, some tumoroids contain subsets of cells that endogenously express FGF19, downstream of Wnt/β-catenin and SOX4. Thus, the embryonic biliary lineage program cooperates with stabilized nuclear β-catenin, inducing FGF19 as a paracrine growth signal that promotes tumor cell proliferation, together with active Wnt signaling. In this pediatric cancer presumed to originate from a multipotent hepatobiliary progenitor, lineage-driven heterogeneity results in a functional growth advantage, a non-genetic mechanism whereby developmental lineage programs influence tumor evolution.

Divergent WNT signaling and drug sensitivity profiles within hepatoblastoma tumors and organoids

Hepatoblastoma, the most prevalent pediatric liver cancer, almost always carries a WNT-activating CTNNB1 mutation, yet exhibits notable molecular heterogeneity. To characterize this heterogeneity and identify novel targeted therapies, we perform comprehensive analysis of hepatoblastomas and tumor-derived organoids using single-cell RNA-seq/ATAC-seq, spatial transcriptomics, and high-throughput drug profiling. We identify two distinct tumor epithelial signatures: hepatic 'fetal' and WNT-high 'embryonal', displaying divergent WNT signaling patterns. The fetal group is enriched for liver-specific WNT targets, while the embryonal group is enriched in canonical WNT target genes. Gene regulatory network analysis reveals enrichment of regulons related to hepatic functions such as bile acid, lipid and xenobiotic metabolism in the fetal subtype but not in the embryonal subtype. In addition, the dichotomous expression pattern of the transcription factors HNF4A and LEF1 allows for a clear distinction between the fetal and embryonal tumor cells. We also perform high-throughput drug screening using patient-derived tumor organoids and identify sensitivity to HDAC inhibitors. Intriguingly, embryonal and fetal tumor organoids are sensitive to FGFR and EGFR inhibitors, respectively, indicating a dependency on EGF/FGF signaling in hepatoblastoma tumorigenesis. In summary, our data uncover the molecular and drug sensitivity landscapes of hepatoblastoma and pave the way for the development of targeted therapies.

Gamma-butyrobetaine hydroxylase (BBOX1) exerts suppressive effects on HepG2 hepatoblastoma cells

Gamma-butyrobetaine hydroxylase (BBOX1) plays a pivotal role in catalyzing the final stage of L-carnitine biosynthesis. Recently, increasing number of studies have reported that BBOX1 is weakly expressed in tumor cells and exhibits antitumor activity. The role of BBOX1 in Hepatoblastoma (HB) has yet to be determined. To substantiate this, we have investigated BBOX1 expression and its clinical relevance in HB, and explored how BBOX1 might inhibit the occurrence and development of HB. The GSE104766 and GSE131329 datasets were used to screen for the core gene BBOX1 in HB and to analyze differences in expression between hepatoblastoma and normal tissues. Based on the clinicopathological features of the GSE131329 dataset, the connections between the expression of BBOX1 and the clinicopathological feature of HB patients were determined. After BBOX1 was overexpressed, CCK-8 and colony formation assays were employed to assess cell proliferation and wound healing experiments were utilized to assess cell migration. The presence of cell apoptosis, cell cycle changes, and reactive oxygen species (ROS) was assayed using flow cytometry. Compared with normal tissues, the expression of BBOX1 in hepatoblastoma tissues was notably decreased. Dysregulated expression of BBOX1 was indicated as a prognostic risk factor closely linked to clinical stag of patients with HB. Furthermore, following BBOX1 overexpression, cell proliferation and migration are decreased, the cell cycle is arrested, and ROS are attenuated. BBOX1 has suppressive effects on HepG2 cells, potentially through its ability to hinder cancer cell proliferation, arrest cell cycle progression, and decrease ROS levels, suggesting its potential as a novel prognostic biomarker and therapeutic candidate for hepatoblastoma.

Multiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in the microenvironment

Mapping the spatial interactions of cancer, immune, and stromal cell states presents novel opportunities for patient stratification and for advancing immunotherapy. While single-cell studies revealed significant molecular heterogeneity in prostate cancer cells, the impact of spatial stromal cell heterogeneity remains poorly understood. Here, we used cyclic immunofluorescent imaging on whole-tissue sections to uncover novel spatial associations between cancer and stromal cells in low- and high-grade prostate tumors and tumor-adjacent normal tissues. Our results provide a spatial map of single cells and recurrent cellular neighborhoods in the prostate tumor microenvironment of treatment-naive patients. We report unique populations of mast cells that show distinct spatial associations with M2 macrophages and regulatory T cells. Our results show disease-specific neighborhoods that are primarily driven by androgen receptor-positive (AR+) stromal cells and identify inflammatory gene networks active in AR+ prostate stroma.

Androgen receptor post-translational modifications and their implications for pathology

A major mechanism to modulate the biological activities of the androgen receptor (AR) involves a growing number of post-translational modifications (PTMs). In this review we summarise the current knowledge on the structural and functional impact of PTMs that affect this major transcription factor. Next, we discuss the cross-talk between these different PTMs and the presence of clusters of modified residues in the AR protein. Finally, we discuss the implications of these covalent modifications for the aetiology of diseases such as spinal and bulbar muscular atrophy (Kennedy's disease) and prostate cancer, and the perspectives for pharmacological intervention.

Digital medicine and minimally invasive surgery in pediatric hepatoblastoma: An update

Hepatoblastoma (HB) is the most common liver malignancy in children, accounting for approximately 60 % of liver tumors in this population. However, the exact cause of HB remains unclear. The combination of surgery and neoadjuvant chemotherapy has significantly improved the overall survival rate of children with HB, increasing it from 40 % in the past to over 70 %. The concept of precise hepatectomy, which aims to achieve the best rehabilitation outcomes with minimal trauma and maximum liver protection, has been widely accepted by hepatobiliary surgeons. This article provides a comprehensive review of the recent advancements in surgical treatment of HB, focusing on digital surgery and minimally invasive techniques.

Predicting response of hepatoblastoma primary lesions to neoadjuvant chemotherapy through contrast-enhanced computed tomography radiomics

OBJECTIVE

To investigate the clinical value of contrast-enhanced computed tomography (CECT) radiomics for predicting the response of primary lesions to neoadjuvant chemotherapy in hepatoblastoma.

METHODS

Clinical and CECT imaging data were retrospectively collected from 116 children with hepatoblastoma who received neoadjuvant chemotherapy. Tumor response was assessed according to the Response Evaluation Criteria in Solid Tumors (RECIST). Subsequently, they were randomly stratified into a training cohort and a test cohort in a 7:3 ratio. The clinical model was constructed using univariate and multivariate logistic regression, while the radiomics model was developed based on selected radiomics features employing the support vector machine algorithm. The combined clinical-radiomics model incorporated both clinical and radiomics features.

RESULTS

The area under the curve (AUC) for the clinical, radiomics, and combined models was 0.704 (95% CI: 0.563-0.845), 0.830 (95% CI: 0.704-0.959), and 0.874 (95% CI: 0.768-0.981) in the training cohort, respectively. In the validation cohort, the combined model achieved the highest mean AUC of 0.830 (95% CI 0.616-0.999), with a sensitivity, specificity, accuracy, precision, and f1 score of 72.0%, 81.1%, 78.5%, 57.2%, and 63.5%, respectively.

CONCLUSION

CECT radiomics has the potential to predict primary lesion response to neoadjuvant chemotherapy in hepatoblastoma.

First Transcriptome Analysis of Hepatoblastoma in Brazil: Unraveling the Pivotal Role of Noncoding RNAs and Metabolic Pathways

Hepatoblastoma stands as the most prevalent liver cancer in the pediatric population. Characterized by a low mutational burden, chromosomal and epigenetic alterations are key drivers of its tumorigenesis. Transcriptome analysis is a powerful tool for unraveling the molecular intricacies of hepatoblastoma, shedding light on the effects of genetic and epigenetic changes on gene expression. In this study conducted in Brazilian patients, an in-depth whole transcriptome analysis was performed on 14 primary hepatoblastomas, compared to control liver tissues. The analysis unveiled 1,492 differentially expressed genes (1,031 upregulated and 461 downregulated), including 920 protein-coding genes (62%). Upregulated biological processes were linked to cell differentiation, signaling, morphogenesis, and development, involving known hepatoblastoma-associated genes (DLK1, MEG3, HDAC2, TET1, HMGA2, DKK1, DKK4), alongside with novel findings (GYNG4, CDH3, and TNFRSF19). Downregulated processes predominantly centered around oxidation and metabolism, affecting amines, nicotinamides, and lipids, featuring novel discoveries like the repression of SYT7, TTC36, THRSP, CCND1, GCK and CAMK2B. Two genes, which displayed a concordant pattern of DNA methylation alteration in their promoter regions and dysregulation in the transcriptome, were further validated by RT-qPCR: the upregulated TNFRSF19, a key gene in the embryonic development, and the repressed THRSP, connected to lipid metabolism. Furthermore, based on protein-protein interaction analysis, we identified genes holding central positions in the network, such as HDAC2, CCND1, GCK, and CAMK2B, among others, that emerged as prime candidates warranting functional validation in future studies. Notably, a significant dysregulation of non-coding RNAs (ncRNAs), predominantly upregulated transcripts, was observed, with 42% of the top 50 highly expressed genes being ncRNAs. An integrative miRNA-mRNA analysis revealed crucial biological processes associated with metabolism, oxidation reactions of lipids and carbohydrates, and methylation-dependent chromatin silencing. In particular, four upregulated miRNAs (miR-186, miR-214, miR-377, and miR-494) played a pivotal role in the network, potentially targeting multiple protein-coding transcripts, including CCND1 and CAMK2B. In summary, our transcriptome analysis highlighted disrupted embryonic development as well as metabolic pathways, particularly those involving lipids, emphasizing the emerging role of ncRNAs as epigenetic regulators in hepatoblastomas. These findings provide insights into the complexity of the hepatoblastoma transcriptome and identify potential targets for future therapeutic interventions.

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

Hepatoblastomas (HB) display heterogeneous cellular phenotypes that influence the clinical outcome, but the underlying mechanisms are poorly understood. Here, we use a single-cell multiomic strategy to unravel the molecular determinants of this plasticity. We identify a continuum of HB cell states between hepatocytic (scH), liver progenitor (scLP) and mesenchymal (scM) differentiation poles, with an intermediate scH/LP population bordering scLP and scH areas in spatial transcriptomics. Chromatin accessibility landscapes reveal the gene regulatory networks of each differentiation pole, and the sequence of transcription factor activations underlying cell state transitions. Single-cell mapping of somatic alterations reveals the clonal architecture of each tumor, showing that each genetic subclone displays its own range of cellular plasticity across differentiation states. The most scLP subclones, overexpressing stem cell and DNA repair genes, proliferate faster after neo-adjuvant chemotherapy. These results highlight how the interplay of clonal evolution and epigenetic plasticity shapes the potential of HB subclones to respond to chemotherapy.

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

BACKGROUND

Hepatoblastoma is the most frequent pediatric liver cancer. The current treatments lead to 80% of survival rate at 5 years. In this study, we evaluated the clinical relevance of molecular features to identify patients at risk of chemoresistance, relapse and death of disease.

METHODS

All the clinical data of 86 children with hepatoblastoma were retrospectively collected. Pathological slides were reviewed, tumor DNA sequencing (by whole exome, whole genome or target) and transcriptomic profiling with RNAseq or 300-genes panel were performed. Associations between the clinical, pathological, mutational and transcriptomic data were investigated.

RESULTS

High-risk patients represented 44% of our series and the median age at diagnosis was 21.9 months (range: 0-208). Alterations of the WNT/ß-catenin pathway and of the 11p15.5 imprinted locus were identified in 98% and 74% of the tumors, respectively. Other cancer driver genes mutations were only found in less than 11% of tumors. After neoadjuvant chemotherapy, disease-specific survival and poor response to neoadjuvant chemotherapy were associated with 'Liver Progenitor' (p = 0.00049, p < 0.0001) and 'Immune Cold' (p = 0.0011, p < 0.0001) transcriptomic tumor subtypes, SBS35 cisplatin mutational signature (p = 0.018, p = 0.001), mutations in rare cancer driver genes (p = 0.0039, p = 0.0017) and embryonal predominant histological type (p = 0.0013, p = 0.0077), respectively. Integration of the clinical and molecular features revealed a cluster of molecular markers associated with resistance to chemotherapy and survival, enlightening transcriptomic 'Immune Cold' and Liver Progenitor' as a predictor of survival independent of the clinical features.

CONCLUSIONS

Response to neoadjuvant chemotherapy and survival in children treated for hepatoblastoma are associated with genomic and pathological features independently of the clinical features.

The expression analysis of SerpinB9 in hepatoblastoma microenvironment

PURPOSE

In this research, we analyzed the expression of serpinB9 in hepatoblastoma and investigated the factors which enhance its expression.

METHOD

SerpinB9 expression in hepatoblastoma cell lines and macrophages co-cultured with each other or stimulated by anticancer agents was examined using RT-qPCR and western blotting. Immunohistochemistry for SerpinB9 in hepatoblastoma specimens was performed. Single-cell RNA-sequence data for hepatoblastoma from an online database were analyzed to investigate which types of cells express SerpinB9.

RESULT

HepG2, a hepatoblastoma cell line, exhibited increased expression of SerpinB9 when indirectly co-cultured with macrophages. Immunohistochemistry for the specimens demonstrated that serpinB9 is positive not in hepatoblastoma cells but in macrophages. Single-cell RNA sequence analysis in tissues from hepatoblastoma patients showed that macrophages expressed SerpinB9 more than tumor cells did. Co-culture of macrophages with hepatoblastoma cell lines led to the enhanced expression of SerpinB9 in both macrophages and cell lines. Anticancer agents induced an elevation of SerpinB9 in hepatoblastomas cell lines.

CONCLUSION

In hepatoblastoma, SerpinB9 is thought to be more highly expressed in macrophages and enhanced by interaction with hepatoblastoma cell.

EZH2 is a key component of hepatoblastoma tumor cell growth

BACKGROUND

Enhancer of zeste homolog 2 (EZH2) catalyzes the trimethylation of histone H3 at lysine 27 via the polycomb recessive complex 2 (PRC2) and plays a time-specific role in normal fetal liver development. EZH2 is overexpressed in hepatoblastoma (HB), an embryonal tumor. EZH2 can also promote tumorigenesis via a noncanonical, PRC2-independent mechanism via proto-oncogenic, direct protein interaction, including β-catenin. We hypothesize that the pathological activation of EZH2 contributes to HB propagation in a PRC2-independent manner.

METHODS AND RESULTS

We demonstrate that EZH2 promotes proliferation in HB tumor-derived cell lines through interaction with β-catenin. Although aberrant EZH2 expression occurs, we determine that both canonical and noncanonical EZH2 signaling occurs based on specific gene-expression patterns and interaction with SUZ12, a PRC2 component, and β-catenin. Silencing and inhibition of EZH2 reduce primary HB cell proliferation.

CONCLUSIONS

EZH2 overexpression promotes HB cell proliferation, with both canonical and noncanonical function detected. However, because EZH2 directly interacts with β-catenin in human tumors and EZH2 overexpression is not equal to SUZ12, it seems that a noncanonical mechanism is contributing to HB pathogenesis. Further mechanistic studies are necessary to elucidate potential pathogenic downstream mechanisms and translational potential of EZH2 inhibitors for the treatment of HB.

An Integrative Bioorthogonal Nanoengineering Strategy for Dynamically Constructing Heterogenous Tumor Spheroids

Although tumor models have revolutionized perspectives on cancer aetiology and treatment, current cell culture methods remain challenges in constructing organotypic tumor with in vivo-like complexity, especially native characteristics, leading to unpredictable results for in vivo responses. Herein, the bioorthogonal nanoengineering strategy (BONE) for building photothermal dynamic tumor spheroids is developed. In this process, biosynthetic machinery incorporated bioorthogonal azide reporters into cell surface glycoconjugates, followed by reacting with multivalent click ligand (ClickRod) that is composed of hyaluronic acid-functionalized gold nanorod carrying dibenzocyclooctyne moieties, resulting in rapid construction of tumor spheroids. BONE can effectively assemble different cancer cells and immune cells together to construct heterogenous tumor spheroids is identified. Particularly, ClickRod exhibited favorable photothermal activity, which precisely promoted cell activity and shaped physiological microenvironment, leading to formation of dynamic features of original tumor, such as heterogeneous cell population and pluripotency, different maturation levels, and physiological gradients. Importantly, BONE not only offered a promising platform for investigating tumorigenesis and therapeutic response, but also improved establishment of subcutaneous xenograft model under mild photo-stimulation, thereby significantly advancing cancer research. Therefore, the first bioorthogonal nanoengineering strategy for developing dynamic tumor models, which have the potential for bridging gaps between in vitro and in vivo research is presented.

Erythroid Cells as Full Participants in the Tumor Microenvironment

The tumor microenvironment is an important factor that can determine the success or failure of antitumor therapy. Cells of hematopoietic origin are one of the most important mediators of the tumor-host interaction and, depending on the cell type and functional state, exert pro- or antitumor effects in the tumor microenvironment or in adjacent tissues. Erythroid cells can be full members of the tumor microenvironment and exhibit immunoregulatory properties. Tumor growth is accompanied by the need to obtain growth factors and oxygen, which stimulates the appearance of the foci of extramedullary erythropoiesis. Tumor cells create conditions to maintain the long-term proliferation and viability of erythroid cells. In turn, tumor erythroid cells have a number of mechanisms to suppress the antitumor immune response. This review considers current data on the existence of erythroid cells in the tumor microenvironment, formation of angiogenic clusters, and creation of optimal conditions for tumor growth. Despite being the most important life-support function of the body, erythroid cells support tumor growth and do not work against it. The study of various signaling mechanisms linking tumor growth with the mobilization of erythroid cells and the phenotypic and functional differences between erythroid cells of different origin allows us to identify potential targets for immunotherapy.

Potential involvement of IL-32 in cell-to-cell communication between macrophages and hepatoblastoma

PURPOSE

This study investigated the expression of interleukin 32 (IL-32) in hepatoblastoma, the most common primary pediatric liver tumor, and its possible roles in tumorigenesis.

METHODS

IL-32 expression was investigated in two hepatoblastoma cell lines (Hep G2 and HuH 6) in the steady state and after co-culture with macrophages by RNA-seq analysis and RT-qPCR, and after stimulation with chemotherapy. Cultured macrophages were stimulated by IL-32 isoforms followed by RT-qPCR and western blot analysis. IL-32 immunohistochemical staining (IHC) was performed using specimens from 21 hepatoblastoma patients. Clustering analysis was also performed using scRNA-seq data downloaded from Gene Expression Omnibus.

RESULTS

The IL-32 gene is expressed by hepatoblastoma cell lines; expression is upregulated by paracrine cell-cell communication with macrophages, also by carboplatin and etoposide. IL-32 causes protumor activation of macrophages with upregulation of PD-L1, IDO-1, IL-6, and IL-10. In the patient pool, IHC was positive only in 48% of cases. However, in the downloaded dataset, IL-32 gene expression was negative.

CONCLUSION

IL-32 was detected in hepatoblastoma cell lines, but not in all hepatoblastoma patients. We hypothesized that stimulation such as chemotherapy might induce expression of IL-32, which might be a critical mediator of chemoresistance in hepatoblastoma through inducing protumor activation in macrophages.

Advances in single-cell RNA sequencing and its applications in cancer research

Cancers are a group of heterogeneous diseases characterized by the acquisition of functional capabilities during the transition from a normal to a neoplastic state. Powerful experimental and computational tools can be applied to elucidate the mechanisms of occurrence, progression, metastasis, and drug resistance; however, challenges remain. Bulk RNA sequencing techniques only reflect the average gene expression in a sample, making it difficult to understand tumor heterogeneity and the tumor microenvironment. The emergence and development of single-cell RNA sequencing (scRNA-seq) technologies have provided opportunities to understand subtle changes in tumor biology by identifying distinct cell subpopulations, dissecting the tumor microenvironment, and characterizing cellular genomic mutations. Recently, scRNA-seq technology has been increasingly used in cancer studies to explore tumor heterogeneity and the tumor microenvironment, which has increased the understanding of tumorigenesis and evolution. This review summarizes the basic processes and development of scRNA-seq technologies and their increasing applications in cancer research and clinical practice.

Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma

A lack of relevant genetic models and cell lines hampers our understanding of hepatoblastoma pathogenesis and the development of new therapies for this neoplasm. Here, we report an improved MYC-driven hepatoblastoma-like murine model that recapitulates the pathological features of embryonal type of hepatoblastoma, with transcriptomics resembling the high-risk gene signatures of the human disease. Single-cell RNA-sequencing and spatial transcriptomics identify distinct subpopulations of hepatoblastoma cells. After deriving cell lines from the mouse model, we map cancer dependency genes using CRISPR-Cas9 screening and identify druggable targets shared with human hepatoblastoma (e.g., CDK7, CDK9, PRMT1, PRMT5). Our screen also reveals oncogenes and tumor suppressor genes in hepatoblastoma that engage multiple, druggable cancer signaling pathways. Chemotherapy is critical for human hepatoblastoma treatment. A genetic mapping of doxorubicin response by CRISPR-Cas9 screening identifies modifiers whose loss-of-function synergizes with (e.g., PRKDC) or antagonizes (e.g., apoptosis genes) the effect of chemotherapy. The combination of PRKDC inhibition and doxorubicin-based chemotherapy greatly enhances therapeutic efficacy. These studies provide a set of resources including disease models suitable for identifying and validating potential therapeutic targets in human high-risk hepatoblastoma.

Intratumoral erythroblastic islands restrain anti-tumor immunity in hepatoblastoma

Erythroblastic islands (EBIs) are the specialized structures for erythropoiesis, but they have never been found functional in tumors. As the most common pediatric liver malignancy, hepatoblastoma (HB) requires more effective and safer therapies to prevent progression and the lifelong impact of complications on young children. However, developing such therapies is impeded by a lack of comprehensive understanding of the tumor microenvironment. By single-cell RNA sequencing of 13 treatment-naive HB patients, we discover an immune landscape characterized by aberrant accumulation of EBIs, formed by VCAM1⁺ macrophages and erythroid cells, which is inversely correlated with survival of HB. Erythroid cells inhibit the function of dendritic cells (DCs) via the LGALS9/TIM3 axis, leading to impaired anti-tumor T cell immune responses. Encouragingly, TIM3 blockades relieve the inhibitory effect of erythroid cells on DCs. Our study provides an immune evasion mechanism mediated by intratumoral EBIs and proposes TIM3 as a promising therapeutic target for HB.