Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

Emerging importance of m6A modification in liver cancer and its potential therapeutic role

Liver cancer refers to malignant tumors that form in the liver and is usually divided into several types, the most common of which is hepatocellular carcinoma (HCC), which originates in liver cells. Other rare types of liver cancer include intrahepatic cholangiocarcinoma (iCCA). m6A modification is a chemical modification of RNA that usually manifests as the addition of a methyl group to adenine in the RNA molecule to form N6-methyladenosine. This modification exerts a critical role in various biological processes by regulating the metabolism of RNA, affecting gene expression. Recent studies have shown that m6A modification is closely related to the occurrence and development of liver cancer, and m6A regulators can further participate in the pathogenesis of liver cancer by regulating the expression of key genes and the function of specific cells. In this review, we provided an overview of the latest advances in m6A modification in liver cancer research and explored in detail the specific functions of different m6A regulators. Meanwhile, we deeply analyzed the mechanisms and roles of m6A modification in liver cancer, aiming to provide novel insights and references for the search for potential therapeutic targets. Finally, we discussed the prospects and challenges of targeting m6A regulators in liver cancer therapy.

Genetic re-classification of combined hepatocellular-cholangiocarcinoma and small duct type intrahepatic cholangiocarcinoma

BACKGROUND

Combined hepatocellular-cholangiocarcinoma (cHCC-CCA) shares various features with small duct type intrahepatic cholangiocarcinoma (SmD-iCCA) and sometimes histological diagnosis may be difficult.

METHODS

We examined genetic alterations such as hTERT promoter (hTERT), p53, and fibroblast growth factor receptor 2 (FGFR2) in 103 PLCs diagnosed as cHCC-CCA or SmD-iCCA. A cluster analysis was performed on the R software for re-classification of PLCs including cHCC-CCA and SmD-iCCA.

RESULTS

The primary liver carcinomas (PLCs) were divided into 5 clusters; 19 tumors (18 %) in Cluster-1 (with alterations in hTERT and/or p53), 24 (23 %) in Cluster-2 (FGFR2 and/or p53), 13 (13 %) in Cluster-3 (IDH2 or null), 19 (18 %) in Cluster-4 (MTAP and/or FGFR2), 28 (27 %) in Cluster-5 (ARID1A and/or PBRM1), being based on genetic alterations. Cluster-1 and Clusters-2 to- 5 formed distinct 2 groups. Cluster-1 was characterized by significantly bigger size, rich and higher histological grade of HCC component, significantly less cholangiolocellular carcinoma (CLC)-component, ductal plate malformation pattern and bile duct adenoma in the background livers. No SmD-iCCA was included in Cluster-1, whereas SmD-iCCA distributed evenly in Clusters 2-5. Cluster-4 was characterized by higher prevalence of hepatitis B and higher histological diversity scores.

CONCLUSION

PLCs diagnosed as cHCC-CCA or SmD-iCCAs could be divided into 5 clusters based on genetic alterations. Cluster-1 was HCC-like cluster characterized by hTERT alteration, rich and higher grade of HCC and bigger size. Clusters-2-5 may be iCCA-like clusters characterized by different genetic alterations. cHCC-CCA in Cluster-1 and Clusters-2-5 may be handled separately for further analysis and treatment.

Autophagy-related gene SQSTM1 predicts the prognosis of hepatocellular carcinoma

BACKGROUND

The relationship between autophagy and the progression of hepatocellular carcinoma (HCC) is notably substantial, yet the underlying mechanisms remain incompletely elucidated. Our objective is to construct a predictive model, thereby providing fresh insights into the diagnosis and treatment of HCC. Autophagy's role in HCC progression is recognized, but the exact mechanisms are still unclear. This study seeks to build a predictive model to offer new diagnostic and therapeutic insights for HCC. Through combining bioinformatics and experiments, we aim to clarify autophagy pathways' part in HCC and spot possible treatment targets, thus aiding future HCC research and treatment.

METHODS

We screened HCC-related prognostic differential genes from the TCGA dataset combined with GeneCards, constructed a prognostic risk model related to autophagy genes and verified it in the GEO dataset and ICGC dataset. We integrated machine learning with protein-protein interaction (PPI) network analysis to pinpoint core targets and performed independent prognostic assessments. Leveraging single-cell sequencing data of hepatocellular carcinoma (HCC) from published literature, we ascertained the cellular distribution of these core genes.We used drug sensitivity analysis to screen clinical drugs for core genes.

RESULTS

We established a prognostic model using 12 differential prognostic genes, which was validated in both the GEO data set and the ICGC data set, and was more effective than the 5 collected prognostic models. Machine learning combined with the PPI network screened the core gene SQSTM1, and It can be a key factor in prognosis. Single-cell analysis showed that it is significantly distributed in Tumor-associated macrophages (TAM) where SQSTM1 is concentrated. Additionally, drug susceptibility analysis showed that patients with HCC and high SQSTM1 expression are responsive to 17-AGG.

CONCLUSIONS

Our study proposed a new risk model for predicting HCC patients based on autophagy-related genes (ARGs). The model has good predictive performance and screened out a potential target for HCC patients, which can be used as an independent prognostic factor. SQSTM1 was significantly enriched in tumor-associated macrophages. We also screened drugs for the treatment of hepatocellular carcinoma.

Precision targeting of β-catenin induces tumor reprogramming and immunity in hepatocellular cancers

First-line immune checkpoint inhibitor (ICI) combinations show responses in subsets of hepatocellular carcinoma (HCC) patients. Nearly half of HCCs are Wnt-active with mutations in CTNNB1 (encoding for β-catenin), AXIN1/2, or APC, and demonstrate heterogeneous and limited benefit to ICI due to an immune excluded tumor microenvironment. We show significant tumor responses in multiple β-catenin-mutated immunocompetent HCC models to a novel siRNA encapsulated in lipid nanoparticle targeting CTNNB1 (LNP-CTNNB1). Both single-cell and spatial transcriptomics reveal cellular and zonal reprogramming, along with activation of immune regulatory transcription factors IRF2 and POU2F1, re-engaged type I/II interferon signaling, and alterations in both innate and adaptive immunity upon β-catenin suppression with LNP-CTNNB1 at early- and advanced-stage disease. Moreover, ICI enhances response to LNP-CTNNB1 in advanced-stage disease by preventing T cell exhaustion and through formation of lymphoid aggregates (LA). In fact, expression of an LA-like gene signature prognosticates survival for patients receiving atezolizumab plus bevacizumab in the IMbrave150 phase III trial and inversely correlates with CTNNB1-mutatational status in this patient cohort. In conclusion, LNP-CTNNB1 is efficacious as monotherapy and in combination with ICI in CTNNB1-mutated HCCs through impacting tumor cell-intrinsic signaling and remodeling global immune surveillance, providing rationale for clinical investigations.

Exploring the association between chemotherapy and prognosis among patients less than 50 years old with hepatocellular carcinoma: a retrospective cohort study based on the SEER database

BACKGROUND/AIM

Hepatic carcinoma, including hepatocellular carcinoma (HCC), is one of the most common malignant tumors globally, with an increasing incidence among younger populations. While chemotherapy is effective for advanced HCC, its impact on the prognosis of younger patients, who typically have better physiological conditions, remains unclear. Younger patients may have different tumor biology and chemotherapy responses than older patients. This study aims to evaluate the impact of chemotherapy on the prognosis and survival rates of younger HCC patients.

METHODS

A retrospective analysis was conducted using the Surveillance, Epidemiology, and End Results Program (SEER) database, which provides information on cancer statistics among the US population. We selected patients diagnosed with primary HCC between 2010 and 2015. The patients were divided into two groups based on whether they received chemotherapy or not. Kaplan-Meier analyses were utilised to evaluate the impact of chemotherapy on prognosis by comparing the overall survival (OS) and cancer-specific survival (CSS) between the two groups. After performing 1:1 propensity score matching (PSM), the differences in OS and CSS were reassessed.

RESULTS

Before PSM, there were 1662 participants with primary HCC. After PSM, the sample was reduced to 1154 participants, with 577 individuals in each chemotherapy and non-chemotherapy group. Before PSM, there was no statistically significant difference in OS and CSS between the chemotherapy and non-chemotherapy groups (P = 0.25 and P = 0.06). After PSM, although the survival time in the chemotherapy group was slightly extended, the difference remained statistically insignificant (P = 0.09 and P = 0.38). Kaplan-Meier curves indicated no significant difference between the chemotherapy and non-chemotherapy groups, both before and after PSM, further supporting the conclusion that chemotherapy did not significantly improve survival in young patients with HCC.

CONCLUSION

Chemotherapy did not significantly improve survival for young patients with HCC. Treatment decisions should be approached cautiously, especially in cases with complex tumor characteristics. Future studies should explore the mechanisms of chemotherapy in younger patients and develop personalized treatment strategies to improve long-term outcomes.

CYP4F11, an NRF2 Target Gene, Promotes Hepatocellular Carcinoma Cell Growth

Hepatocellular carcinoma (HCC), the most common form of primary liver cancer, is the third leading cause of cancer-related mortality globally. Current systemic therapies for HCC are limited and often exhibit unsatisfactory efficacy, underscoring the need for novel therapeutic approaches. Nuclear factor erythroid 2-related factor-2 (NRF2), a master transcription factor regulating cellular redox and metabolic homeostasis, is frequently overexpressed in HCC due to mutations in NFE2L2/NRF2 or its negative regulator Kelch-like ECH-associated protein 1 (KEAP1), contributing to tumor progression. In this study, we identify CYP4F11, a member of the Cytochrome P450 family, as a direct target gene of NRF2. CYP4F11, primarily expressed in the liver, is crucial in fatty acid oxidation and eicosanoid metabolism. We demonstrate that CYP4F11 expression is driven by NRF2 and is significantly elevated in HCC patients harboring NFE2L2 gain of function or KEAP1 loss of function mutations. Functionally, CYP4F11 promotes HCC cell growth, and reduced expression of CYP4F11 not only suppresses HCC cell proliferation but also enhances sorafenib-induced HCC cell death. Further, NRF2 inhibition sensitizes HCC to sorafenib through downregulation of CYP4F11. These findings position CYP4F11 as a novel contributor to HCC progression and highlight the potential of targeting the NRF2-CYP4F11 axis for HCC treatment.

Pathogenesis and Systemic Treatment of Hepatocellular Carcinoma: Current Status and Prospects

Hepatocellular carcinoma (HCC) remains one of the major threats to human health worldwide. The emergence of systemic therapeutic options has greatly improved the prognosis of patients with HCC, particularly those with advanced stages of the disease. In this review, we discussed the pathogenesis of HCC, genetic alterations associated with the development of HCC, and alterations in the tumor immune microenvironment. Then, important indicators and emerging technologies related to the diagnosis of HCC are summarized. Also, we reviewed the major advances in treatments for HCC, offering insights into future prospects for next-generation managements.

Keap1-independent Nrf2 regulation: A novel therapeutic target for treating kidney disease

The transcription factor NF-E2-related factor 2 (Nrf2) is a master regulator of antioxidant responses in mammals, where it plays a critical role in detoxification, maintaining cellular homeostasis, combating inflammation and fibrosis, and slowing disease progression. Kelch-like ECH-associated protein 1 (Keap1), an adaptor subunit of Cullin 3-based E3 ubiquitin ligase, serves as a critical sensor of oxidative and electrophilic stress, regulating Nrf2 activity by sequestering it in the cytoplasm, leading to its proteasomal degradation and transcriptional repression. However, the clinical potential of targeting the Keap1-dependent Nrf2 regulatory pathway has been limited. This is evidenced by early postnatal lethality in Keap1 knockout mice, as well as significant adverse events after pharmacological blockade of Keap1 in human patients with Alport syndrome as well as in those with type 2 diabetes mellitus and chronic kidney disease. The exact underlying mechanisms remain elusive, but may involve non-specific and systemic activation of the Nrf2 antioxidant response in both injured and normal tissues. Beyond Keap1-dependent regulation, Nrf2 activity is modulated by Keap1-independent mechanisms, including transcriptional, epigenetic, and post-translational modifications. In particular, GSK3β has emerged as a critical convergence point for these diverse signaling pathways. Unlike Keap1-dependent regulation, GSK3β-mediated Keap1-independent Nrf2 regulation does not affect basal Nrf2 activity but modulates its response at a delayed/late phase of cellular stress. This allows fine-tuning of the inducibility, magnitude, and duration of the Nrf2 response specifically in stressed or injured tissues. As one of the most metabolically active organs, the kidney is a major source of production of reactive oxygen and nitrogen species and also a vulnerable organ to oxidative damage. Targeting the GSK3β-mediated Nrf2 regulatory pathway represents a promising new approach for the treatment of kidney disease.

Molecular Testing and Targeted Therapies in Hepatobiliary Cancers: A Review

Importance

Hepatobiliary cancers are heterogeneous and molecularly complex. Recent advances in next-generation sequencing (NGS) have enhanced the understanding of their molecular landscape and enabled deployment of biomarker-based gene- and immune-targeted therapies. This review examines the role of molecular testing and targeted therapies in these malignant neoplasms.

Observations

Patients with hepatobiliary cancers have poor outcomes. Precision oncology studies have shown that while many common molecular alterations are not currently targetable in hepatocellular carcinoma (HCC), a large number of actionable alterations characterize biliary tract cancers (BTCs), with several therapies now approved by the US Food and Drug Administration. Immunotherapy is increasingly adopted in clinical practice, either as monotherapy or combined with cytotoxic chemotherapy, for both HCC and BTCs. Moreover, multiple solid cancer tumor-agnostic therapies are approved (larotrectinib, entrectinib, and repotrectinib for NTRK fusions; selpercatinib for RET fusions; dabrafenib and trametinib combination for BRAF V600E mutations; dostarlimab or pembrolizumab for tumors with high microsatellite instability and pembrolizumab for tumor mutation burden ≥10 mutations/megabase), highlighting the need for NGS as well as ERBB2 (formerly HER2) immunohistochemistry (IHC) (with the recent approval of solid tissue-agnostic deruxtecan trastuzumab for ERBB2-positive [IHC 3+] cancer) across cancers. N-of-1 clinical trials using customized drug combinations matched to the tumor's molecular profile have yielded encouraging results and provide a promising framework for future clinical trial design.

Conclusions and Relevance

Molecular testing and gene- and immune-targeted therapies are transforming hepatobiliary cancer treatment. Tumor-agnostic and N-of-1 clinical trials have challenged traditional clinical trial paradigms and provide the foundation for truly personalized oncology for patients with these aggressive cancers. Further work is needed to determine how to leverage these novel approaches into the management of operable disease.

Dysregulation of the SREBP pathway is associated with poor prognosis and serves as a potential biomarker for the diagnosis of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a severe disease associated with a poor prognosis. The role of aberrant lipid metabolism in the development and progression of HCC necessitates detailed characterization. Sterol regulatory element‑binding proteins (SREBPs), pivotal transcription factors governing lipogenesis, are central to this process. The present study aimed to assess the regulation of HCC by the SREBP signaling pathway, examining the expression levels of genes in this pathway, the clinical implications and its prognostic value using the Kaplan‑Meier method. Pearson's correlation coefficient was used to identify the co‑expression of SREBP pathway genes in HCC. Genomic analysis examined the frequency of TP53 mutations in groups with and without SREBP pathway alterations. In addition, small interfering RNAs targeting genes of the SREBP pathway were transfected into Huh‑7 and HCC‑LM3 cell lines. Subsequently, Cell Counting Kit‑8 and Transwell assays were carried out to evaluate the viability and invasion of these cells. Reverse transcription‑quantitative PCR and western blotting were performed to investigate the expression of TP53 in response to silencing of SREBP pathway genes. Dysregulation of SREBP pathway genes was detected in HCC tissues compared with in normal liver tissues, and predicted a poor prognosis. Silencing these genes reduced the viability and invasion of HCC cells. Furthermore, abnormal SREBP pathway gene expression was associated with poor survival rates, vascular invasion, advanced tumor stage and an increased incidence of TP53 mutations. By contrast, knockdown of SREBP pathway genes decreased mutant TP53 expression at both the mRNA and protein levels in HCC cells. The findings of the present study suggested that SREBP pathway genes could serve as promising prognostic biomarkers for HCC. The combined analysis of individual gene expression levels offers offer novel insights into the pathogenesis and progression of HCC.

Differences between hepatocellular carcinoma caused by alcohol and other aetiologies

Alcohol-related liver disease is the third leading cause of hepatocellular carcinoma worldwide and the leading cause in Europe. Additionally, the recent definition of metabolic dysfunction-associated steatotic liver disease with increased alcohol intake (MetALD) will enrich this population with a more nuanced phenotype, reflecting recent epidemiological trends. In these patients, the hepatocellular carcinoma diagnosis is often delayed and less frequently detected through screening programmes. Moreover, at the time of diagnosis, patients with alcohol-related hepatocellular carcinoma tend to have a poorer general condition, more severely impaired liver function, and a higher prevalence of comorbidities, leading to increased competitive mortality. However, when hepatocellular carcinoma is diagnosed during surveillance programmes in patients with alcohol-related liver disease or MetALD, the rate of allocation to first-line curative treatments is high (56%) and comparable to that of patients with virus-related hepatocellular carcinoma. As a consequence, the aetiology of the underlying cirrhosis cannot be considered an independent prognostic factor in patients with hepatocellular carcinoma. Instead, prognosis is driven by liver function, general condition, and tumour burden. This underscores the crucial role of early diagnosis through periodic surveillance in patients with alcohol- or MetALD-related cirrhosis.

Hepatic Expression of Fibroblast Growth Factor 19 Significantly Correlates With Serum Bile Acids in Neonatal Cholestasis

BACKGROUND

Bile acids in the ileum act as a feedback regulator of their own synthesis by inducing the release of ileal fibroblast growth factor 19 (FGF19), which inhibits the cholesterol-7-alpha hydroxylase enzyme. In cholestasis, this feedback mechanism is dysregulated. FGF19 is not expressed in the healthy liver. We aimed to assess the hepatic expression of FGF19 in neonatal cholestasis (NC) and its relation to serum bile acids.

METHODS

The study included 41 patients with NC. FGF19 immunohistochemical staining in liver tissue (hepatocytes, endothelial cells, bile ducts, and bile canaliculi) was evaluated as negative, weak, moderate, and strong staining. FGF19 staining in 6 liver samples from explants of children with Crigler-Najjar syndrome type-1 served as controls.

RESULTS

Hepatocyte, endothelial, and canalicular FGF19 expression was significantly higher in cholestasis group compared to controls (P = .039, .006, and .028 respectively). Serum bile acids had significant correlation with hepatocyte FGF19, endothelial, and bile duct FGF19 expressions (P = .002, .003, and .01, respectively) but not with canalicular FGF19 expression. Hepatocyte FGF19 expression significantly associated with cholestasis severity in terms of serum total bilirubin, direct bilirubin, and aspartate transaminase levels (P = .01, .02, and .02, respectively).

CONCLUSION

Hepatic FGF19 expression significantly upregulated in NC and correlated with cholestasis severity.

BEND3 promotes hepatocellular carcinoma progression and metastasis by activating the PI3K/AKT/mTOR pathway and inducing epithelial-mesenchymal transition

OBJECTIVE

This study aimed to investigate the expression of BEND3 in hepatocellular carcinoma (HCC), its correlation with clinical characteristics, and its functional and mechanistic impacts on HCC progression.

METHODS

Bioinformatics analyses identified BEND3 as highly expressed in HCC and associated with poor clinical prognosis, which was further validated using qRT-PCR, western blotting and immunohistochemistry. Stable BEND3-overexpressing and silenced cell lines were constructed to evaluate its functional effects. CCK-8 and colony formation assays assessed its influence on cell proliferation, while wound healing and Transwell assays evaluated its role in migration and invasion. WB and immunofluorescence were employed to analyze the effects of BEND3 on epithelial-mesenchymal transition (EMT) and the PI3K/AKT/mTOR signaling pathway.

RESULTS

Public database analysis, alongside qRT-PCR, western blotting, and immunohistochemical, confirmed that BEND3 expression is significantly elevated in HCC tissues compared to normal liver tissues and is closely associated with poor prognosis. Functional assays demonstrated that BEND3 promotes HCC cell proliferation, migration, and invasion. Mechanistic studies revealed that BEND3 drives HCC progression by inducing EMT and activating the PI3K/AKT/mTOR signaling pathway.

CONCLUSION

BEND3 is highly expressed in HCC and strongly correlates with poor clinical outcomes. Functional and mechanistic analyses indicate that BEND3 enhances HCC progression by promoting proliferation, migration and invasion via EMT induction and PI3K/AKT/mTOR pathway activation.

Clinically Uncertain Liver Masses: A Guide to Distinguishing Poorly Differentiated Primary Liver Cancer

Objectives: The distinction of clinically uncertain, poorly differentiated liver masses into primary liver cancer (PLC) of cholangiocytic origin (intrahepatic cholangiocarcinoma; CCA) or hepatocellular origin (hepatocellular carcinoma; HCC) vs. metastasis is highly relevant to guiding patient treatment. Protocols differ in terms of resection, local ablation, liver transplantation, or systemic therapies with immune checkpoint inhibitors (ICIs) and tyrosine kinase inhibitors (TKIs). Methods: This retrospective case series exemplifies a multidisciplinary, practical guide to clinically uncertain liver masses using imaging, histomorphology, immune phenotyping, and mutational testing of telomerase promoter (TERT) combined with a literature review. Results: In 2/3 patients with uncertain liver masses and inconclusive immunohistochemistry profiles, TERT testing supported the diagnosis of poorly differentiated hepatocellular carcinoma. The third case with a history of sclerosing cholangitis and vague adenoid morphology yielded mutations in ARID1a and TP53 and was identified as primary liver cancer, consistent with poorly differentiated intrahepatic cholangiocarcinoma or mixed hepatocellular cholangiocarcinoma (cHCC/CCA). Conclusions: Finding HCC-typical TERT promoter mutations is a useful diagnostic tool in poorly differentiated primary liver cancer.

Machine learning-based ultrasound radiomics for predicting TP53 mutation status in hepatocellular carcinoma

Objectives

To explore the utility of machine learning-based ultrasound radiomics for predicting TP53 gene mutation in hepatocellular carcinoma (HCC).

Methods

154 HCC patients with 182 lesions from 2019 to 2024 were reviewed retrospectively. All lesions were randomly split into the training set (n = 129) and the test set (n = 53), and ultrasound radiomics features were extracted and selected. Extreme gradient boosting tree (XGBoost), decision tree (DT), random forest (RF), support vector machine (SVM), and logistic regression (LR) were used to construct the ultrasound radiomics models, the clinical models, and the combined models. The predictive performance of various models was evaluated by the area under the curve (AUC), accuracy, calibration curve, and decision curve analysis (DCA).

Results

Among the 182 lesions, 102 were confirmed as mutant TP53 and 80 were confirmed as wild-type TP53. The ultrasound radiomics model obtained an AUC of 0.778 and an accuracy of 0.774 in the test set. The clinical model achieved an AUC of 0.761 and an accuracy of 0.710 in the test set. Notably, integrating clinical features with ultrasound radiomics further enhanced predictive performance. The XGBoost-based combined model exhibited the highest predictive performance among all models, achieving an AUC of 0.846 and an accuracy of 0.823 in the test set. The decision curve analysis and calibration curve revealed that the XGBoost-based combined model provided the highest clinical benefit and exhibited strong predictive consistency.

Conclusion

Machine learning-based ultrasound radiomics signatures accurately predict TP53 gene mutations in HCC. The XGBoost-based combined model, which combined ultrasound radiomics features with clinical features, showed the best performance and represented a promising noninvasive approach for screening TP53-mutated HCC.

Unraveling the Role of the Wnt Pathway in Hepatocellular Carcinoma: From Molecular Mechanisms to Therapeutic Implications

Hepatocellular carcinoma (HCC) is one of the deadliest malignant tumors in the world, and its incidence and mortality have increased year by year. HCC research has increasingly focused on understanding its pathogenesis and developing treatments.The Wnt signaling pathway, a complex and evolutionarily conserved signal transduction system, has been extensively studied in the genesis and treatment of several malignant tumors. Recent investigations suggest that the pathogenesis of HCC may be significantly influenced by dysregulated Wnt/β-catenin signaling. This article aimed to examine the pathway that controls Wnt signaling in HCC and its mechanisms. In addition, we highlighted the role of this pathway in HCC etiology and targeted treatment.

Predictive factors and prognostic models for Hepatic arterial infusion chemotherapy in Hepatocellular carcinoma: a comprehensive review

Hepatocellular carcinoma (HCC) is a prevalent and lethal cancer, often diagnosed at advanced stages where traditional treatments such as surgical resection, liver transplantation, and locoregional therapies provide limited benefits. Hepatic arterial infusion chemotherapy (HAIC) has emerged as a promising treatment modality for advanced HCC, enhancing anti-tumor efficacy through targeted drug delivery while minimizing systemic side effects. However, the heterogeneous nature of HCC leads to variable responses to HAIC, highlighting the necessity for reliable predictive indicators to tailor personalized treatment strategies. This review explores the factors influencing HAIC success, including patient demographics, tumor characteristics, biomarkers, genomic profiles, and advanced imaging techniques such as radiomics and deep learning models. Additionally, the synergistic potential of HAIC combined with immunotherapy and molecular targeted therapies is examined, demonstrating improved survival outcomes. Prognostic scoring systems and nomograms that integrate clinical, molecular, and imaging data are discussed as superior tools for individualized prognostication compared to traditional staging systems. Understanding these predictors is essential for optimizing HAIC efficacy and enhancing survival and quality of life for patients with advanced HCC. Future research directions include large-scale prospective studies, integration of multi-omics data, and advancements in artificial intelligence to refine predictive models and further personalize treatment approaches.

Insights from the bottom-up development of LGR5-targeting immunotherapeutics

Leucine-rich repeat-containing G-protein coupled receptor 5 (LGR5), a transcriptional target gene of the Wnt signalling pathway, is overexpressed in multiple cancers, including colorectal cancer (CRC), hepatocellular carcinoma (HCC) and pre-B acute lymphoblastic leukaemia (pre-B ALL) and has emerged as a promising therapeutic target. Here, we reflect on the bottom-up development of a novel α-LGR5 therapeutic antibody we have recently reported, into a palette of LGR5-targeting immunotherapeutic modalities: antibody-drug conjugates (ADCs), bispecific T cell engagers (bispecific engagers), and chimeric antigen receptor (CAR) T cells. The α-LGR5 antibody is highly specific and accurately detects LGR5 protein expression levels, enabling its use as a prognostic biomarker for identifying LGR5+ tumour types. Preclinical studies road-testing the various α-LGR5-based modalities established potent and safe elimination of LGR5-expressing cancer cells in vitro and efficacy in a mouse model of human cancer in vivo. In this review, we discuss the utility of our antibody as the building block for a novel set of immunotherapeutics and highlight the importance of matching specific α-LGR5-based therapeutic modalities to individual tumour type and patient characteristics.

The impact of an RNA-binding protein group on regulating the RSPO-LGR4/5-ZNRF3/RNF43 module and the immune microenvironment in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality. RNA-binding proteins (RBPs) are potential therapeutic targets because of their role in tumor progression. This study investigated the interactions between specific HCC progression-associated RBPs (HPARBPs), namely, ILF3, PTBP1, U2AF2, NCBP2, RPS3, and SSB, in HCC and their downstream targets, as well as their impact on the immune microenvironment and their clinical value.

METHODS

Tissue samples from human HCC, collected from 28 patients who experienced recurrence following postoperative adjuvant therapy were examined. The mRNA levels of RBPs and their prospective targets were quantified through RNA isolation and quantitative real-time PCR. Data from two public datasets were scrutinized for both expression and clinical relevance. Through Student's t test and logistic regression, HPARBPs were identified. Enhanced cross-linking immunoprecipitation (eCLIP) experiments revealed RBP-RNA interactions in HepG2 cells. For functional enrichment, Metascape was used, whereas CIBERSORT was used to characterize the immune microenvironment.

RESULTS

Public database analysis confirmed widespread RBP expression abnormalities in HCC (false discovery rate < 0.00001 and fold change ≥ 1.15 or ≤ 0.85), leading to the identification of 42 HPARBPs and core modules. eCLIP data analysis revealed the specificity of downstream target genes and binding site features for core HPARBPs (signal value > 3, P value < 0.01). Four core HPARBPs may bind to RNAs of genes in the RSPO-LGR4/5-ZNRF3/RNF43 module, affecting the Wnt pathway and HCC progression. Immunoinfiltration analysis revealed changes in the HCC immune microenvironment due to altered expression of relevant genes.

CONCLUSION

In our study, we identified core HPARBPs that might contribute to HCC progression by binding to RNAs in the RSPO-LGR4/5-ZNRF3/RNF43 module. Changes in the expression of HPARBPs affect the HCC immune microenvironment. Our findings offer novel insights into the regulatory network of Wnt pathway-related RBPs and their potential clinical value in HCC.

Other Primary Epithelial Neoplasms of the Liver

Primary liver carcinoma (PLC) is the sixth most common malignancy worldwide and the third leading cause of cancer-related mortalities. Hepatocellular carcinoma (HCC) is the most prevalent form of PLC, followed by intrahepatic cholangiocarcinoma (iCCA). In addition, there is a group of rarer PLCs that do not fit neatly into the HCC or iCCA categories. This review explores this heterogeneous group, including combined hepatocellular-cholangiocarcinoma (cHCC-CCA), intermediate cell carcinoma (ICC), mixed hepatocellular-neuroendocrine carcinoma, and undifferentiated primary liver carcinoma. cHCC-CCA is a rare subtype of PLC, characterized by both hepatocytic and cholangiocytic differentiation within the same tumor. The latest WHO classification (2019, fifth edition) redefined cHCC-CCA by eliminating the "stem cell subtypes" and emphasized that diagnosis should primarily rely on morphologic features, supported by immunohistochemical staining to better define subtypes. Intermediate cell carcinoma is a subtype of cHCC-CCA and is comprised of monomorphic tumor cells that exhibit characteristics intermediate between hepatocytes and cholangiocytes, with immunohistochemical expression of hepatocytic and cholangiocytic markers within the same cell. Another rare entity, combined HCC and neuroendocrine carcinoma (NEC), contains an admixture of HCC and NEC components within the same tumor. Undifferentiated primary liver carcinoma, on the other hand, lacks definitive lineage differentiation beyond an epithelial phenotype. These heterogeneous PLCs pose diagnostic challenges owing to their mixed/unusual histologic features and overlapping immunohistochemical markers. They tend to have poor prognoses, highlighting the critical importance of accurate and timely diagnosis.

Traditional Chinese Medicine as a Tool for the Treatment of Hepatocellular Carcinoma by Targeting Pathophysiological Mechanism

Liver cancer is a significant global health concern, with projections indicating that the incidence of morbidity may surpass one million cases by 2025. Hepatocellular carcinoma (HCC) is the predominant subtype of liver cancer, constituting approximately 90% of all liver cancer diagnoses. Infections caused by the hepatitis B virus (HBV) and hepatitis C virus (HCV) are recognized as primary risk factors for the development of HCC. However, non-alcoholic steatohepatitis (NASH), which is often linked to metabolic syndrome or diabetes, is increasingly being recognized as a prevalent risk factor in Western populations. Furthermore, HCC associated with NASH exhibits distinct molecular pathogenesis. Patients diagnosed with HCC have access to a range of therapeutic interventions, including liver transplantation, surgical resection, percutaneous ablation, radiation therapy, and transarterial and systemic therapies. Consequently, effective clinical decision-making requires a multidisciplinary approach to adapt individualized treatment plans based on the patient's tumor stage, liver function, and overall performance status. The approval of new first- and second-line pharmacological agents, along with the establishment of immune checkpoint inhibitor therapies as standard treatment modalities, has contributed to an improved prognosis for patients with HCC. Nevertheless, the optimal sequencing of these therapeutic agents remains to be elucidated, highlighting the urgent need for predictive biomarkers to inform treatment selections. Traditional Chinese Medicine (TCM) has demonstrated potential as a complementary and alternative therapeutic approach for liver cancer, warranting further investigation. This review aimed to examine the comprehensive treatment of HCC through the lens of TCM, informed by the current understanding of its epidemiology, diagnosis, and pathophysiology.

An overview of BAP1 biological functions and current therapeutics

BRCA1-associated protein 1 (BAP1) is a tumor suppressor gene that was first identified in 1998. Germline loss-of-function variants in BAP1 are associated with a tumor predisposition syndrome with at least four cancers: uveal melanoma (UM), malignant mesothelioma (MMe), renal cell carcinoma (RCC), and cutaneous melanoma (CM). Furthermore, somatic BAP1 mutations are important drivers for several cancers most notably UM, MMe, RCC, intrahepatic cholangiocarcinoma (ICC) and hepatocellular carcinoma (HCC). Emerging evidence substantiates the fundamental role of BAP1 in suppressing cancer initiation and progression by tuning DNA damage repair, apoptosis, ferroptosis, immune response, Warburg phenomenon, and metastasis. Multiple treatment strategies such as poly (ADP-ribose) polymerase (PARP) inhibitors, EZH2 inhibitors, alkylating agents, and immunotherapy have been used as potential therapies for BAP1-mutated tumors. Although these agents showed promising results in BAP1-mutated tumors in preclinical studies, the results of most clinical trials are still dismal. The objectives of this review are to summarize the current state of knowledge regarding the biological functions of BAP1, the implications of these functions in tumorigenesis, and the current progress in BAP1-targeted therapy.

Alpha-1 antitrypsin deficiency and primary liver cancers

Primary liver cancers (PLCs) remain a major challenge to global health and an escalating threat to human life, with a growing incidence worldwide. PLCs are composed of hepatocellular carcinoma (HCC), cholangiocarcinoma (CCA), and mixed HCC-CCA, accounting for 85 %, 10 %, and 5 % of cases, respectively. Among the numerous identified risk factors associated with liver cancers, Alpha 1-AntiTrypsin Deficiency (AATD) genetic disease emerges as an intriguing one. AATD-related liver disease may lead to chronic hepatitis, cirrhosis, and PLCs in adulthood. Although our knowledge about the natural history of AATD-liver disease has improved recently, liver cancers associated with AATD remain poorly understood and explored, while this specific population is at a 20 to 50 times higher risk of developing PLC. Thus, we review here current knowledge about AATD-associated PLCs, describing the impact of AATD genotypes on their occurrence. We also discuss emerging hypotheses regarding the AATD PiZZ genotype-related hepatic carcinogenesis process. Finally, we perform an updated analysis of the United Kingdom Biobank database that highlights and confirms AATD PiZZ genotype as an important HCC risk factor.

Integrated molecular characterization of sarcomatoid hepatocellular carcinoma

BACKGROUNDS/AIMS

Sarcomatoid hepatocellular carcinoma (HCC) is a rare histological subtype of HCC characterized by extremely poor prognosis; however, its molecular characterization has not been elucidated.

METHODS

In this study, we conducted an integrated multiomics study of whole-exome sequencing, RNA-seq, spatial transcriptome, and immunohistochemical analyses of 28 paired sarcomatoid tumor components and conventional HCC components from 10 patients with sarcomatoid HCC, in order to identify frequently altered genes, infer the tumor subclonal architectures, track the genomic evolution, and delineate the transcriptional characteristics of sarcomatoid HCCs.

RESULTS

Our results showed that the sarcomatoid HCCs had poor prognosis. The sarcomatoid tumor components and the conventional HCC components were derived from common ancestors, mostly accessing similar mutational processes. Clonal phylogenies demonstrated branched tumor evolution during sarcomatoid HCC development and progression. TP53 mutation commonly occurred at tumor initiation, whereas ARID2 mutation often occurred later. Transcriptome analyses revealed the epithelial-mesenchymal transition (EMT) and hypoxic phenotype in sarcomatoid tumor components, which were confirmed by immunohistochemical staining. Moreover, we identified ARID2 mutations in 70% (7/10) of patients with sarcomatoid HCC but only 1-5% of patients with non-sarcomatoid HCC. Biofunctional investigations revealed that inactivating mutation of ARID2 contributes to HCC growth and metastasis and induces EMT in a hypoxic microenvironment.

CONCLUSION

We offer a comprehensive description of the molecular basis for sarcomatoid HCC, and identify genomic alteration (ARID2 mutation) together with the tumor microenvironment (hypoxic microenvironment), that may contribute to the formation of the sarcomatoid tumor component through EMT, leading to sarcomatoid HCC development and progression.

Geographic and Viral Etiology Patterns of TERT Promoter and CTNNB1 Exon 3 Mutations in Hepatocellular Carcinoma: A Comprehensive Review

Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and a leading cause of cancer-related mortality worldwide. Genetic alterations play a critical role in hepatocarcinogenesis, with mutations in the telomerase reverse transcriptase promoter (TERTp) and CTNNB1 exon 3 representing two of the most frequently reported somatic events in HCC. However, the frequency and distribution of these mutations vary across geographic regions and viral etiologies, particularly hepatitis B virus (HBV) and hepatitis C virus (HCV). This study aimed to assess the global distribution and etiological associations of TERTp and CTNNB1 exon 3 mutations in HCC through a comprehensive literature review. Our analysis, encompassing over 4000 HCC cases, revealed that TERTp mutations were present in 49.2% of tumors, with C228T being the predominant variant (93.3% among mutated cases). A striking contrast was observed between viral etiologies: TERTp mutations were detected in 31.6% of HBV-related HCCs, compared to 66.2% in HCV-related cases. CTNNB1 exon 3 mutations were identified in 23.1% of HCCs, showing a similar association with viral etiology, being more common in HCV-related cases (30.7%) than in HBV-related tumors (12.8%). Geographically, both mutations exhibited comparable patterns, with higher frequencies in Europe, Japan, and the USA, while lower rates were observed in China, Taiwan, and South Korea. Our findings underscore the distinct molecular profiles of HCC according to viral etiology and geographic origin, highlighting the need for region- and etiology-specific approaches to HCC prevention, diagnosis, and targeted therapy.

Hepatoma-Derived Growth Factor Promotes Liver Carcinogenesis by Inducing Phosphatase and Tensin Homolog Inactivation

Hepatoma-derived growth factor (HDGF) is located on chromosome 1q21-23, a locus frequently amplified in hepatocellular carcinoma (HCC), and has been proposed as an oncogenic factor by stimulating PI3K/Akt signaling. Phosphatase and tensin homolog (PTEN) acts as a tumor suppressor that antagonizes PI3K/Akt signaling, suggesting a possible regulatory effect of HDGF on PTEN. In this study, we aimed to investigate the regulatory role of HDGF on PTEN. The Cancer Genome Atlas cohort study was used to explore molecular significance and outcomes in liver cancer. Resected clinical specimens, consisting of paired tumor and adjacent nontumor tissue, were analyzed for expression of HDGF and PTEN in the liver cancer cohort. Liver tissue and primary hepatocytes derived from HDGF knockout mice were analyzed for PTEN status. The influence of HDGF on PTEN was investigated through in vitro and in vivo genetic manipulation studies. The Cancer Genome Atlas cohort study revealed an inverse correlation between HDGF and PTEN, with HDGF overexpression emerging as a dominant factor independent of PTEN levels and correlated with poor outcomes in patients with HCC. Paired clinical specimens revealed HDGF upregulation in tumor tissue is relevant to elevated alpha-fetoprotein, and poor survival and recurrent outcomes in the liver cancer cohort. HDGF knockout mice exhibited decreased liver C-tail--phosphorylated PTEN (p-PTEN) levels and increased PTEN expression. Furthermore, an in vitro study validated that overexpression of HDGF increased p-PTEN levels and tumor growth, whereas knockdown of HDGF yielded inverse results. Treatment with recombinant HDGF confirmed the stimulation of p-PTEN and accumulation of phosphatidylinositol 3,4,5-trisphosphate. Blockade of HDGF and casein kinase 2 signaling using anti-HDGF and a casein kinase 2 inhibitor validated the stimulation of p-PTEN. Our results reveal that HDGF is an oncogene frequently amplified and upregulated, leading to suppression of PTEN expression and activity, thereby contributing to malignant progression in liver cancer. HDGF upregulation in resected paired-HCC specimens may constitute a valuable prognostic biomarker for patients with HCC.

Tumor protein 53 gene polymorphism, demographic attributes and associated risk factors among liver cancer patients in Calabar, Nigeria

Mutations in the TP53 gene had been attributed to the development of liver cancer. Hepatocellular carcinoma (HCC) and liver tumour are liver diseases having high mortality rates in several populations. There is no information on the TP53 gene polymorphism among liver diseases patients in Calabar, Nigeria. This study investigated the genetic polymorphism of TP53 among HCC and liver tumour in Calabar. This research was carried out in the University of Calabar Teaching Hospital, Calabar. Blood samples were collected from 35 clinically diagnosed hepatocellular carcinoma and 10 tumour patients and 10 healthy controls. DNA was extracted from all blood samples and Polymerase Chain Reaction (PCR) was performed using specific primers. The PCR amplicons were digested using Hae III restriction enzyme and the genotypic and allelic frequencies was determined. Demographic data among participants showed that males were 68.9% (31), females (31.1%; 14), sex ratio (2.2: 0.5), mean age was 41.51 ± 2.13 years with an odds ratio of 1.25. The distribution of participants according to marital status were 33(73.3%), 10(22.2%), and 2(4.4%) for married, single, and widowed respectively. The participants were from different extractions with varied representations of Yakurr (22.2%, 10), Efik (20%, 9), Boki (13.3%, 6), Ogoja (13.3%, 6), Annang (8.8%, 4), Ibibio (2.2%, 1) and Igbo (2.2%, 1) and respectively. Approximately, 64.7% (30) of the chronic liver diseases were from the Central and Northern part of Cross River State. The risk factors were HCV infection, HBsAg+, alcoholism, smoking, consumption of groundnuts that may have been contaminated with aflatoxin and family history of the disease. PCR product yielded 254 bp and digested PCR product showed homozygous TT mutation (27), heterozygous GT mutation (17) and homozygous GG wild type (1) in cases. The overall TP53 gene mutation frequency was 46.32% (44). The frequency of G allele, T allele, GG, GT and TT were 0.21, 0.79, 0.04, 0.33 and 0.62 respectively among cases, while GG (wild type) was only detected among controls in the study population. The genotypic and allelic frequencies conform to Hardy-Weinberg equilibrium meaning that the forces of evolution were not acting on the locus. There were significant differences in the genotypic proportions of the TP53 gene polymorphism among patients and controls. This study on the TP53 gene polymorphism will serve as baseline information on the molecular etiology of hepatocellular carcinoma and liver tumour in Cross River State.

NOTCH1 Drives Sexually Dimorphic Immune Responses in Hepatocellular Carcinoma

Hepatocellular carcinoma presents strong sexual dimorphism, being two to three times more frequent in males than in females; however, the role of sex in response to immunotherapies in HCC remains unknown. We demonstrate that NOTCH1, an understudied oncogene in HCC, elicits sexually dimorphic antitumor immunity and response to FDA-approved immunotherapies. Surprisingly, males harboring NOTCH1-driven tumors displayed enhanced antitumor immune responses, which, in mice, were mediated by dendritic and T cells. Conversely, females harboring NOTCH1-driven tumors presented immune evasion and resistance to immunotherapies through a defect in dendritic cell (DC)-mediated priming and activation of CD8+ T cells in mice, which was restored therapeutically with CD40 agonism. Mechanistically, the sexually dimorphic immunity was mediated by genes in the sex chromosomes but not by sex hormones. Together, our study unravels an unexpected association between NOTCH1 and sex in cancer immunity and highlights the potential of restoring the DC-CD8+ T-cell axis with CD40 agonism to improve outcomes. Significance: Although HCC presents strong sexual dimorphism, the role of sex in response to immunotherapies remains elusive. With a novel HCC mouse model and validation in patients with HCC, we demonstrate that NOTCH1 disrupts antitumor immunity specifically in females through a mechanism mediated by sex chromosome genes, which is reversed with CD40 agonism. See related commentary by Zhu and Koltsova, p. 452.

Next-generation sequencing demonstrates racial and sex differences in genomic profiling of hepatocellular carcinoma patients: an AACR GENIE project analysis

BACKGROUND

Genomic variations related to racial and sex differences among patients with hepatocellular carcinoma (HCC) have not been investigated. We sought to characterize the mutational landscape of patients with HCC relative to race and sex.

METHODS

The American Association for Cancer Research GENIE project (v16.0) was used to assess data on genomic variations among adult patients (>18 years) with HCC who underwent next-generation sequencing. Variations in 787 genes were identified and characterized relative to race and sex.

RESULTS

Among 832 patients, 60.8 % of individuals were White, 7.7 % Black, and 12.4 % Asian (other/unknown:19.1 %). Most patients had genetic data from the primary tumor (71.2 %), whereas 17.2 % had metastatic disease sequenced (unknown:11.6 %). TERT mutations occurred more frequently in White (48.0 %) and Black (46.7 %) versus Asian (23.4 %) patients (q = 0.003), while TP53 mutations were more common in Asian (48.6 %) versus Black (45.5 %) or White (33.1 %) individuals (q = 0.03). TERT (46.1 % vs. 28.6 %) and CTNNB1 mutations (47.7 % vs. 29.3 %) were more likely to occur in males than females (both q < 0.05). Marked variations in prevalence of other common genetic HCC mutations were noted across different races and sexes.

CONCLUSIONS

Differences in mutational profiles of HCC patients highlight the importance of accruing diverse populations of patients to clinical trials.

Molecular and immune landscape of hepatocellular carcinoma for therapeutic development

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide, with an estimated 750,000 deaths in 2022. Recent emergence of molecular targeted agents and immune checkpoint inhibitors and their combination therapies have been transforming HCC care, but their prognostic impact in advanced-stage disease remains unsatisfactory. In addition, their application to early-stage disease is still an unmet need. Omics profiling studies have elucidated recurrent and heterogeneously present molecular aberrations involved in pro-cancer tumor (immune) microenvironment that may guide therapeutic strategies. Recurrent aberrations such somatic mutations in TERT promoter and TP53 have been regarded undruggable, but recent studies have suggested that these may serve as new classes of therapeutic targets. HCC markers such as alpha-fetoprotein, glypican-3, and epithelial cell adhesion molecule have also been explored as therapeutic targets. These molecular features may be utilized as biomarkers to guide the application of new approaches as companion biomarkers to maximize therapeutic benefits in patients who are likely to benefit from the therapies, while minimizing unnecessary harm in patients who will not respond. The explosive number of new agents in the pipelines have posed challenges in their clinical testing. Novel clinical trial designs guided by predictive biomarkers have been proposed to enable their efficient and cost-effective evaluation. These new developments collectively facilitate clinical translation of personalized molecular-targeted therapies in HCC and substantially improve prognosis of HCC patients.

Molecular and immune landscape of hepatocellular carcinoma to guide therapeutic decision-making

Liver cancer, primarily HCC, exhibits highly heterogeneous histological and molecular aberrations across tumors and within individual tumor nodules. Such intertumor and intratumor heterogeneities may lead to diversity in the natural history of disease progression and various clinical disparities across the patients. Recently developed multimodality, single-cell, and spatial omics profiling technologies have enabled interrogation of the intertumor/intratumor heterogeneity in the cancer cells and the tumor immune microenvironment. These features may influence the natural history and efficacy of emerging therapies targeting novel molecular and immune pathways, some of which had been deemed undruggable. Thus, comprehensive characterization of the heterogeneities at various levels may facilitate the discovery of biomarkers that enable personalized and rational treatment decisions, and optimize treatment efficacy while minimizing the risk of adverse effects. Such companion biomarkers will also refine HCC treatment algorithms across disease stages for cost-effective patient management by optimizing the allocation of limited medical resources. Despite this promise, the complexity of the intertumor/intratumor heterogeneity and ever-expanding inventory of therapeutic agents and regimens have made clinical evaluation and translation of biomarkers increasingly challenging. To address this issue, novel clinical trial designs have been proposed and incorporated into recent studies. In this review, we discuss the latest findings in the molecular and immune landscape of HCC for their potential and utility as biomarkers, the framework of evaluation and clinical application of predictive/prognostic biomarkers, and ongoing biomarker-guided therapeutic clinical trials. These new developments may revolutionize patient care and substantially impact the still dismal HCC mortality.

Increased Synthetic Cytotoxicity of Combinatorial Chemoradiation Therapy in Homologous Recombination Deficient Tumors

PURPOSE

Homologous recombination deficient (HRD) tumors are exquisitely sensitive to platinum-based chemotherapy and when combined with radiation therapy (RT), leads to improved overall survival in multiple cancer types. Whether a subset of tumors with distinct molecular characteristics demonstrate increased benefit from cisplatin and RT (c-RT) is unclear. We hypothesized that HRD tumors, whether associated with BRCA mutations or genomic scars of HRD, exhibit exquisite sensitivity to c-RT, and that HRD may be a significant driver of c-RT benefit.

METHODS AND MATERIALS

Sensitivity to c-RT was examined using isogenic and sporadic breast cancer cell lines. HRD was assessed using 4 assays: RT-induced Rad51 foci, a DR-GFP reporter assay, a genomic scar score (large-scale state transitions [LST]), and clonogenic survival assays. Whole-genome sequencing of 4 breast tumors from a phase 2 clinical trial of neoadjuvant c-RT in triple-negative breast cancer was performed and HRD was defined using HRDetect.

RESULTS

BRCA1/2 deficient cell lines displayed functional HRD based on the Rad51 functional assay, with c-RT to RT or cisplatin interaction ratios (IR) of 1.11 and 26.84 for the BRCA1 isogenic pair at 2 μM cisplatin and 6 Gy, respectively. The highest LST lines demonstrated HRD and synthetic cytotoxicity to c-RT with IR at 2 Gy and cisplatin 20 μM of 7.50, and the lowest LST line with IR of 0.65. Of 4 evaluable patients in the phase 2 trial, one achieved a pathologic complete response with corresponding HRD based on multiple genomic scar scores including HRDetect and LST scores, compared with patients without a pathologic complete response.

CONCLUSIONS

HRD breast cancers, whether identified by BRCA1/2 mutation status, functional tests, or mutational signatures, appear to be significantly more sensitive to c-RT compared with isogenic controls or tumors without HRD mutational signatures. HRD tumors may be exquisitely sensitive to c-RT which warrants further clinical investigation to guide a precision oncology approach.

PAXIP1 is regulated by NRF1 and is a prognosis‑related biomarker in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is characterized by a poor prognosis globally. PAX-interacting protein 1 (PAXIP1) serves a key role in the development of numerous human cancer types. Nevertheless, its specific involvement in HCC remains poorly understood. Public repository systems (Integrative Molecular Database of HCC, Gene Expression Omnibus, The Cancer Genome Atlas, University of Alabama at Birmingham Cancer Data Analysis Portal, Tumor Immune Estimation Resource and Human Protein Atlas) were utilized to explore PAXIP1 expression in HCC and evaluate the prognostic value of PAXIP1 in patients with HCC. PAXIP1 expression was investigated, and a notable relationship between PAXIP1 expression and various cancer types was found through analysis of The Cancer Genome Atlas data. More specifically, patients with HCC and lower PAXIP1 levels had improved survival rates. Furthermore, using LinkedOmics, the co-expression network of PAXIP1 in HCC was determined. Colocalization analysis of PAXIP1 using chromatin immunoprecipitation-sequencing data suggested that PAXIP1 might act as a cofactor for MYB proto-oncogene like 2 or FOXO1 in HCC. In addition, by predicting and analyzing the potential transcription factors related to PAXIP1, nuclear respiratory factor 1 was identified as a factor upstream of PAXIP1 in HCC. Notably, PAXIP1 expression exhibited a positive association with the infiltration of CD4+ and CD8+ T cells, macrophages, neutrophils and myeloid dendritic cells. Furthermore, PAXIP1 expression was associated with a range of immune markers such as programmed cell death protein 1, programmed death-ligand 1 and cytotoxic T-lymphocyte associated protein 4 in HCC. The findings of the present study highlighted the prognostic relevance of PAXIP1 and its function in modulating immune cell recruitment in HCC.

Precision models in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) represents a global health challenge, and ranks among one of the most prevalent and deadliest cancers worldwide. Therapeutic advances have expanded the treatment armamentarium for patients with advanced HCC, but obstacles remain. Precision oncology, which aims to match specific therapies to patients who have tumours with particular features, holds great promise. However, its implementation has been hindered by the existence of numerous 'HCC influencers' that contribute to the high inter-patient heterogeneity. HCC influencers include tumour-related characteristics, such as genetic alterations, immune infiltration, stromal composition and aetiology, and patient-specific factors, such as sex, age, germline variants and the microbiome. This Review delves into the intricate world of HCC, describing the most innovative model systems that can be harnessed to identify precision and/or personalized therapies. We provide examples of how different models have been used to nominate candidate biomarkers, their limitations and strategies to optimize such models. We also highlight the importance of reproducing distinct HCC influencers in a flexible and modular way, with the aim of dissecting their relative contribution to therapy response. Next-generation HCC models will pave the way for faster discovery of precision therapies for patients with advanced HCC.

Advancements in proteogenomics for preclinical targeted cancer therapy research

Advancements in molecular characterization technologies have accelerated targeted cancer therapy research at unprecedented resolution and dimensionality. Integrating comprehensive multi-omic molecular profiling of a tumor, proteogenomics, marks a transformative milestone for preclinical cancer research. In this paper, we initially provided an overview of proteogenomics in cancer research, spanning genomics, transcriptomics, and proteomics. Subsequently, the applications were introduced and examined from different perspectives, including but not limited to genetic alterations, molecular quantifications, single-cell patterns, different post-translational modification levels, subtype signatures, and immune landscape. We also paid attention to the combined multi-omics data analysis and pan-cancer analysis. This paper highlights the crucial role of proteogenomics in preclinical targeted cancer therapy research, including but not limited to elucidating the mechanisms of tumorigenesis, discovering effective therapeutic targets and promising biomarkers, and developing subtype-specific therapies.

Precision oncology through next generation sequencing in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a primary liver cancer that originates from underlying inflammation, often associated with Hepatitis B virus (HBV) or Hepatitis C virus (HCV) infections. Despite the availability of treatments, there are high rates of tumour relapse due to the development of drug resistance in infected cells. Next-Generation Sequencing (NGS) plays a crucial role in overcoming this issue by sequencing both viral and host genomes to identify mutations and genetic heterogeneity. The knowledge gained from sequencing is then utilised to develop countermeasures against these mutants through different combination therapies. Advances in NGS have led to sequencing with higher accuracy and throughput, thereby enabling personalized and effective treatments. The purpose of this article is to highlight how NGS has contributed to precision medicine in HCC and the possible integration of artificial intelligence (AI) to bolster the advancement.

Develop a prognostic and drug therapy efficacy prediction model for hepatocellular carcinoma based on telomere maintenance-associated genes

Background

Hepatocellular carcinoma (HCC) poses a substantial global health challenge because of its grim prognosis and limited therapeutic options. Telomere maintenance mechanisms (TMM) significantly influence cancer progression, yet their prognostic value in HCC remains largely unexamined. This research aims to establish a telomere maintenance-associated genes(TMGs)-based prognostic model using transcriptomic and clinical data to evaluate its effectiveness in predicting patient outcomes in HCC.

Methods

The identified differentially expressed genes (DEGs) were derived from the analysis of transcriptomic and clinical information sourced from the database of the Cancer Genome Atlas (TCGA) and were cross-referenced with TMGs. Candidate risk factors were initially assessed using univariate Cox regression, subsequently followed by LASSO, and then refined through multivariate Cox regression to establish a risk prediction model. This model's predictive accuracy was validated through Kaplan-Meier(K-M) survival analysis, with external validation in the Gene Expression Omnibus (GEO) dataset. Additionally, a nomogram incorporating age and tumor stage was developed. Tumor mutation burden (TMB), immune profile, and drug sensitivity in HCC were also analyzed. Furthermore, we employed RT-PCR to confirm the expression levels of the genes related to TMGs in HepG2 cell lines.

Results

A prognostic model comprising 3 core genes was constructed, with high-risk individuals showing significantly lower overall survival (OS). The association between elevated TMB and diminished survival in high-risk patients was uncovered through TMB analysis. Immune profiling indicated notable disparities in immune infiltration among these groups, with high-risk patients displaying elevated Tumor Immune Dysfunction and Exclusion (TIDE) scores, suggesting potential immune evasion.

Conclusion

In short, our prognosis model based on TMGs effectively categorized HCC patients using risk scores, enabling dependable prognostic forecasts and identification of potential therapeutic targets for personalized treatment in HCC management. Future studies should explore integrating this model into clinical practice to improve patient outcomes.

Fifty Years of Aflatoxin Research in Qidong, China: A Celebration of Team Science to Improve Public Health

The Qidong Liver Cancer Institute (QDLCI) and the Qidong Cancer Registry were established in 1972 with input from doctors, other medical practitioners, and non-medical investigators arriving from urban centers such as Shanghai and Nanjing. Medical teams were established to quantify the extent of primary liver cancer in Qidong, a corn-growing peninsula on the north side of the Yangtze River. High rates of liver cancer were documented and linked to several etiologic agents, including aflatoxins. Local corn, the primary dietary staple, was found to be consistently contaminated with high levels of aflatoxins, and bioassays using this corn established its carcinogenicity in ducks and rats. Observational studies noted a positive association between levels of aflatoxin in corn and incidence of liver cancer across townships. Biomarker studies measuring aflatoxin B1 and its metabolite aflatoxin M1 in biofluids reflected the exposures. Approaches to decontamination of corn from aflatoxins were also studied. In 1993, investigators from Johns Hopkins University were invited to visit the QDLCI to discuss chemoprevention studies in some townships. A series of placebo-controlled clinical trials were conducted using oltipraz (a repurposed drug), chlorophyllin (an over-the-counter drug), and beverages prepared from 3-day-old broccoli sprouts (rich in the precursor phytochemical for sulforaphane). Modulation of biomarkers of aflatoxin DNA and albumin adducts established proof of principle for the efficacy of these agents in enhancing aflatoxin detoxication. Serendipitously, by 2012, aflatoxin exposures quantified using biomarker measurements documented a many hundred-fold reduction. In turn, the Cancer Registry documents that the age-standardized incidence rate of liver cancer is now 75% lower than that seen in the 1970s. This reduction is seen in Qidongese who have never received the hepatitis B vaccination. Aflatoxin mitigation driven by economic changes switched the dietary staple of contaminated corn to rice coupled with subsequent dietary diversity leading to lower aflatoxin exposures. This 50-year effort to understand the etiology of liver cancer in Qidong provides the strongest evidence for aflatoxin mitigation as a public health strategy for reducing liver cancer burden in exposed, high-risk populations. Also highlighted are the challenges and successes of international team science to solve pressing public health issues.

Hepatocellular carcinoma: signaling pathways and therapeutic advances

Liver cancer represents a major global health concern, with projections indicating that the number of new cases could surpass 1 million annually by 2025. Hepatocellular carcinoma (HCC) constitutes around 90% of liver cancer cases and is primarily linked to factors incluidng aflatoxin, hepatitis B (HBV) and C (HCV), and metabolic disorders. There are no obvious symptoms in the early stage of HCC, which often leads to delays in diagnosis. Therefore, HCC patients usually present with tumors in advanced and incurable stages. Several signaling pathways are dis-regulated in HCC and cause uncontrolled cell propagation, metastasis, and recurrence of HCC. Beyond the frequently altered and therapeutically targeted receptor tyrosine kinase (RTK) pathways in HCC, pathways involved in cell differentiation, telomere regulation, epigenetic modification and stress response also provide therapeutic potential. Investigating the key signaling pathways and their inhibitors is pivotal for achieving therapeutic advancements in the management of HCC. At present, the primary therapeutic approaches for advanced HCC are tyrosine kinase inhibitors (TKI), immune checkpoint inhibitors (ICI), and combination regimens. New trials are investigating combination therapies involving ICIs and TKIs or anti-VEGF (endothelial growth factor) therapies, as well as combinations of two immunotherapy regimens. The outcomes of these trials are expected to revolutionize HCC management across all stages. Here, we provide here a comprehensive review of cellular signaling pathways, their therapeutic potential, evidence derived from late-stage clinical trials in HCC and discuss the concepts underlying earlier clinical trials, biomarker identification, and the development of more effective therapeutics for HCC.

Involvement of β-catenin expression in hepatocellular carcinoma prognosis in a cohort of patients undergoing curative treatment

BACKGROUND

Hepatocellular carcinoma is a tumor of epithelial origin that arises from the action of different carcinogens on the hepatocytes and has a high worldwide incidence. The prognostic markers of this disease have not been completely established. Mutations in the gene encoding β-catenin are overexpressed in hepatocellular carcinoma. The objective of our study was to correlate the molecular expression of β-catenin in hepatocellular carcinoma with the already known prognostic markers.

METHODS

We conducted an observational and prospective cohort study on adult patients diagnosed with hepatocellular carcinoma from whom samples of nontumor and tumor liver parenchyma were taken intraoperatively to correlate the molecular expression of β-catenin in hepatocellular carcinoma with the known prognostic markers.

RESULTS

A total of 81 samples were collected, of which 48 met the inclusion criteria. The final sample was divided into patients with a diagnosis of hepatocellular carcinoma on a cirrhotic liver, corresponding to 31 patients (64.6%), and patients with a diagnosis of hepatocellular carcinoma on a noncirrhotic liver, corresponding to 17 patients (35.4%). We found that overexpression of β-catenin and the neutrophil/lymphocyte ratio are independently related to disease-free survival, and both overexpression and molecular repression of β-catenin are independently related.

CONCLUSION

Molecular overexpression of β-catenin in hepatocellular carcinoma compared with nontumor tissue is associated with worse disease-free survival, and its combination with a high neutrophil-lymphocyte ratio worsens this prognosis.

Molecular and pathological landscape of the AT-rich interaction domain 1A (ARID1A) mutation in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, with complex etiological factors and a diverse genetic landscape. Among the critical genetic mutations in HCC, the AT-rich interaction domain 1 A (ARID1A) gene, a key component of the SWI/SNF chromatin remodeling complex, stands out due to its significant role in both tumor suppression and oncogenesis. This review comprehensively examines the molecular and pathological impacts of ARID1A mutations in HCC. ARID1A mutations, which occur in approximately 7.9 % of HCC cases, predominantly involve truncating mutations leading to loss of function. These mutations are associated with various aggressive cancer features, including larger tumor size, higher rates of metastasis, and poor prognosis. The dual role of ARID1A in HCC is context-dependent, acting as a tumor suppressor by regulating cell cycle control, DNA damage repair, and gene expression, while also displaying oncogenic properties in specific contexts by promoting early tumorigenesis through oxidative stress pathways. Understanding the molecular mechanisms of ARID1A, including its interactions with key cellular pathways such as PI3K/AKT/mTOR, β-catenin, and PD-L1, provides insights into its complex role in HCC pathogenesis. Furthermore, ARID1A's impact on cancer stem cell maintenance, metabolic reprogramming, and immune evasion underscores its potential as a therapeutic target. This review highlights the need for context-specific therapeutic strategies targeting ARID1A, which could lead to more effective treatments for HCC, addressing both its tumor-suppressive and oncogenic activities.

Advances and challenges in molecular understanding, early detection, and targeted treatment of liver cancer

In this review, we explore the application of next-generation sequencing in liver cancer research, highlighting its potential in modern oncology. Liver cancer, particularly hepatocellular carcinoma, is driven by a complex interplay of genetic, epigenetic, and environmental factors. Key genetic alterations, such as mutations in TERT, TP53, and CTNNB1, alongside epigenetic modifications such as DNA methylation and histone remodeling, disrupt regulatory pathways and promote tumorigenesis. Environmental factors, including viral infections, alcohol consumption, and metabolic disorders such as nonalcoholic fatty liver disease, enhance hepatocarcinogenesis. The tumor microenvironment plays a pivotal role in liver cancer progression and therapy resistance, with immune cell infiltration, fibrosis, and angiogenesis supporting cancer cell survival. Advances in immune checkpoint inhibitors and chimeric antigen receptor T-cell therapies have shown potential, but the unique immunosuppressive milieu in liver cancer presents challenges. Dysregulation in pathways such as Wnt/β-catenin underscores the need for targeted therapeutic strategies. Next-generation sequencing is accelerating the identification of genetic and epigenetic alterations, enabling more precise diagnosis and personalized treatment plans. A deeper understanding of these molecular mechanisms is essential for advancing early detection and developing effective therapies against liver cancer.

Personalized Immunity: Neoantigen-Based Vaccines Revolutionizing Hepatocellular Carcinoma Treatment

Hepatocellular carcinoma (HCC), the most prevalent form of primary liver cancer, presents significant therapeutic challenges due to its molecular complexity, late-stage diagnosis, and inherent resistance to conventional treatments. The intermediate to low mutational burden in HCC and its ability to evade the immune system through multiple mechanisms complicate the development of effective therapies. Recent advancements in immunotherapy, particularly neoantigen-based vaccines, offer a promising, personalized approach to HCC treatment. Neoantigens are tumor-specific peptides derived from somatic mutations in tumor cells. Unlike normal cellular antigens, neoantigens are foreign to the immune system, making them highly specific targets for immunotherapy. Neoantigens arise from genetic alterations such as point mutations, insertions, deletions, and gene fusions, which are expressed as neoepitopes that are not present in healthy tissues, thus evading the immune tolerance mechanisms that typically protect normal cells. Preclinical and early-phase clinical studies of neoantigen-based vaccines have shown promising results, demonstrating the ability of these vaccines to elicit robust T cell responses against HCC. The aim of the current review is to provide an in-depth exploration of the therapeutic potential of neoantigen-based vaccines in HCC, focusing on neoantigen identification, vaccine platforms, and their integration with immune checkpoint inhibitors to enhance immunogenicity. It also evaluates preclinical and clinical data on efficacy and safety while addressing challenges in clinical translation. By taking advantage of the unique antigenic profile of each patient's tumor, neoantigen-based vaccines represent a promising approach in the treatment of HCC, offering the potential for improved patient outcomes, long-term remission, and a shift towards personalized, precision medicine in liver cancer therapy.

TP53 Mutation Predicts Worse Survival and Earlier Local Progression in Patients with Hepatocellular Carcinoma Treated with Transarterial Embolization

The aim of this study was to evaluate associations between TP53 status and outcomes after transarterial embolization (TAE) for the treatment of patients with hepatocellular carcinoma (HCC). This single-institution study included patients from 1/2014 to 6/2022 who underwent TAE of HCC and genomic analysis of tumoral tissue. The primary outcome was overall survival (OS) with relation to TP53 status, and the secondary outcome was the time to progression. Survival analysis was performed using the Kaplan-Meier method. The time to progression with death or the last patient contact without progression as competing risks were used to obtain a cumulative incidence function, and the association with TP53 status was evaluated using the Gray test. In total, 75 patients (63 men) with a median age of 70.0 (IQR 62.0-76.3) years were included. Of these, 26/75 (34.7%) patients had TP53-mutant HCC. Patients with TP53-mutant HCC had a significantly worse median OS of 15.2 (95% CI, 9.5-29.3) months, versus 31.2 (95% CI, 21.2-52.4) months as the median OS (p = 0.023) for TP53 wild-type HCC. Competing risk analysis showed a shorter time to local hepatic progression (at the site of the previously treated tumor) after TAE in patients with TP53-mutant HCC. The cumulative incidences of local progression at 6 and 12 months for TP53-mutant HCC were 65.4% and 84.6%, versus 40.8% and 55.1% for TP53 wild-type HCC (p = 0.0072). A TP53 mutation may predict a worse overall survival and a shorter time to local progression in HCC patients treated with TAE.

Iron metabolism in a mouse model of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) remains the most prevalent type of primary liver cancer worldwide. p53 is one of the most frequently mutated tumor-suppressor genes in HCC and its deficiency in hepatocytes triggers tumor formation in mice. To investigate iron metabolism during liver carcinogenesis, we employed a model of chronic carbon tetrachloride injections in liver-specific p53-deficient mice to induce liver fibrosis, cirrhosis and subsequent carcinogenesis. A transcriptome analysis of liver carcinoma was employed to identify p53-dependent gene expression signatures with subsequent in-depth analysis of iron metabolic parameters being conducted locally within liver cancers and at systemic levels. We show that all mutant mice developed liver cancer by 36-weeks of age in contrast to 3.4% tumors identified in control mice. All liver cancers with a p53-deficient background exhibited a local iron-poor phenotype with a "high transferrin receptor 1 (Tfr1) and low hepcidin (Hamp)" signature. At systemic levels, iron deficiency was restricted to female mice. Additionally, liver tumorigenesis correlated with selective deficits of selenium, zinc and manganese. Our data show that iron deficiency is a prevalent phenomenon in p53-deficient liver cancers, which is associated with alterations in Hamp and Tfr1 and a poor prognosis in mice and patients.

The Distinct Roles of NEIL1 and XPA in Limiting Aflatoxin B1-Induced Mutagenesis in Mice

Dietary exposure to aflatoxin B1 (AFB1) is a risk factor for the development of hepatocellular carcinomas. Following metabolic activation, AFB1 reacts with guanines to form covalent DNA adducts, which induce high-frequency G > T transversions. The molecular signature associated with these mutational events aligns with the single-base substitution signature 24 (SBS24) in the Catalog of Somatic Mutations in Cancer database. Deficiencies in either base excision repair due to the absence of Nei-like DNA glycosylase 1 (NEIL1) or nucleotide excision repair due to the absence of xeroderma complementation group A protein (XPA) contribute to hepatocellular carcinomas in murine models. In the current study, ultra-low error duplex sequencing was used to characterize mutational profiles in liver DNAs of NEIL1-deficient, XPA-deficient, and DNA repair-proficient mice following neonatal injection of 1 mg/kg AFB1. Analyses of AFB1-induced mutations showed high cosine similarity to SBS24 regardless of repair proficiency status. The absence of NEIL1 resulted in an approximately 30% increase in the frequency of mutations, with the distribution suggesting preferential NEIL1-dependent repair of AFB1 lesions in open chromatin regions. A trend of increased mutagenesis was also observed in the absence of XPA. Consistent with the role of XPA in transcription-coupled repair, mutational profiles in XPA-deficient mice showed disruption of the transcriptional bias in mutations associated with SBS24. Implications: Our findings define the roles of DNA repair pathways in AFB1-induced mutagenesis and carcinogenesis in murine models, with these findings having implications in human health for those with base excision repair and nucleotide excision repair deficiencies.