DNA methylation markers in the detection of hepatocellular carcinoma

The epigenetic basis of hepatocellular carcinoma - mechanisms and potential directions for biomarkers and therapeutics

Hepatocellular carcinoma (HCC) is the sixth leading cancer worldwide and has complex pathogenesis due to its heterogeneity, along with poor prognoses. Diagnosis is often late as current screening methods have limited sensitivity for early HCC. Moreover, current treatment regimens for intermediate-to-advanced HCC have high resistance rates, no robust predictive biomarkers, and limited survival benefits. A deeper understanding of the molecular biology of HCC may enhance tumor characterization and targeting of key carcinogenic signatures. The epigenetic landscape of HCC includes complex hallmarks of 1) global DNA hypomethylation of oncogenes and hypermethylation of tumor suppressors; 2) histone modifications, altering chromatin accessibility to upregulate oncogene expression, and/or suppress tumor suppressor gene expression; 3) genome-wide rearrangement of chromatin loops facilitating distal enhancer-promoter oncogenic interactions; and 4) RNA regulation via translational repression by microRNAs (miRNAs) and RNA modifications. Additionally, it is useful to consider etiology-specific epigenetic aberrancies, especially in viral hepatitis and metabolic dysfunction-associated steatotic liver disease (MASLD), which are the main risk factors of HCC. This article comprehensively explores the epigenetic signatures in HCC, highlighting their potential as biomarkers and therapeutic targets. Additionally, we examine how etiology-specific epigenetic patterns and the integration of epigenetic therapies with immunotherapy could advance personalized HCC treatment strategies.

Integrated Analysis of PSMB8 Expression and Its Potential Roles in Hepatocellular Carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) represents a highly aggressive malignancy with significant global health implications. The proteasome subunit beta type-8 (PSMB8) gene, known for its association with hepatitis B virus susceptibility, has emerged as a potential regulator of tumor progression. However, its functional role and clinical significance in HCC remain poorly characterized.

METHODS

We conducted a comprehensive multi-omics analysis to elucidate the role of PSMB8 in HCC. PSMB8 expression profiles were derived from The Cancer Genome Atlas and validated using the GSE76427 dataset. Prognostic significance was assessed through Kaplan-Meier survival analysis. Then, we systematically evaluated the relationships between PSMB8 expression and clinicopathological features, somatic mutations, immune cell infiltration, immune regulatory genes, and immune checkpoint responses. Single-cell RNA sequencing data from the Tumor Immune Single-cell Hub database were analyzed to determine cell type-specific PSMB8 expression. Tissue-level validation was performed using multiplex immunofluorescence staining on HCC tissue microarrays.

RESULTS

PSMB8 demonstrated significant overexpression in HCC tissues and exhibited strong prognostic value. Single-cell analysis revealed predominant PSMB8 expression in T and B cell populations. Notably, PSMB8 expression showed significant positive correlations with immune checkpoint molecules PD-L1/CD274 and CD27. Functional enrichment analysis implicated PSMB8 in multiple oncogenic pathways, particularly proteasome-related processes.

CONCLUSION

Our findings position PSMB8 as a promising prognostic biomarker and potential therapeutic target in HCC. The observed associations with immune checkpoint molecules and proteasomal pathways suggest its potential role in modulating tumor immunity and protein homeostasis, warranting further investigation into its mechanistic contributions to HCC progression.

Astrocyte Elevated Gene-1/Metadherin (AEG-1/MTDH): A Promising Molecular Marker and Therapeutic Target for Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths. The 5-year survival rate has been estimated to be less than 20% while its incidence rates have more than tripled since the 1980s. Astrocyte elevated gene-1/Metadherin (AEG-1/MTDH) has been demonstrated to have an influential role in HCC progression and the development of an aggressive phenotype. AEG-1 has been shown to be upregulated in many cancers, including HCC. Studies have shown that it plays a crucial role in the proliferation, invasion and metastasis, and evasion of apoptosis in HCC. Its relationship with proteins and pathways, such as MYC, SND1, PI3K/AKT, and other signaling pathways demonstrates its pertinent role in oncogenic development and relevance as a biomarker and therapeutic target. Recent studies have shown that AEG-1 is present in tumor tissues, and the anti-AEG-1 antibody is detected in the blood of cancer patients, demonstrating its viability as a diagnostic/prognostic marker. This review paper shines light on recent findings regarding the molecular implications of AEG-1, with emphasis on its role of regulating metabolic dysfunction-associated steatohepatitis (MASH), a key predisposing factor for HCC, new treatment strategies targeting AEG-1, and challenges associated with analyzing this intriguing molecule.

Therapeutic Effects of DNase I on Peripheral and Local Markers of Liver Injury and Neutrophil Extracellular Traps in a Model of Alcohol-Related Liver Disease

Alcohol-related liver disease (ALD) is a leading cause of chronic liver conditions globally. Chronic alcohol consumption induces liver damage through various mechanisms, including neutrophil extracellular trap (NET) formation. Extracellular DNA (ecDNA), released from damaged hepatocytes and NETotic neutrophils, has emerged as a potential biomarker and contributor to liver disease pathology. Enzyme DNases could be an effective therapy for the denaturation of immunogenic ecDNA. This study investigated the circulating ecDNA and NET markers in ALD and therapeutic effect of DNase I in a murine model of ALD. Female C57BL/6J mice were fed a control diet (n = 13) or Lieber-DeCarli ethanol diet for 10 days followed by a binge ethanol dose to mimic acute-on-chronic alcoholic liver injury. From day 5, mice fed ethanol were randomized into an ethanol diet group (n = 17) and ethanol + DNase group (n = 5), which received additional DNase I treatment every 12 h. Liver damage markers were analyzed. Circulating ecDNA and NETosis were measured by fluorometry and cytometry, respectively. DNase I activity was analyzed with single radial enzyme dispersion assay. The ethanol-fed mice exhibited increased mortality, neutrophil infiltration and structural damage in the liver. Total circulating ecDNA levels and NET markers did not differ between groups. DNase activity was higher in ethanol-fed mice compared to controls and additional daily administration of DNase prevented liver injury. These findings suggest that alcohol-induced liver injury modestly influences systemic NETosis and ecDNA levels. However, increased DNase activity can prevent disease progression and enhanced systemic degradation of ecDNA using DNase I.

Molecular mechanism of genetic, epigenetic, and metabolic alteration in lung cancer

Lung cancer, a leading cause of cancer-related deaths worldwide, is primarily linked to smoking, tobacco use, air pollution, and exposure to hazardous chemicals. Genetic alterations, particularly in oncogenes like RAS, EGFR, MYC, BRAF, HER, and P13K, can lead to metabolic changes in cancer cells. These cells often rely on glycolysis for energy production, even in the presence of oxygen, a phenomenon known as aerobic glycolysis. This metabolic shift, along with other alterations, contributes to cancer cell growth and survival. To develop effective therapies, it's crucial to understand the genetic and metabolic changes that drive lung cancer. This review aims to identify specific genes associated with these metabolic alterations and screen phytochemicals for their potential to target these genes. By targeting both genetic and metabolic pathways, we hope to develop innovative therapeutic approaches to combat lung cancer.

Biomarkers of hepatocellular carcinoma: status and prospects

Hepatocellular carcinoma (HCC) also known as hepatocellular cancer is one of the most common and aggressive types of primary malignant liver neoplasms. This type of cancer accounts for up to 90% of all primary liver tumors and is the third leading cause of cancer death worldwide. Despite the advances in modern medicine, diagnostics and treatment of HCC remain challenging, especially in the later stages, when the patient's prognosis significantly worsens and treatment options are very limited. More than half a century has passed since Yu.S. Tatarinov discovered embryo-specific α-globulin in the blood of people with primary liver cancer in 1963, which was later called alpha-fetoprotein (AFP), but unfortunately, the number of specific and sensitive biomarkers for HCC remains very limited. In this regard, many scientific papers are devoted to the search and study of potential HCC biomarkers, which are essential for early diagnostics, prognosis, and development of new therapeutic strategies. Proteomic studies represent one of the promising approaches to investigate both molecular mechanisms of HCC occurrence and HCC biomarkers. Identification of specific protein profiles characteristic of tumor cells can contribute to the identification of new biomarkers that can be used not only for early detection of the disease, but also for monitoring its progression, assessing the response to therapy and predicting the clinical outcome. This review discusses current achievements in the search for potential biomarkers of HCC, as well as the prospects for their clinical use.

DNA Methylation Profile in Buffy Coat Identifies Methylation Differences Between Cirrhosis with and Without Hepatocellular Carcinoma

BACKGROUND/OBJECTIVES

Cirrhosis is the precursor to most cases of hepatocellular carcinoma (HCC). Understanding the mechanisms leading to the transition from cirrhosis to HCC and identifying key biomarkers is crucial to developing effective screening strategies and reducing HCC-related mortality. DNA methylation is associated with gene inactivation and plays an important role in physiological and pathological processes; however, its role in cirrhosis progression to HCC is unknown.

METHODS

We performed genome-wide DNA methylation profiling using Illumina Infinium MethylationEPI BeadChip in pre-diagnostic samples from 22 cirrhosis patients who subsequently developed HCC and 22 cirrhosis patients who remained HCC-free during an average 4-year follow-up. In a secondary analysis, we examined a subset of patients without hepatitis C virus (HCV) infection.

RESULTS

We identified three differentially methylated positions (DMPs) located in ADAM12 (cg13674437) and PSD3 (cg06758847 and cg24595678) that show a strong association with HCC risk (lower median vs. higher median hazards ratio (HR): HR cg13674437 = 0.34, 95% CI = 0.14-0.83; HR cg06758847 = 4.89, 95% CI = 1.79-13.33; HR cg24595678 = 11.19, 95% CI = 3.27-38.35). After excluding all HCV-active patients from our analysis, the HR for the DMPs remained significant.

CONCLUSIONS

In conclusion, the findings in this study support the theory that buffy coat-derived DNA methylation markers could be used to identify biomarkers among cirrhosis patients at high risk for HCC before clinical symptoms appear. A further study with a large prospective cohort is required to validate these findings.

Hepatocellular Carcinoma: The Search for an Optimal Screening Test

Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and the third leading cause of cancer-related death, with a 5-year survival rate of 10%-12%. It usually develops in the setting of chronic liver disease (CLD), with chronic viral hepatitis, alcohol, and non-alcoholic fatty liver disease (NAFLD) being the most common risk factors. Some patients are at higher risk of developing hepatocellular cancer, so it is important to screen them regularly to diagnose the disease at an early stage and improve their chances for curative treatment. Six-monthly ultrasound with or without alpha-fetoprotein (AFP) is the currently recommended surveillance method. AFP has been used as a biomarker for liver cancer; however, it has low sensitivity and specificity, which necessitates the search for other, more accurate biomarkers. Promising biomarkers include lens culinaris agglutinin-reactive AFP, des-gamma-carboxy prothrombin, methylated DNA markers, plasma microRNA expression, circulating tumor DNA, and circulating tumor cells. In addition, combinations of biomarkers, like the GALAD score and the Doylestown algorithm, may help in the early detection of HCC. In this review, we summarize the screening tests for early detection of HCC that have been studied over the last decade.

Antimicrobial activity and cytotoxic and epigenetic effects of tannic acid-loaded chitosan nanoparticles

Tannic acid (TA) is a potent antitumor agent, but its low bioavailability and absorption limit its use. In this study, it was loaded into chitosan-based nanoparticles (Chi-NPs) to overcome these limitations and to improve its antimicrobial and anticancer activities. TA-loaded Chi-NPs (Chi-TA-NPs) were synthesized using the ionic gelation method and physicochemically characterized by FE-SEM, FTIR, XRD, PDI, DLS, and zeta potential analysis. Additionally, the antimicrobial activity of Chi-TA-NPs against two G+ bacterial strains, two G- bacterial strains, and a fungal strain (Candida albicans) was investigated using the microbroth dilution method. MTT assay was used to examine the cytotoxic effects of Chi-TA-NPs on HepG2 cells. The expression of DNA methyltransferase 1 (DNMT1), DNMT3A, and DNMT3B was examined in HepG2 cells using RT-qPCR. The amount of 5-methylcytosine in the HepG2 cell-derived genomic DNA was measured using ELISA. FE-SEM micrographs showed the loading of TA into the chitosan-based formulation. The peaks detected in the XRD and FTIR analyses confirmed the formation of the Chi-TA-NPs. The PDI value (0.247 ± 0.03), size (567.0 ± 25.84 nm), and zeta potential (17.0 ± 5.86 mV) confirmed the relative stability of Chi-TA-NPs. A constant release profile in line with the Korsmeyer-Peppas model was detected for Chi-TA-NPs, such that approximately 44% of TA was released after 300 min. In addition, Chi-TA-NPs exhibited effective antimicrobial activity against the studied microbial strains, as manifested by MIC values ranging from 250 to 1000 µg/mL. Chi-TA-NPs induced cytotoxicity in liver tumor cell line, with an IC50 value of 500 µg/mL. Furthermore, Chi-TA-NPs considerably decreased the expression of DNMT1 (2.52-fold; p = 0.01), DNMT3A (2.96-fold; p = 0.004), and DNMT3B (2.94-fold; p < 0.0001). However, 5-methylcytosine levels in HepG2 cells were unaffected by Chi-TA-NPs treatment (p = 0.62). Finally, the antimicrobial, cytotoxic, and epigenetic effects of Chi-TA-NPs were more pronounced than those of free TA and the unloaded Chi-NPs. In conclusion, Chi-TA-NPs exhibit promising potential for reducing microbial growth and promoting cytotoxicity in liver cancer cells.

Comprehensive review and updated analysis of DNA methylation in hepatocellular carcinoma: From basic research to clinical application

Hepatocellular carcinoma (HCC) is a primary malignant tumour, ranking second in global mortality rates and posing significant health threats. Epigenetic alterations, particularly DNA methylation, have emerged as pivotal factors associated with HCC diagnosis, therapy, prognosis and malignant progression. However, a comprehensive analysis of the DNA methylation mechanism driving HCC progression and its potential as a therapeutic biomarker remains lacking. This review attempts to comprehensively summarise various aspects of DNA methylation, such as its mechanism, detection methods and biomarkers aiding in HCC diagnosis, treatment and prognostic assessment of HCC. It also explores the role of DNA methylation in regulating HCC's malignant progression and sorafenib resistance, alongside elaborating the therapeutic effects of DNA methyltransferase inhibitors on HCC. A detailed examination of these aspects underscores the significant research on DNA methylation in tumour cells to elucidate malignant progression mechanisms, identify diagnostic markers and develop new tumour-specific inhibitors for HCC. KEY POINTS: A comprehensive summary of various aspects of DNA methylation, such as its mechanism, detection methods and biomarkers aiding in diagnosis and treatment. The role of DNA methylation in regulating hepatocellular carcinoma's (HCC) malignant progression and sorafenib resistance, alongside elaborating therapeutic effects of DNA methyltransferase inhibitors. Deep research on DNA methylation is critical for discovering novel tumour-specific inhibitors for HCC.

Measuring the differential expression of the major hypermethylated tumor suppressor genes in tissues of primary hepatocellular carcinoma

BACKGROUND

Hepatocarcinogenesis is a multifactorial process that arises from a integration of genetic and epigenetic anomalies leading to abnormal gene expression and function. It is difficult to characterize HCC with a single biomarker. Our study aimed at detecting the expression of a panel of 8 methylated genes (SOCS1, APC, Gadd45b, CDKN1B, P15, PAX6, STAT1 and MSH2) as regulatory factors among Egyptian patients with HCC.

METHODS

This study was conducted on HCC tissue samples of 30 Egyptian patients in comparison with their non-cancerous adjacent cirrhotic tissue as a control. Tissue samples were obtained from patients who have undergone living donor liver transplantation (LDLT) or liver resection at El Sahel Teaching Hospital (Cairo, Egypt). A special Custom designed PCR Arrays was used to analyze the expression profiles of chosen methylated genes associated with HCC.

RESULTS

Expression of SOCS1, APC, Gadd45b, CDKN1B, P15, PAX6, STAT1 and MSH2 were lower in the HCC tissue compared to the cirrhotic tissue (pvalue = 0.015, 0.081, 0.004, 0.027, 0.211, 0.015, 0.025 and 0.0001 respectively). 5 genes (SOCS1, APC, GAdd45b, CDKN1B, and MSH2) showed the ability to be used as diagnostic biomarkers for HCC with high sensitivity and specificity values at cut off values: 1.05, 1.17, 0.995, 0.546, and 0.125 respectively. As for the other 3 genes (P15, PAX6, STAT1), PAX6 gene has the highest sensitivity at a cut off value of 0.3364. A significant negative correlation was shown between alpha fetoprotein (AFP) and 5 of the studied genes (SOCS1, APC, Gadd45b, STAT1, and MSH2).

CONCLUSIONS

Expression of the selected hypermethylated genes (SOCS1, APC, Gadd45b, CDKN1B, P15, PAX6, STAT1 and MSH2) in HCC tissue samples was lower than adjacent tissue. Their role should be further studied to solve the mystery that surrounds the pathogenesis of HCC.

CTHRC1 modulates cell proliferation and invasion in hepatocellular carcinoma by DNA methylation

BACKGROUND

Collagen triple helix repeat containing-1 (CTHRC1), an extracellular matrix protein, is highly expressed in hepatocellular carcinoma (HCC) and linked to poor prognosis. Nevertheless, the precise mechanism of CTHRC1 in HCC is unclear.

METHODS

Agena MassARRAY® Methylation Analysis assessed the methylation level of CTHRC1 in the promoter region. Functional assays were conducted to investigate the effects of CTHRC1 knockdown in Hep3B2.1 cells. RNA sequencing identified differentially expressed genes and lncRNAs associated with angiogenesis after CTHRC1 knockdown. Furthermore, differential alternative splicing (AS) and gene fusion events were analyzed using rMATS and Arriba.

RESULTS

In HCC cell lines, CTHRC1 was highly expressed and associated with hypomethylation. Downregulation of CTHRC1 inhibited Hep3B2.1 cell proliferation, migration, and invasion, blocked cells in the G1/S phase, and promoted apoptosis. We obtained 34 mRNAs and 7 lncRNAs differentially expressed between the NC and CTHRC1 inhibitor groups. Additionally, we found 4 angiogenesis-related mRNAs and lncRNAs significantly correlated with CTHRC1. RT-qPCR results showed that knockdown of CTHRC1 in Hep3B2.1 cells resulted in significantly aberrant expression of CXCL6, LINC02127, and AC020978.8. Moreover, the role of CTHRC1 in HCC development may be associated with events, like 12 AS events and 5 pairs of fusion genes.

CONCLUSIONS

High expressed CTHRC1 is associated with hypomethylation and may promote HCC development, involving events like angiogenesis, alternative splicing, and gene fusion.

Metabolomics biomarkers of hepatocellular carcinoma in a prospective cohort of patients with cirrhosis

Background & Aims

The effectiveness of surveillance for hepatocellular carcinoma (HCC) in patients with cirrhosis is limited, due to inadequate risk stratification and suboptimal performance of current screening modalities.

Methods

We developed a multicenter prospective cohort of patients with cirrhosis undergoing surveillance with MRI and applied global untargeted metabolomics to 612 longitudinal serum samples from 203 patients. Among them, 37 developed HCC during follow-up.

Results

We identified 150 metabolites with significant abundance changes in samples collected prior to HCC (Cases) compared to samples from patients who did not develop HCC (Controls). Tauro-conjugated bile acids and gamma-glutamyl amino acids were increased, while acyl-cholines and deoxycholate derivatives were decreased. Seven amino acids including serine and alanine had strong associations with HCC risk, while strong protective effects were observed for N-acetylglycine and glycerophosphorylcholine. Machine learning using the 150 metabolites, age, gender, and PNPLA3 and TMS6SF2 single nucleotide polymorphisms, identified 15 variables giving optimal performance. Among them, N-acetylglycine had the highest AUC in discriminating Cases and Controls. When restricting Cases to samples collected within 1 year prior to HCC (Cases-12M), additional metabolites including microbiota-derived metabolites were identified. The combination of the top six variables identified by machine learning (alpha-fetoprotein, 6-bromotryptophan, N-acetylglycine, salicyluric glucuronide, testosterone sulfate and age) had good performance in discriminating Cases-12M from Controls (AUC 0.88, 95% CI 0.83-0.93). Finally, 23 metabolites distinguished Cases with LI-RADS-3 lesions from Controls with LI-RADS-3 lesions, with reduced abundance of acyl-cholines and glycerophosphorylcholine-related lysophospholipids in Cases.

Conclusions

This study identified N-acetylglycine, amino acids, bile acids and choline-derived metabolites as biomarkers of HCC risk, and microbiota-derived metabolites as contributors to HCC development.

Impact and implications

The effectiveness of surveillance for hepatocellular carcinoma (HCC) in patients with cirrhosis is limited. There is an urgent need for improvement in risk stratification and new screening modalities, particularly blood biomarkers. Longitudinal collection of paired blood samples and MRI images from patients with cirrhosis is particularly valuable in assessing how early blood and imaging markers become positive during the period when lesions are observed to obtain a diagnosis of HCC. We generated a multicenter prospective cohort of patients with cirrhosis under surveillance with contrast MRI, applied untargeted metabolomics on 612 serum samples from 203 patients and identified metabolites associated with risk of HCC development. Such biomarkers may significantly improve early-stage HCC detection for patients with cirrhosis undergoing HCC surveillance, a critical step to increasing curative treatment opportunities and reducing mortality.

Recent Advances in Biosensor Technology for Early-Stage Detection of Hepatocellular Carcinoma-Specific Biomarkers: An Overview

Hepatocellular carcinoma is currently the most common malignancy of the liver. It typically occurs due to a series of oncogenic mutations that lead to aberrant cell replication. Most commonly, hepatocellular carcinoma (HCC) occurs as a result of pre-occurring liver diseases, such as hepatitis and cirrhosis. Given its aggressive nature and poor prognosis, the early screening and diagnosis of HCC are crucial. However, due to its plethora of underlying risk factors and pathophysiologies, patient presentation often varies in the early stages, with many patients presenting with few, if any, specific symptoms in the early stages. Conventionally, screening and diagnosis are performed through radiological examination, with diagnosis confirmed by biopsy. Imaging modalities tend to be limited by their requirement of large, expensive equipment; time-consuming operation; and a lack of accurate diagnosis, whereas a biopsy's invasive nature makes it unappealing for repetitive use. Recently, biosensors have gained attention for their potential to detect numerous conditions rapidly, cheaply, accurately, and without complex equipment and training. Through their sensing platforms, they aim to detect various biomarkers, such as nucleic acids, proteins, and even whole cells extracted by a liquid biopsy. Numerous biosensors have been developed that may detect HCC in its early stages. We discuss the recent updates in biosensing technology, highlighting its competitive potential compared to conventional methodology and its prospects as a tool for screening and diagnosis.

Periodic magnetic modulation enhanced electrochemical analysis for highly sensitive determination of genomic DNA methylation

DNA methylation aberrations have a strong correlation with cancer in early detection, diagnosis, and prognosis, which make them possible candidate biomarkers. Electrochemical biosensors offer rapid protocols for detecting DNA methylation status with minimal pretreatment of samples. However, the inevitable presence of background current in the time domain, including electrochemical noise and variations, limits the detection performance of these biosensors, especially for low concentration analytes. Here, we propose an ultrasensitive frequency-domain electrochemical analysis strategy to effectively separate the weak signals from background current. To achieve this, we employed periodic magnetic field modulation of magnetic beads (MBs) on and off the electrode surface to generate a periodic electrochemical signal for subsequent frequency-domain analysis. By capturing labeled MBs with as low as 0.5 pg of DNA, we successfully demonstrated a highly sensitive electrochemical method for determination of genome-wide DNA methylation levels. We also validated the effectiveness of this methodology using DNA samples extracted from three types of hepatocellular carcinoma (HCC) cell lines. The results revealed varying genomic methylation levels among different HCC cell lines, indicating the potential application of this approach for early-stage cancer detection in terms of DNA methylation status.

Construction of a prognostic model based on genome-wide methylation analysis of miRNAs for hepatocellular carcinoma

Aim: Using the methylation level of miRNA genes to develop a prognostic model for patients with hepatocellular carcinoma (HCC). Materials & methods: least absolute shrinkage and selection operator and multivariate Cox regression analyses were performed to develop a prognostic model. One miRNA in the model was selected for verification. Results: A prognostic model was developed using eight miRNAs. The areas under the curve for predicting overall survival at 1, 3 and 5 years were 0.75, 0.81 and 0.81. miR-223 was found to be hypomethylated in 160 HCC tissues, and its methylation level was associated with Barcelona Clinic Liver Cancer stages and the prognosis of patients with HCC. Conclusion: The prognostic model based on miRNA methylation levels has the capability to partially forecast the prognosis of patients with HCC.

RNA 5-methylcytosine writer NSUN5 promotes hepatocellular carcinoma cell proliferation via a ZBED3-dependent mechanism

Hepatocellular carcinoma (HCC) is one of the leading contributors to cancer-related mortality worldwide. Nop2/Sun domain family member 5 (NSUN5), a conserved RNA 5-methylcytosine methyltransferase, is conventionally recognized as oncogenic. However, its role in HCC development remains unknown. In this study, we observed a remarkable upregulation of NSUN5 expression in both tumor tissues from patients with HCC, establishing a correlation with unfavorable clinical outcomes. NSUN5 knockdown and overexpression significantly inhibited and promoted HCC cell proliferation, respectively. Additionally, employing a combination of methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RIP-seq techniques, we identified zinc finger BED domain-containing protein 3 (ZBED3) as a novel downstream target of NSUN5. Additionally, we found that the overexpression of ZBED3 counteracted the tumor-suppressing effect of NSUN5 knockdown and simultaneously reversed the inhibition of the Wnt/β-catenin signaling pathway. In summary, we elucidated the oncogenic role of NSUN5 in HCC development and identified the ZBED3/Wnt/β-catenin signaling pathway as its downstream target. This study provides a novel therapeutic target for further development in HCC treatment.

Plasma Cell-Free Tumor Methylome as a Biomarker in Solid Tumors: Biology and Applications

DNA methylation is a fundamental mechanism of epigenetic control in cells and its dysregulation is strongly implicated in cancer development. Cancers possess an extensively hypomethylated genome with focal regions of hypermethylation at CPG islands. Due to the highly conserved nature of cancer-specific methylation, its detection in cell-free DNA in plasma using liquid biopsies constitutes an area of interest in biomarker research. The advent of next-generation sequencing and newer computational technologies have allowed for the development of diagnostic and prognostic biomarkers that utilize methylation profiling to diagnose disease and stratify risk. Methylome-based predictive biomarkers can determine the response to anti-cancer therapy. An additional emerging application of these biomarkers is in minimal residual disease monitoring. Several key challenges need to be addressed before cfDNA-based methylation biomarkers become fully integrated into practice. The first relates to the biology and stability of cfDNA. The second concerns the clinical validity and generalizability of methylation-based assays, many of which are cancer type-specific. The third involves their practicability, which is a stumbling block for translating technologies from bench to clinic. Future work on developing pan-cancer assays with their respective validities confirmed using well-designed, prospective clinical trials is crucial in pushing for the greater use of these tools in oncology.

Hepatocellular carcinoma

An update on the management of Hepatocellular carcinoma (HCC) is provided in the present article for those interested in the UEMS/EBSQ exam in Surgical Oncology. The most recent publications in HCC, including surveillance, guidelines, and indications for liver resection, liver transplantation, and locoregional or systemic therapies, are summarised. The objective is to yield a set of main points regarding HCC that are required in the core curriculum of hepatobiliary oncological surgery.

Benefit and harm of waiting time in liver transplantation for HCC

Liver transplantation is the most successful treatment for limited-stage HCC. The waiting time for liver transplantation (LT) can be a critical factor affecting the oncological prognosis and outcome of patients with HCC. Efficient strategies to optimize waiting time are essential to maximize the benefits of LT and to reduce the harm of delay in transplantation. The ever-increasing demand for donor livers emphasizes the need to improve the organization of the waiting list for transplantation and to optimize organ availability for patients with and without HCC. Current progress in innovations to expand the donor pool includes the implementation of living donor LT and the use of grafts from extended donors. By expanding selection criteria, an increased number of patients are eligible for transplantation, which necessitates criteria to prevent futile transplantations. Thus, the selection criteria for LT have evolved to include not only tumor characteristics but biomarkers as well. Enhancing our understanding of HCC tumor biology through the analysis of subtypes and molecular genetics holds significant promise in advancing the personalized approach for patients. In this review, the effect of waiting time duration on outcome in patients with HCC enlisted for LT is discussed.

An integrative analysis reveals the prognostic value and potential functions of MTMR2 in hepatocellular carcinoma

Abnormal expression of myotubularin-related protein 2 (MTMR2) has been identified in certain types of cancer, leading to varying effects on tumor genesis and progression. However, the various biological significances of MTMR2 in hepatocellular carcinoma (HCC) have not been systematically and comprehensively studied. The aim of this study was to explore the role of MTMR2 in HCC. We obtained the raw data from Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Afterward, we analyzed the data using R and cBioPortal. We investigated the connection between MTMR2 and its expression, prognosis, clinical significance, methylation, genetic alterations, tumor microenvironment (TME), tumor mutation burden (TMB), and drug reactivity in HCC patients. MTMR2 expression levels in HCC cells were validated through western blotting and RT-qPCR. MTMR2 exhibits high levels of expression across a wide range of cancer types, including HCC. MTMR2 is diagnostically valuable in detecting HCC, with its up-regulated expression often being indicative of poor prognosis among HCC patients. The in vitro experiments confirmed elevated MTMR2 expression in HepG2, HUH-7, and MHCC-97H cells. Univariate and multivariate Cox analysis demonstrated that MTMR2 was an independent prognostic factor in HCC patients. The cg20195272 site has the highest degree of methylation in MTMR2, and it is positively correlated with MTMR2 expression. Patients with high levels of methylation at the cg20195272 site show poor prognosis. Analysis of the TME indicates that high expression of MTMR2 is associated with elevated ESTIMATE score and that MTMR2 expression correlates positively with infiltration by resting memory CD4 T cells, activated dendritic cells, as well as several immune checkpoints. There is a negative correlation between MTMR2 expression and TMB, and drug sensitivity analyses have shown that higher MTMR2 expression is associated with lower IC50 values. This study indicates that increased expression of MTMR2 may play a crucial role in the occurrence, progression, diagnosis, prognostic prediction and drug therapy of HCC.

Hypermethylation of DNA Methylation Markers in Non-Cirrhotic Hepatocellular Carcinoma

Aberrant DNA methylation changes have been reported to be associated with carcinogenesis in cirrhotic HCC, but DNA methylation patterns for these non-cirrhotic HCC cases were not examined. Therefore, we sought to investigate DNA methylation changes on non-cirrhotic HCC using reported promising DNA methylation markers (DMMs), including HOXA1, CLEC11A, AK055957, and TSPYL5, on 146 liver tissues using quantitative methylation-specific PCR and methylated DNA sequencing. We observed a high frequency of aberrant methylation changes in the four DMMs through both techniques in non-cirrhotic HCC compared to cirrhosis, hepatitis, and benign lesions (p < 0.05), suggesting that hypermethylation of these DMMs is specific to non-cirrhotic HCC development. Also, the combination of the four DMMs exhibited 78% sensitivity at 80% specificity with an AUC of 0.85 in discriminating non-cirrhotic HCC from hepatitis and benign lesions. In addition, HOXA1 showed a higher aberrant methylation percentage in non-cirrhotic HCC compared to cirrhotic HCC (43.3% versus 13.3%, p = 0.039), which was confirmed using multivariate linear regression (p < 0.05). In summary, we identified aberrant hypermethylation changes in HOXA1, CLEC11A, AK055957, and TSPYL5 in non-cirrhotic HCC tissues compared to cirrhosis, hepatitis, and benign lesions, providing information that could be used as potentially detectable biomarkers for these unusual HCC cases in clinical practice.