ARID2 Chromatin Remodeler in Hepatocellular Carcinoma

Circulating tumor DNA and its role in detection, prognosis and therapeutics of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is considered the fifth most prevalent cancer among all types of cancers and has the third most morbidity value. It has the most frequent duplication time and a high recurrence rate. Recently, the most unique technique used is liquid biopsies, which carry many markers; the most prominent is circulating tumor DNA (ctDNA). Varied methods are used to investigate ctDNA, including various forms of polymerase chain reaction (PCR) [emulsion PCR (ePCR), digital PCR (dPCR), and bead, emulsion, amplification, magnetic (BEAMing) PCR]. Hence ctDNA is being recognized as a potential biomarker that permits early cancer detection, treatment monitoring, and predictive data on tumor burden are subjective to therapy or surgery. Numerous ctDNA biomarkers have been investigated based on their alterations such as 1) single nucleotide variations (either insertion or deletion of a nucleotide) markers including TP53, KRAS, and CCND1; 2) copy number variations which include markers such as CDK6, EFGR, MYC and BRAF; 3) DNA methylation (RASSF1A, SEPT9, KMT2C and CCNA2); 4) homozygous mutation includes ctDNA markers as CDKN2A, AXIN1; and 5) gain or loss of function of the genes, particularly for HCC. Various researchers have conducted many studies and gotten fruitful results. Still, there are some drawbacks to ctDNA namely low quantity, fragment heterogeneity, less stability, limited mutant copies and standards, and differential sensitivity. However, plenty of investigations demonstrate ctDNA's significance as a polyvalent biomarker for cancer and can be viewed as a future diagnostic, prognostic and therapeutic agent. This article overviews many conditions in genetic changes linked to the onset and development of HCC, such as dysregulated signaling pathways, somatic mutations, single-nucleotide polymorphisms, and genomic instability. Additionally, efforts are also made to develop treatments for HCC that are molecularly targeted and to unravel some of the genetic pathways that facilitate its early identification.

Screening of potential biomarkers of system lupus erythematosus based on WGCNA and machine learning algorithms

Systemic lupus erythematosus (SLE) is an autoimmune disease involving multiple systems. Its recurrent episodes and fluctuating disease courses have a severe impact on patients. Biomarkers to predict disease prognosis and remission are still lacking in SLE. We downloaded the GSE50772 dataset from the Gene Expression Omnibus database and identified differentially expressed genes (DEGs) between SLE and healthy controls. Weighted gene co-expression network analysis was used to identify key gene modules and corresponding genes in SLE. The overlapped genes in DEGs and key modules are used as key genes for subsequent analysis. These key genes were analyzed using 3 machine learning algorithms, including the least absolute shrinkage and selection operator, support vector machine recursive elimination, and random forest algorithms. The overlapped genes were obtained as potential biomarkers for further analysis, investigating and validating the potential biomarkers' possible functions, regulatory mechanisms, diagnostic value, and expression levels. And finally studied the differences between groups in level of immune cell infiltration and explored the relationship between potential biomarkers and immunity. A total of 234 overlapped genes in DEGs and key modules are used as key genes for subsequent analysis. After taking the intersection of the key genes obtained by 3 algorithms, we got 4 potential biomarkers (ARID2, CYSTM1, DDIT3, and RNASE1) with high diagnostic values. Finally, further immune infiltration analysis showed differences in various immune cells in the SLE and healthy control samples. ARID2, CYSTM1, DDIT3, and RNASE1 can affect the immune function of SLE patients. ARID2, CYSTM1, DDIT3, and RNASE1 could be used as immune-related potential biomarkers and therapeutic or diagnostic targets for further research.

Impact of tumor suppressor genes inactivation on the multidrug resistance phenotype of hepatocellular carcinoma cells

The response of advanced hepatocellular carcinoma (HCC) to pharmacological treatments is unsatisfactory and heterogeneous. Inactivation of tumor suppressor genes (TSGs) by genetic and epigenetic events is frequent in HCC. This study aimed at investigating the impact of frequently altered TSGs on HCC chemoresistance. TSG alterations were screened by in silico analysis of TCGA-LIHC database, and their relationship with survival was investigated. These TSGs were silenced in HCC-derived cell lines using CRISPR/Cas9. TLDA was used to determine the expression of a panel of 94 genes involved in the resistome. Drug sensitivity, cell proliferation, colony formation and cell migration were assessed. The in silico study revealed the down-regulation of frequently inactivated TSGs in HCC (ARID1A, PTEN, CDH1, and the target of p53, CDKN1A). The presence of TP53 and ARID1A variants and the low expression of PTEN and CDH1 correlated with a worse prognosis of HCC patients. In PLC/PRF/5 cells, ARID1A knockout (ARID1AKO) induced increased sensitivity to cisplatin, doxorubicin, and cabozantinib, without affecting other characteristics of malignancy. PTENKO and E-CadKO showed minimal changes in malignancy, resistome, and drug response. In p53KO HepG2 cells, enhanced malignant properties and higher resistance to cisplatin, doxorubicin, sorafenib, and regorafenib were found. This was associated with changes in the resistome. In conclusion, the altered expression and function of several TSGs are involved in the heterogeneity of HCC chemoresistance and other features of malignancy, contributing to the poor prognosis of these patients. Individual identification of pharmacological vulnerabilities is required to select the most appropriate treatment for each patient.

JARID2 and EZH2, The Eminent Epigenetic Drivers In Human Cancer

Cancer has become a prominent cause of death, accounting for approximately 10 million death worldwide as per the World Health Organization reports 2020. Epigenetics deal with the alterations of heritable phenotypes, except for DNA alterations. Currently, we are trying to comprehend the role of utmost significant epigenetic genes involved in the burgeoning of human cancer. A sundry of studies reported the Enhancer of Zeste Homologue2 (EZH2) as a prime catalytic subunit of Polycomb Repressive Complex2, which is involved in several pivotal activities, including embryogenesis. In addition, EZH2 has detrimental effects leading to the onset and metastasis of several cancers. Jumonji AT Rich Interacting Domain2 (JARID2), an undebated crucial nuclear factor, has strong coordination with the PRC2 family. In this review, we discuss various epigenetic entities, primarily focusing on the possible role and mechanism of EZH2 and the significant contribution of JARID2 in human cancers.

The Use of ctDNA in the Diagnosis and Monitoring of Hepatocellular Carcinoma-Literature Review

Hepatocellular carcinoma (HCC) is the most common primary liver cancer and is one of the leading causes of cancer-related deaths worldwide. Despite advances in medicine, it is still a cancer with a very poor prognosis. Both imaging and liver biopsy still have important limitations, especially in very small nodules and those which show atypical imaging features. In recent years, liquid biopsy and molecular analysis of tumor breakdown products have become an attractive source of new biomarkers. Patients with liver and biliary malignancies, including hepatocellular carcinoma (HCC), may greatly benefit from ctDNA testing. These patients are often diagnosed at an advanced stage of the disease, and relapses are common. Molecular analysis may indicate the best cancer treatment tailored to particular patients with specific tumor DNA mutations. Liquid biopsy is a minimally invasive technique that facilitates the early detection of cancer. This review summarizes the knowledge of ctDNA in liquid biopsy as an indicator for early diagnosis and monitoring of hepatocellular cancer.

ARID2 mitigates hepatic steatosis via promoting the ubiquitination of JAK2

Non-alcoholic fatty liver disease (NAFLD) has become a growing public health problem. However, the complicated pathogenesis of NAFLD contributes to the deficiency of effective clinical treatment. Here, we demonstrated that liver-specific loss of Arid2 induced hepatic steatosis and this progression could be exacerbated by HFD. Mechanistic study revealed that ARID2 repressed JAK2-STAT5-PPARγ signaling pathway by promoting the ubiquitination of JAK2, which was mediated by NEDD4L, a novel E3 ligase for JAK2. ChIP assay revealed that ARID2 recruited CARM1 to increase H3R17me2a level at the NEDD4L promoter and activated the transcription of NEDD4L. Moreover, inhibition of Jak2 by Fedratinib in liver-specific Arid2 knockout mice alleviated HFD-induced hepatic steatosis. Downregulation of ARID2 and the reverse correlation between ARID2 and JAK2 were also observed in clinical samples. Therefore, our study has revealed an important role of ARID2 in the development of NAFLD and provided a potential therapeutic strategy for NAFLD.

Regulation of Gene Expression in Cancer-An Overview

Regulation of gene expression takes a central place in normal cells to maintain tissue homeostasis but also in cancer cells to respond to intra- and extra-cellular stimuli, such as therapeutic drugs [...].

Pathogenesis and Current Treatment Strategies of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is the most frequent liver cancer with high lethality and low five-year survival rates leading to a substantial worldwide burden for healthcare systems. HCC initiation and progression are favored by different etiological risk factors including hepatitis B virus (HBV) and hepatitis C virus (HCV) infection, non-/and alcoholic fatty liver disease (N/AFLD), and tobacco smoking. In molecular pathogenesis, endogenous alteration in genetics (TP53, TERT, CTNNB1, etc.), epigenetics (DNA-methylation, miRNA, lncRNA, etc.), and dysregulation of key signaling pathways (Wnt/β-catenin, JAK/STAT, etc.) strongly contribute to the development of HCC. The multitude and complexity of different pathomechanisms also reflect the difficulties in tailored medical therapy of HCC. Treatment options for HCC are strictly dependent on tumor staging and liver function, which are structured by the updated Barcelona Clinic Liver Cancer classification system. Surgical resection, local ablative techniques, and liver transplantation are valid and curative therapeutic options for early tumor stages. For multifocal and metastatic diseases, systemic therapy is recommended. While Sorafenib had been the standalone HCC first-line therapy for decades, recent developments had led to the approval of new treatment options as first-line as well as second-line treatment. Anti-PD-L1 directed combination therapies either with anti-VEGF directed agents or with anti-CTLA-4 active substances have been implemented as the new treatment standard in the first-line setting. However, data from clinical trials indicate different responses on specific therapeutic regimens depending on the underlying pathogenesis of hepatocellular cancer. Therefore, histopathological examinations have been re-emphasized by current international clinical guidelines in addition to the standardized radiological diagnosis using contrast-enhanced cross-sectional imaging. In this review, we emphasize the current knowledge on molecular pathogenesis of hepatocellular carcinoma. On this occasion, the treatment sequences for early and advanced tumor stages according to the recently updated Barcelona Clinic Liver Cancer classification system and the current algorithm of systemic therapy (first-, second-, and third-line treatment) are summarized. Furthermore, we discuss novel precautional and pre-therapeutic approaches including therapeutic vaccination, adoptive cell transfer, locoregional therapy enhancement, and non-coding RNA-based therapy as promising treatment options. These novel treatments may prolong overall survival rates in regard with quality of life and liver function as mainstay of HCC therapy.

ARID2 suppression promotes tumor progression and upregulates cytokeratin 8, 18 and β-4 integrin expression in TP53-mutated tobacco-related oral cancer and has prognostic implications

Mutations in ARID2 and TP53 genes are found to be implicated in the tobacco related tumorigeneses. However, the effect of loss of ARID2 in the TP53 mutated background in tobacco related cancer including oral cancer has not been investigated yet. Hence, in this study we knockdown ARID2 using shRNA mediated knockdown strategy in TP53 mutated oral squamous cell carcinoma (OSCC) cell line and studied its tumorigenic role. Our study revealed that suppression of ARID2 in TP53 mutated oral cancer cells increases cell motility and invasion, induces drastic morphological changes and leads to a marked increase in the expression levels of cytokeratins, and integrins, CK8, CK18 and β4-Integrin, markers of cell migration/invasion in oral cancer. ARID2 suppression also showed early onset and increased tumorigenicity in-vivo. Interestingly, transcriptome profiling revealed differentially expressed genes associated with migration and invasion in oral cancer cells including AKR1C2, NCAM2, NOS1, ADAM23 and genes of S100A family in ARID2 knockdown TP53 mutated oral cancer cells. Pathway analysis of differentially regulated genes identified "cancer pathways" and "PI3K/AKT Pathway" to be significantly dysregulated upon suppression of ARID2 in TP53 mutated OSCC cells. Notably, decreased ARID2 expression and increased CK8, CK18 expression leads to poor prognosis in Head and Neck cancer (HNSC) patients as revealed by Pan-Cancer TCGA data analysis. To conclude, our study is the first to demonstrate tumor suppressor role of ARID2 in TP53 mutated background indicating their cooperative role in OSCC, and also highlights its prognostic implications suggesting ARID2 as an important therapeutic target in OSCC.

3D chromatin architecture and transcription regulation in cancer

Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.

Hepatocellular carcinoma after a sustained virological response by direct-acting antivirals harbors TP53 inactivation

Introduction

The genomic characteristics of hepatocellular carcinoma (HCC) after a sustained virological response (SVR) and its differences according to whether an SVR was achieved by treatment with direct‐acting antivirals (DAA) or interferon (IFN) are still not fully understood.

Methods

Sixty‐nine surgically resected HCCs from patients with hepatitis C virus infection were analyzed by gene expression profiling and whole‐exome sequencing.

Results

Among the 69 HCC patients, 34 HCCs in which an SVR was not achieved at the time of surgery were classified as HCV‐positive, and 35 HCCs in which an SVR was achieved at the time of surgery were classified as HCV‐SVR. According to the HCV treatment, 35 HCV‐SVR HCCs were classified into two groups: eight tumors with DAA (HCV‐SVR‐DAA) and 24 tumors with interferon (HCV‐SVR‐IFN). The frequency of samples with ARID2 mutations was significantly lower in HCV‐SVR than in HCV‐positive tumors (p = 0.048). In contrast, the frequency of samples with PREX2 mutations was significantly higher in HCV‐SVR samples than in HCV‐positive samples (p = 0.048). Among the patients with HCV‐SVR, the frequency of samples with TP53 mutations was significantly higher in HCV‐SVR‐DAA tumors than in HCV‐SVR‐IFN tumors (p = 0.030). TP53 inactivation scores in HCV‐SVR‐DAA tumors were found to be significantly enhanced in comparison to HCV‐SVR‐IFN tumors (p = 0.022). In addition, chromosomal instability and PI3K/AKT/mTOR pathway signatures were enhanced in HCV‐SVR‐DAA tumors. HCV‐SVR‐DAA was significantly associated with portal vein invasion (p = 0.003) in comparison to HCV‐SVR‐IFN.

Conclusion

Our dataset potentially serves as a fundamental resource for the genomic characteristics of HCV‐SVR‐DAA tumors. Our comprehensive genetic profiling by WES revealed significant differences in the mutation rate of several driver genes between HCV‐positive tumors and HCV‐SVR tumors. Furthermore, it was revealed that the frequency of samples with mutations in TP53 was significantly higher in HCV‐SVR‐DAA tumors than in HCV‐SVR‐IFN tumors.

Expression Signature of the AT-Rich Interactive Domain Gene Family Identified in Digestive Cancer

Background

The AT-rich interactive domain (ARID) gene family of 15 proteins has an important role in development and proliferation. Gene expression alterations of the ARID family are correlated with the pathogenesis of digestive cancer, but systematic research has not been conducted.

Methods

We obtained transcriptome sequencing data, clinical characteristics and stemness indices of the seven main types of digestive cancer (cholangiocarcinoma, colon adenocarcinoma, oesophageal carcinoma, liver hepatocellular carcinoma, pancreatic adenocarcinoma, rectum adenocarcinoma and stomach adenocarcinoma) from public pan-cancer data to combine the analysis of the expression and prognostic signature of the ARID gene family. The stromal and immune scores for each sample were calculated to explore the correlations between the ARID gene family members and the tumour microenvironment.

Results

After screening, 1,920 digestive cancer samples were included in our study. ARID3C was expressed at low levels throughout the digestive cancer samples. The expression levels of ARID1A and JARID1C were relatively high, but there was striking heterogeneity across the different cancer types for specific family members. The survival analysis indicated that many genes were significantly related to the prognosis of patients with liver hepatocellular carcinoma. The stemness indices, stromal score, and immune score analysis showed that the expression of a single ARID gene had characteristic consistency in each tumour, but the levels among the different genes still varied.

Conclusion

Our systematic study of the ARID gene family and its association with the immune infiltrate, tumour microenvironment and outcomes of digestive cancer patients focus on the complex relations and indicate the need to study each ARID member as an individual in a specific cancer type.

BRD4 inhibition induces synthetic lethality in ARID2-deficient hepatocellular carcinoma by increasing DNA damage

Hepatocellular carcinoma (HCC) has emerged as the third cause of cancer-related death owing to lacking effective systemic therapies. Genomic DNA sequencing revealed the high frequency of loss-of-function mutations in ARID2, which encodes a subunit of SWI/SNF chromatin remodeling complex, however, the therapeutic strategy for the HCC patients with ARID2 mutations is still completely unclear. In this study, we first performed a high-throughput screening approach using a compound library consisting of 2 180 FDA-approved drugs and other compounds, to elicit the potential drugs for synthetic lethality to target ARID2-deficient HCC cells. Interestingly, JQ1, a selective inhibitor of bromodomain protein BRD4, uniquely suppressed the growth of ARID2- deficient HCC cells. Next JQ1 is further confirmed to predominantly induce cell lethality upon ARID2 depletion through exacerbating DNA damage, especially double strand breaks (DSBs). Functional assays demonstrated that both BRD4 inhibition and ARID2 deficiency synergistically impede two main DNA damage repair pathways, homologous recombination (HR) and non-homologous end-joining (NHEJ), through attenuating the transcription of BRCA1, RAD51, and 53BP1, which encode the core molecules responsible for DSB repair. Mechanistically, both ARID2 and BRD4 exert a synergistic effect for maintaining transcriptional enhancer-promoter loops of these genes within chromatin conformation. However, as both ARID2 and BRD4 are disrupted, the expression of these DNA repair-related genes in response to DNA damage are hindered, resulting in DSB accumulation and cell apoptosis. Taken together, this study discloses that BRD4 inhibition may induce synthetic lethality in ARID2-deficient HCC cells, which might provide a potential therapeutic strategy for HCC patients with ARID2 mutations.