Downregulation of ARID4A and ARID4B promote tumor progression and directly regulated by microRNA-30d in patient with prostate cancer

ARID4B Promotes the Progression of Hepatocellular Carcinoma Through the PI3K/AKT Pathway

BACKGROUND

AT-rich interaction domain 4B (ARID4B) is a transcriptional activator that regulates the phosphatidylinositol 3-kinase (PI3K)/AKT pathway in prostate cancer. However, the role of ARID4B in hepatocellular carcinoma (HCC) has remained unclear.

METHODS

This study included 162 patients who had undergone primary hepatic resection for HCC between 2008 and 2019. Their HCC samples were immunohistochemically stained for ARID4B, and ARID4B score was calculated from the intensity and percentage of staining. We retrospectively investigated the association of ARID4B score with disease-free and overall survival, and primary recurrence patterns of HCC. Furthermore, human HCC cell lines (HuH-1 and HuH-7) were knocked down for ARID4B using small-interfering RNA (siRNA), and the expression of PI3K/AKT proteins, cell proliferation, migration, and invasion ability were assessed.

RESULTS

In multivariate analyses, negative HBs-antigen (p = 0.02), multiple tumors (p < 0.01), microvascular invasion (p = 0.03), and high ARID4B score (p = 0.01) were independent predictors of disease-free survival, while tumor size >5 cm (p = 0.03), microvascular invasion (p < 0.01), and high ARID4B score (p = 0.04) were independent predictors of overall survival. A high ARID4B score was associated with high serum α-fetoprotein (AFP) level (p = 0.04), poor tumor differentiation (p < 0.01), and microvascular invasion (p < 0.01). ARID4B scores were significantly lower in the no recurrence, intrahepatic recurrence, and extrahepatic recurrence groups, in that order. Knockdown of ARID4B using siRNA in human HCC cell lines significantly suppressed the PI3K/AKT pathway, cell proliferation, migration, and invasion.

CONCLUSIONS

ARID4B may activate the PI3K/AKT signaling pathway in HCC and may be a prognostic factor after hepatic resection for HCC.

Single-cell integrated transcriptomics reveals the role of keratinocytes in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a prevalent malignant tumor with significant morbidity and mortality. Understanding the molecular mechanisms of HNSCC and identifying prognostic markers and therapeutic targets are crucial for improving patient outcomes. In this study, we utilized single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data to comprehensively analyze HNSCC at the cellular level. We identified keratinocytes as the predominant cell type in tumor samples, suggesting their potential role in HNSCC development. Through hdWGCNA co-expression network analysis, we identified gene modules associated with HNSCC progression. Furthermore, we constructed a prognostic model based on specific genes and demonstrated its robust predictive performance in multiple datasets. The model exhibited strong correlations with immune cell infiltration patterns and signaling pathways related to tumor progression. Additionally, drug sensitivity analysis revealed potential chemotherapeutic targets for HNSCC treatment. Our findings provide valuable insights into the molecular characteristics and immune microenvironment of HNSCC, offering new perspectives for prognosis prediction and therapeutic interventions in clinical practice. Further research is warranted to validate and expand upon these findings, ultimately improving patient outcomes in HNSCC.

Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18

Alternative splicing (AS) plays a crucial role in regulating gene expression, function, and diversity. However, limited reports exist on the identification and comparison of AS in Eastern and Western pigs. Here, we analyzed 243 transcriptome data from eight tissues, integrating information on transcription factors (TFs), selection signals, splicing factors (SFs), and quantitative trait loci (QTL) to comprehensively study alternative splicing events (ASEs) in pigs. Five ASE types were identified, with Mutually Exclusive Exon (MXE) and Skipped Exon (SE) ASEs being the most prevalent. A significant portion of genes with ASEs (ASGs) showed conservation across all eight tissues (63.21-76.13% per tissue). Differentially alternative splicing genes (DASGs) and differentially expressed genes (DEGs) exhibited tissue specificity, with blood and adipose tissues having more DASGs. Functional enrichment analysis revealed coDASG_DEGs in adipose were enriched in pathways associated with adipose deposition and immune inflammation, while coDASG_DEGs in blood were enriched in pathways related to immune inflammation and metabolism. Adipose deposition in Eastern pigs might be linked to the down-regulation of immune-inflammation-related pathways and reduced insulin resistance. The TFs, selection signals, and SFs appeared to regulate ASEs. Notably, ARID4A (TF), NSRP1 (SF), ANKRD12, IFT74, KIAA2026, CCDC18, NEXN, PPIG, and ROCK1 genes in adipose tissue showed potential regulatory effects on adipose-deposition traits. NSRP1 could promote adipogenesis by regulating alternative splicing and expression of CCDC18. Conducting an in-depth investigation into AS, this study has successfully identified key marker genes essential for pig genetic breeding and the enhancement of meat quality, which will play important roles in promoting the diversity of pork quality and meeting market demand.

Heterozygous Knockout of ARID4B Using CRISPR/Cas9 Attenuates Some Aggressive Phenotypes in a Breast Cancer Cell Line

Breast cancer is one of the leading causes of death in women around the world. Over time, many genes and mutations that are associated with the development of this disease have been identified. However, the specific role of many genes has not yet been fully elucidated. Higher ARID4B expression has been identified as a risk factor for diverse cancer types. Silencing experiments also showed that ARID4B is associated with developing cancer-associated characteristics. However, no transcriptomic studies have shown the overall cellular effect of loss of function in breast cancer in humans. This study addresses the impact of loss-of-function mutations in breast cancer MCF-7 cells. Using the CRISPR/Cas9 system, we generated mutations that caused heterozygous truncated proteins, isolating three monoclonal lines carrying insertions and deletions in ARID4B. We observed reduced proliferation and migration in in vitro experiments. In addition, from RNA-seq assays, a differential expression analysis shows known and novel deregulated cancer-associate pathways in mutated cells supporting the impact of ARID4B. For example, we found the AKT-PI3K pathway to be altered at the transcript level but through different genes than those reported for ARID4B. Our transcriptomic results also suggest new insights into the role of ARID4B in aggressiveness by the epithelial-to-mesenchymal transition and TGF-β pathways and in metabolism through cholesterol and mevalonate pathways. We also performed exome sequencing to show that no off-target effects were apparent. In conclusion, the ARID4B gene is associated with some aggressive phenotypes in breast cancer cells.

The Prognostic Value of AT-Rich Interaction Domain (ARID) Family Members in Patients with Hepatocellular Carcinoma

Objective

Hepatocellular carcinoma (HCC) is one of the most lethal malignancies with a poor prognosis. The AT-rich interaction domain (ARID) family plays an essential regulatory role in the pathogenesis and progression of cancers. This study aims to evaluate the prognostic value and clinical significance of human ARID family genes in HCC.

Methods

ONCOMINE and The Cancer Genome Atlas (TCGA) databases were employed to retrieve ARIDs expression profile and clinicopathological information of HCC. Kaplan–Meier plotter and MethSurv were applied to the survival analysis of patients with HCC. CBioPortal was used to analyze genetic mutations of ARIDs. Gene Expression Profiling Interactive Analysis (GEPIA) and Metascape were used to perform hub gene identification and functional enrichment.

Results

Expression levels of 11 ARIDs were upregulated in HCC, and 2 ARIDs were downregulated. Also, 4 ARIDs and 5 ARIDs were correlated with pathologic stages and histologic grades, respectively. Furthermore, higher expression of ARID1A, ARID1B, ARID2, ARID3A, ARID3B, ARID5B, KDM5A, KDM5B, KDM5C, and JARID2 was remarkably correlated with worse overall survival of patients with HCC, and the high ARID3C/KDM5D expression was related to longer overall survival. Multivariate Cox analysis indicated that ARID3A, KDM5C, and KDM5D were independent risk factors for HCC prognosis. Moreover, ARIDs mutations and 127 CpGs methylation in all ARIDs were observed to be significantly associated with the prognosis of HCC patients. Besides, our data showed that ARIDs could regulate tumor-related pathways and distinct immune cells in the HCC microenvironment.

Conclusions

ARIDs present the potential prognostic value for HCC. Our findings suggest that ARID3A, KDM5C, and KDM5D may be the prognostic biomarkers for patients with HCC.

The Emerging Roles of circSMARCA5 in Cancer

Circular RNAs have a unique covalent closed-loop structure, which is mainly formed by the reverse splicing of exons from a precursor mRNA. With the development of key technologies such as high-throughput sequencing and the advancement of bioinformatics in recent years, our understanding of circular RNAs has become increasingly more detailed, and their abnormal expression in a variety of cancers has attracted increasing attention. Studies have shown that circSNARCA5 not only plays a crucial role in the occurrence and development of cancer but may also serve as a reliable indicator for tumor screening or a good marker for evaluating cancer prognosis. Nevertheless, there are no reviews focusing on the relationship between circSMARCA5 and cancer. Therefore, we will first explain the main biological characteristics of circSMARCA5, such as biogenesis and biological effects. Then, the focus will be on its role and significance in cancer. Finally, we will summarize the known information on circSMARCA5 in cancer and discuss future research prospects.

A novel heterozygous missense variant of the ARID4A gene identified in Han Chinese families with schizophrenia-diagnosed siblings that interferes with DNA-binding activity

ARID4A plays an important role in regulating gene expression and cell proliferation. ARID4A belongs to the AT-rich interaction domain (ARID)-containing family, and a PWWP domain immediately precedes its ARID region. The molecular mechanism and structural basis of ARID4A are largely unknown. Whole-exome sequencing (WES) revealed that a novel heterozygous missense variant, ARID4A c.1231 C > G (p.His411Asp), was associated with schizophrenia (SCZ) in this study. We determined the crystal structure of the PWWP-ARID tandem at 2.05 Å, revealing an unexpected mode in which ARID4A assembles with its PWWP and ARID from a structural and functional supramodule. Our results further showed that compared with the wild type, the p.His411Asp ARID mutant protein adopts a less compact conformation and exhibits a weaker dsDNA-binding ability. The p.His411Asp mutation decreased the number of cells that were arrested in the G0-G1 phase and caused more cells to progress to the G2-M phase. In addition, the missense mutation promoted the proliferation of HEK293T cells. In conclusion, our data provide evidence that ARID4A p.His411Asp could cause a conformational change in the ARID4A ARID domain, influence the DNA binding function, and subsequently disturb the cell cycle arrest in the G1 phase. ARID4A is likely a susceptibility gene for SCZ; thus, these findings provide new insight into the role of ARID4A in psychiatric disorders.

miR-184 delays cell proliferation, migration and invasion in prostate cancer by directly suppressing DLX1

A number of previous studies have reported that dysregulated miR-184 expression is associated with the development of cancer. The aim of the present study was to investigate the role of miR-184 in prostate cancer (PC) and the mechanism underlying its effects. Data from human tumor tissue samples were collected from The CEancer Genome Atlas to determine the expression levels of miR-184 and DLX1. The miR-184 mimic and pcDNA3.1-DLX1 plasmid were utilized to induce overexpression of miR-184 and DLX1 in Du145 cells, respectively. Cell Counting Kit-8, wound healing and Transwell assays were performed to examine the effects of miR-184 on the aggressiveness of PC cells. Dual-luciferase reporter gene assay was used to investigate the association between miR-184 and DLX1, and reverse transcription-quantitative PCR and western blot analyses were utilized to determine the mRNA and protein levels. miR-184 expression was found to be downregulated whereas DLX1 was upregulated in PC tissues compared with normal prostate tissues. Cell propagation, migration and invasion were all inhibited by miR-184 upregulation in Du145 cells. Dual luciferase reporter assay confirmed the association between miR-184 and DLX1. The inhibitory effect of miR-184 mimic on cell behaviors was reversed by upregulation of DLX1. These findings suggest that miR-184 plays a beneficial role in suppressing the tumorigenesis of PC by directly targeting DLX1, and it may represent a potential therapeutic strategy for PC.

miR-30d suppresses proliferation and invasiveness of pancreatic cancer by targeting the SOX4/PI3K-AKT axis and predicts poor outcome

Aberrant expression of miR-30d is associated with the development and progression of several human cancers. However, its biological roles and underlying mechanisms in pancreatic cancer are largely unknown. The expression of miR-30d in pancreatic cancer was evaluated in public databases and further valuated by real-time quantitative PCR, western blot, and immunohistochemistry in a cohort of pancreatic cancer patients. The role of miR-30d in the proliferation and metastasis of pancreatic cancer cells was determined using in vitro and in vivo assays. Bioinformatics analyses were performed to examine potential target genes of miR-30d. Luciferase reporter assay and functional rescue experiments were used to elucidate the mechanisms of miR-30d. miR-30d was found frequently decreased in pancreatic cancer compared with nontumor tissues, and downregulation of miR-30d predicted poor prognosis and early relapse of pancreatic cancer patients. Overexpression of miR-30d significantly repressed the growth and metastasis of pancreatic cancer cells both in vitro and in vivo. Bioinformatics analyses identified sex-determining region Y-box 4 (SOX4) as a target gene of miR-30d. Mechanically, miR-30d exerted its tumor suppressive effect by directly targeting SOX4, which caused inhibition of the PI3K-AKT signaling pathway. Overexpression of SOX4 partially antagonized the inhibitory effects of miR-30d. Our study demonstrated that dysregulation of the miR-30d/SOX4/PI3K-AKT axis promotes the development and progression of pancreatic cancer. These findings suggest miR-30d as a promising and reliable therapeutic target for pancreatic cancer.

Expression and prognostic values of ARID family members in breast cancer

The ARID family is a superfamily of 15 members containing a domain that interacts with AT-rich DNA elements. However, the expression and prognostic roles of each ARID in breast cancer are still elusive.

We used the TCGA and Kaplan-Meier plotter databases to assess the expression and prognostic values of ARID mRNA levels in breast cancer respectively. In the present study, 6 members were significantly lower in tumor tissues than those in the normal tissues, while 6 members were significantly higher. Further assessment of ARID expression in breast cancer with different molecular subtypes, 3 members were significantly higher in no-luminal molecular subtype than those in the luminal molecular subtype, and 6 members were significantly higher. In regard to prognostic values, high expression of ARID1A, ARID2, ARID3B, ARID4A, ARID5A, ARID5B, JARID1A were associated with favorable outcome, while ARID4B and JARID1B were correlated to a worse outcome. We further analyzed the prognostic value of ARID in different intrinsic subtypes and clinicopathological features of breast cancer. We found many meaningful ARID family biomarkers in breast cancer. The relevant results will expound the role of ARID in breast cancer and may further provide new insight to explore the ARID-targeting reagents for treating breast cancer patients.

WITHDRAWN: Circ_0000517 contributes to hepatocellular carcinoma progression by upregulating ARID4B via sponging miR-328-3p

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Pericardial fluid proteomic label-free quantification of differentially expressed proteins in ischemic heart disease patients with systolic dysfunction by nano-LC-ESI-MS/MS analysis

Left ventricular systolic dysfunction (LVSD) is common in patients with pre-existing ischemic heart disease (IHD) and myocardial infarction. An untargeted proteomic approach is used to improve the understanding of the molecular mechanisms associated with LVSD and to find out potential proteomic signatures in pericardial fluid. The pericardial fluid of IHD (n = 45) patients was grouped into two categories according to the left ventricular ejection fraction, LVEF ≥45 (n = 33) and LVEF <45 (n = 12), and analyzed by using nano-liquid chromatography-mass spectrometry (nano-LC-MS/MS) technique. The nano-LC-MS/MS analysis resulted in the identification of 709 pericardial fluid (PF) proteins in both normal and impaired systolic functional groups (LVEF ≥45 vs. LVEF <45). Sixteen proteins were found to be differentially expressed (p < 0.05, fold change >2) including 12 down-regulated and 4 up-regulated in the impaired systolic functional group (LVEF <45) compared to the normal group (LVEF ≥45). Among the differentially expressed proteins the inflammatory marker albumin, atherosclerosis marker apolipoprotein A-IV and hedgehog-interacting protein marker of angiogenesis were predominantly associated with the impaired LVEF <45 group. KEGG pathway analysis revealed that the hedgehog (Hh) signalling pathway is up-regulated in LVSD reflecting the underlying molecular and pathophysiological processes.

Circ-SMARCA5 suppresses colorectal cancer progression via downregulating miR-39-3p and upregulating ARID4B

BACKGROUND

Circular RNAs are crucial in tumorigenesis. However, little is known about their functions in colorectal cancer (CRC). Circ-SMARCA5 was found to be an oncogene or tumor suppresser in different types of cancers, but its exact role in CRC remains unknown. Here, we aim to identify the role of circ-SMARCA5 in CRC development.

METHODS

Circ-SMARCA5 expression was determined by qRT-PCR. CRC cell proliferation, migration, and invasion were detected by CCK-8, wound healing, and Transwell assays, respectively. Bioinformatics analysis was performed to predict target genes. The interaction of microRNA (miR) with circ-SMARCA5 or target genes was detected using luciferase reporter assay. Xenograft model was established to determine the effect of circ-SMARCA5 on CRC tumor growth in vivo.

RESULTS

Circ-SMARCA5 expression was dramatically decreased in CRC cell lines and tissues. Circ-SMARCA5 overexpression inhibited CRC cell proliferation, migration and invasion. MiR-93-3p was predicted as a target of circ-SMARCA5 and its overexpression attenuated the anti-tumor effect of circ-SMARCA5 on CRC cells. Furthermore, we predicted AT-rich interaction domain 4B (ARID4B) as the target of miR-39-3p. Functional analysis showed that circ-SMARCA5 upregulated ARID4B expression via miR-39-3p. Additionally, in vivo studies demonstrated that circ-SMARCA5 suppressed CRC tumor progression.

CONCLUSION

Circ-SMARCA5 functions as a tumor suppressor by upregulating ARID4B expression via sponging miR-39-3p, and thereby inhibited CRC progression.