Protein In Hepatocellular Carcinoma Research Articles

Identification and validation of ATP6V1G1-regulated phosphorylated proteins in hepatocellular carcinoma.

V-ATPase Subunit G1 (ATP6V1G1) is one of the subunits of Vacuolar ATPases. Previous studies have indicated that ATP6V1G1 plays important roles in hepatocellular carcinoma (HCC) and is associated with HCC progression. However, the effect of ATP6V1G1 in HCC requires further elucidation. The aim of the present study was to explore the roles of ATP6V1G1 in HCC and further decipher the detailed mechanism. To identify the phosphorylated proteins regulated by ATP6V1G1 in HCC, phosphoproteomics and LC-MS/MS analysis were performed on HepG2 with overexpression of ATP6V1G1 and empty vector. Western blotting was applied to validate the differentially expressed phosphorylated proteins (DEPPs). As a result, 163 DEPPs were identified by proteomics; two up-regulated phosphorylated proteins (p-RPS6(Ser235)) and (p-SQSTM1(Ser272)) and two down-regulated phosphorylated proteins (p-PDPK1(Ser241)) and (p-EEF2 (Ser57)) were validated. Taken together, this study highlighted the potential impact of ATP6V1G1 on tumor progression, which may be beneficial to liver cancer related basic research.

The role of kinesin superfamily proteins in hepatocellular carcinoma.

The most prevalent form of primary liver cancer, hepatocellular carcinoma (HCC) poses a significant global health challenge due to its limited therapeutic options. Researchers are currently focused on the complex molecular landscape that governs the initiation and progression of HCC in order to identify new avenues for diagnosis, prognosis, and treatment. In the context of HCC, the Kinesin Superfamily Proteins (KIFs) have become critical regulators of cellular processes, prompting a growing interest in their function among the diverse array of molecular actors implicated in cancer. The KIFs, a family of microtubule-based molecular motors, are renowned for their essential roles in the dynamics of mitotic spindles and intracellular transport. Beyond their well-established functions in normal cellular physiology, emerging evidence indicates that dysregulation of KIFs significantly contributes to the pathogenesis of HCC. Novel therapeutic targets and diagnostic markers are revealed through the unique opportunity to comprehend the complex interplay between KIFs and the molecular events that drive HCC.

A proteomic atlas of glypican‐3 interacting partners: Identification of alpha‐fetoprotein and other extracellular proteins as potential immunotherapy targets in liver cancer

AbstractAntibody and cell‐based therapeutics targeting cell surface receptors have emerged as a major class of immune therapeutics for treating cancer. However, the number of cell surface targets for cancer immunotherapy remains limited. Glypican‐3 (GPC3) is a cell surface proteoglycan and an oncofetal antigen. In this study, we report a large‐scale tumor‐associated GPC3 co‐immunoprecipitation‐proteomic study using liver cancer xenograft tumors in mice. We identified 153 GPC3‐associated proteins through mass spectrometry. To identify potential drug targets, we categorized GPC3‐associated proteins based on their subcellular locations using UniProt annotations, with a focus on extracellular proteins. Additionally, we annotated differentially expressed proteins in hepatocellular carcinoma versus nontumor liver samples based on the literature, analyzed expression levels in tumor versus normal tissues using TCGA and GTEx databases via GEPIA, and identified prognostic liver cancer markers according to GEPIA. Among GPC3‐associated proteins, immunoglobulin superfamily member 1, alpha‐fetoprotein (AFP), FAT atypical cadherin 1, formin 1, and guanylate cyclase 2 C, were identified as potential therapeutic targets. Furthermore, we validated the direct protein interaction between GPC3 and AFP through immunoprecipitation with purified proteins and through co‐localization imaging using immunofluorescence microscopy. This study provides large proteomic datasets related to GPC3‐associated proteins, enhancing our understanding of glypican biology in cancer cells and offering a new approach to identifying immunotherapy targets.

Prognostic value of CMTM6 protein in hepatocellular carcinoma involving the regulation of the immune microenvironment

There have been notable irregularities in CMTM6 expression observed in hepatocellular carcinoma (HCC), with an evident correlation between CMTM6 dysregulation and patient prognosis. The cell cycle progression came to a halt at the G2/M phase. In-depth RNA-sequencing analysis of CMTM6 knockdown Hep3B cells revealed that the most prominent effect of CMTM6 perturbation was on the expression of CXCL8, a chemokine involved in immune responses, particularly through the interleukin-17F (IL-17F) signaling pathway. By carefully examining the RNA-sequencing data obtained from CMTM6 knockdown Hep3B cells and cross-referencing it with the TCGA-LIHC database, we were able to discern that CMTM6 and programmed death-ligand 1 (PD-L1) collaboratively partake in immune regulation within T cells. Furthermore, CMTM6 exerted an influential role in modulating the infiltration of CD4+ and CD8+ T cells in the HCC microenvironment, thereby impacting the overall immune response. Our investigation found that HCC cases characterized by an elevated co-expression of CMTM6 and PD-L1, along with augmented CD4+ T cell infiltration, demonstrated comparatively longer overall and progression-free survival rates when contrasted with those displaying lower CD4+ T cell infiltration.

Prediagnostic plasma proteomics profile for hepatocellular carcinoma.

Proteomics may discover pathophysiological changes related to hepatocellular carcinoma, an aggressive and lethal type of cancer with low sensitivity for early stage diagnosis. We measured 1305 prediagnostic (median = 12.7 years) SomaScan proteins from 54 pairs of healthy individuals who subsequently developed hepatocellular carcinoma and matched non-hepatocellular carcinoma control individuals from the Nurses' Health Study (NHS) and the Health Professionals Follow-up Study (HPFS). Candidate proteins were validated in the independent, prospective UK Biobank Pharma Proteomics Project (UKB-PPP). In NHS and HPFS, we identified 56 elevated proteins in hepatocellular carcinoma with an absolute fold change of more than 1.2 and a Wald test P value less than .05 in conditional logistic regression analysis. Ingenuity pathway analysis identified enrichment of pathways associated with cell viability, adhesion, proteolysis, apoptosis, and inflammatory response. Four proteins-chitinase-3-like protein 1, growth differentiation factor 15, interleukin-1 receptor antagonist protein, and E-selectin-showed strong positive associations with hepatocellular carcinoma and were thus validated by enzyme-linked immunosorbent assay (odds ratio = 2.48-14.7, all P < .05) in the NHS and HPFS and by Olink platform (hazard ratio = 1.90-3.93, all P < .05) in the UKB-PPP. Adding these 4 proteins to a logistic regression model of traditional hepatocellular carcinoma risk factors increased the area under the curve from 0.67 to 0.87 in the NHS and HPFS. Consistently, model area under the curve was 0.88 for hepatocellular carcinoma risk prediction in the UKB-PPP. However, the limited number of hepatocellular carcinoma patients in the cohorts necessitates caution in interpreting our findings, emphasizing the need for further validation in high-risk populations.

Expression of LC3A, LC3B and p62/SQSTM1 autophagy proteins in hepatocellular carcinoma (HCC) tissues and the predicted microRNAs involved in the autophagy-related pathway.

Autophagy plays multifaceted roles in regulating hepatocellular carcinoma (HCC) and the mechanisms involved are under-explored. Regulatory microRNAs (miRNAs) have been reported to target autophagy proteins but their roles in HCC is not well studied. Using HCC patient tissues, this study aims to investigate the association of autophagy with several clinicopathological parameters as well as identifying the autophagy-related miRNAs and the possible pathways. Autophagy level in the HCC patient-derived cancer and non-cancer tissues was determined by immunohistochemistry (IHC) targeting SQSTM1, LC3A and LC3B proteins. Significance tests of clinicopathological variables were tested using the Fisher's exact or Chi-square tests. Gene and miRNA expression assays were carried out and analyzed using Nanostring platform and software followed by validation of other online bioinformatics tools, namely String and miRabel. Autophagy expression was significantly higher in cancerous tissues compared to adjacent non-cancer tissues. High LC3B expression was associated with advanced tumor histology grade and tumor location. Nanostring gene expression analysis revealed that SQSTM1, PARP1 and ATG9A genes were upregulated in HCC tissues compared to non-cancer tissues while SIRT1 gene was downregulated. These genes are closely related to an autophagy pathway in HCC. Further, using miRabel tool, three downregulated miRNAs (hsa-miR-16b-5p, hsa-miR-34a-5p, and hsa-miR-660-5p) and one upregulated miRNA (hsa-miR-539-5p) were found to closely interact with the abovementioned autophagy-related genes. We then mapped out the possible pathway involving the genes and miRNAs in HCC tissues. We conclude that autophagy events are more active in HCC tissues compared to the adjacent non-cancer tissues. We also reported the possible role of several miRNAs in regulating autophagy-related genes in the autophagy pathway in HCC. This may contribute to the development of potential therapeutic targets for improving HCC therapy. Future investigations are warranted to validate the target genes reported in this study using a larger sample size and more targeted molecular technique.

Ferroptosis in liver cancer: a key role of post-translational modifications.

Ferroptosis is an emerging form of regulated cell death in an oxidative stress- and iron-dependent manner, primarily induced by the over-production of reactive oxygen species (ROS). Manipulation of ferroptosis has been considered a promising therapeutic approach to inhibit liver tumor growth. Nevertheless, the development of resistance to ferroptosis in liver cancer poses a significant challenge in cancer treatment. Post-translational modifications (PTMs) are crucial enzymatic catalytic reactions that covalently regulate protein conformation, stability and cellular activities. Additionally, PTMs play pivotal roles in various biological processes and divergent programmed cell death, including ferroptosis. Importantly, key PTMs regulators involved in ferroptosis have been identified as potential targets for cancer therapy. PTMs function of two proteins, SLC7A11, GPX4 involved in ferroptosis resistance have been extensively investigated in recent years. This review will summarize the roles of PTMs in ferroptosis-related proteins in hepatocellular carcinoma (HCC) treatment.

Abstract 2785: Beyond the role of transcobalamin 1 (TCN1) as a vitamin B12-binding protein in hepatocellular carcinoma

Abstract Hepatocellular carcinoma (HCC) is a common form of primary liver cancer and is associated with poor prognosis. Although sorafenib and lenvatinib have shown promising results in HCC treatment, their clinical benefits for patients have been limited owing to drug resistance and tumor relapse. This may be associated with the presence of tumor-initiating cells (T-ICs), which require further investigation to identify the key pathways or molecules involved in their regulation. Through in vitro enrichment of liver T-IC populations via a series of sphere passages under treatment with chemotherapeutic drugs, subsequent bulk RNA sequencing analysis identified a vitamin B-12 binding protein, transcobalamin 1 (TCN1), as the most upregulated molecule in such enriched T-IC populations. This result was consistent with the enrichment profiles of the stem cell signature in TCN1High HCC samples in the clinical dataset. TCN1 is a secretory protein expressed at high levels in salivary glands and glandular cells; however, its function beyond its native role as a vitamin B12-binding protein in the regulation of T-ICs is unclear. Using lentiviral shRNA overexpression and knockdown approaches, we identified a critical role for TCN1 in regulating the properties of T-ICs, including self-renewal, invasiveness, tumorigenicity, and drug resistance, through in vitro and in vivo assays. Clinically, we also observed a substantial increase in TCN1 mRNA signatures in HCC samples, which was associated with poor prognosis of HCC patients. By analyzing the TCGA-LIHC dataset with confirmation by immunoprecipitation, we report, for the first time, that TCN1 directly interacts with integrin subunit alpha 3 (ITGA3), thereby regulating the Notch signaling pathway. Furthermore, ELISA results revealed the presence of the secretory form of TCN1 in HCC cells, which exerts a T-IC-enhancing effect on HCC cells via autocrine regulation. In conclusion, our study provides novel insights into how TCN1 functions in HCC via a non-canonical mechanism, which goes beyond its conventional role as a vitamin B12-binding protein and uncovers a potential novel therapeutic target for HCC. Citation Format: Gregory Kenneth Muliawan, Carmen Oi Ning Leung, Terence Kin Wah Lee. Beyond the role of transcobalamin 1 (TCN1) as a vitamin B12-binding protein in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2785.

Abstract 1482: FKBP52 drives diverse HCC phenotypes through context-dependent targeting of p53

Abstract p53 is notably the most frequently mutated protein in hepatocellular carcinoma (HCC), one of the major causes of cancer-related fatalities globally. These mutations often result in some of the most adverse outcomes in HCC, making p53 a prime target for therapeutic intervention. The concept of “hyperstability”of p53 is essential in understanding its gain-of-function and dominant-negative effects in tumorigenesis. However, the mechanisms driving this hyperstability are not completely understood. In this study, we have identified FKBP52, a member of the FK506-binding protein family, as a crucial factor in stabilizing and accumulating p53, irrespective of the type of mutation. Furthermore, our study suggests that FKBP52 could be a valuable biomarker for predicting HCC outcomes. We observed a notable link between FKBP52 levels and the histological differentiation in HCC samples. To corroborate these observations, we performed a series of in vitro and in vivo experiments using liver cancer models. These experiments highlighted the dual nature of FKBP52’s impact on hepatocytes, which varies according to cell type. Given its connection to HCC severity, FKBP52 seems to contribute negatively to the disease’s progression. The insights gained from this study on how FKBP52 influences p53 stabilization are critical. We suggest that targeting the processes upstream of FKBP52 could lead to more effective HCC treatments. These findings emphasize the importance of further investigating this pathway, potentially paving the way for new strategies in liver cancer therapy. Citation Format: Xing Wang, Jingfeng Wu, Chengyan Tang, Xiang Li, Li Zhu, Yaoyu Liu. FKBP52 drives diverse HCC phenotypes through context-dependent targeting of p53 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1482.

Functions and Therapeutic Use of Heat Shock Proteins in Hepatocellular Carcinoma

Heat shock proteins are intracellular proteins expressed in prokaryotes and eukaryotes that help protect the cell from stress. They play an important role in regulating cell cycle and cell death, work as molecular chaperons during the folding of newly synthesized proteins, and also in the degradation of misfolded proteins. They are not only produced under stress conditions like acidosis, energy depletion, and oxidative stress but are also continuously synthesized as a result of their housekeeping functions. There are different heat shock protein families based on their molecular weight, like HSP70, HSP90, HSP60, HSP27, HSP40, etc. Heat shock proteins are involved in many cancers, particularly hepatocellular carcinoma, the main primary tumor of the liver in adults. Their deregulations in hepatocellular carcinoma are associated with metastasis, angiogenesis, cell invasion, and cell proliferation and upregulated heat shock proteins can be used as either diagnostic or prognostic markers. Targeting heat shock proteins is a relevant strategy for the treatment of patients with liver cancer. In this review, we provide insights into heat shock proteins and heat shock protein-like proteins (clusterin) in the progression of hepatocellular carcinoma and their use as therapeutic targets.

Expression of p53 and beta-catenin proteins in hepatocellular carcinoma

Expression of p53 and beta-catenin proteins in hepatocellular carcinoma

Study on F9 gene expression downregulation and its clinical value in hepatocellular carcinoma

Objective: To analyze the expression levels of the F9 gene and F9 protein in hepatocellular carcinoma by combining multiple gene chip data, real-time fluorescence quantitative PCR (RT qPCR), and immunohistochemistry. Additionally, explore their correlation with the occurrence and development of hepatocellular carcinoma, as well as with various clinical indicators and prognosis. Methods: The mRNA microarray dataset from the GEO database was analyzed to identify the F9 gene with significant expression differences associated with hepatocellular carcinoma. Liver cancer and adjacent tissues were collected from 18 cases of hepatocellular carcinoma. RT-qPCR method was used to detect the F9 gene expression level. Immunohistochemistry was used to detect the F9 protein level. Combined with the TCGA database information, the correlation between F9 gene expression level and prognostic and clinicopathological parameters was analyzed. The biological function of F9 co-expressed genes associated with hepatocellular carcinoma was analyzed by the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Statistical analysis was performed using Graphpad Prism software. Results: Meta-analysis results showed that the expression of the F9 gene was lower in HCC tissues than in non-cancerous tissues. Immunohistochemistry results were basically consistent with those of RT-qPCR. The data obtained from TCGA showed that the F9 gene had lower expression values in stages III-IV, T3-T4, and patients with vascular invasion. A total of 127 genes were selected for bioinformatics analysis as co-expressed genes of F9, which were highly enriched in redox processes and metabolic pathways. Conclusion: This study validates that the F9 gene and F9 protein are lower in HCC. The down-regulation of the F9 gene predicts adverse outcomes, which may provide a new therapeutic target for HCC.

Transcriptional analysis of the expression and prognostic value of lipid droplet-localized proteins in hepatocellular carcinoma

The accumulation of lipid droplets (LDs) in hepatocytes is the main pathogenesis in nonalcoholic fatty liver disease (NAFLD), which is also the key risk factor for the progression of hepatocellular carcinoma (HCC). LDs behaviors are demonstrated to be associated with HCC advancement, and are tightly regulated by a subset protein localized on the surface of LDs. However, the role of LDs-localized protein in HCC has been rarely investigated. This study is focused on the transcriptional dynamic and prognostic value of LDs-localized protein in HCC. Firstly, we summarized the known LDs-localized proteins, which are demonstrated by immunofluorescence according to previous studies. Next, by the use of GEPIA/UALCAN/The Human Protein Atlas databases, we screened the transcriptional change in tumor and normal liver tissues, and found that 13 LDs-localized proteins may involve in the progression of HCC. Then we verified the transcriptional changes of 13 LDs-localized proteins by the use of HCC samples. Moreover, based on the assays of fatty liver of mice and human NAFLD liver samples, we found that the hepatic steatosis mainly contributed to the transcriptional change of selected LDs-localized proteins, indicating the involvement of these LDs-localized proteins in the negative role of NAFLD in HCC progression. Finally, we focused on the role of PLIN3 in HCC, and revealed that NAFLD status significantly promoted PLIN3 transcription in HCC tissue. Functional studies revealed that PLIN3 knockdown significantly limited the migration and chemosensitivity of hepatoma cells, suggesting the positive role of PLIN3 in HCC progression. Our study not only revealed the transcriptional change and prognostic value of lipid droplet-localized proteins in HCC, but also built the correlation between HCC and hepatic steatosis.

The functions and roles of C2H2 zinc finger proteins in hepatocellular carcinoma.

C2H2 zinc finger (C2H2-ZF) proteins are the majority group of human transcription factors and they have many different molecular functions through different combinations of zinc finger domains. Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors and the main reason for cancer-related deaths worldwide. More and more findings support the abnormal expression of C2H2-ZF protein in the onset and progression of HCC. The C2H2-ZF proteins are involved in various biological functions in HCC, such as EMT, stemness maintenance, metabolic reprogramming, cell proliferation and growth, apoptosis, and genomic integrity. The study of anti-tumor drug resistance also highlights the pivotal roles of C2H2-ZF proteins at the intersection of biological functions (EMT, stemness maintenance, autophagy)and chemoresistance in HCC. The involvement of C2H2-ZF protein found recently in regulating different molecules, signal pathways and pathophysiological activities indicate these proteins as the possible therapeutic targets, and diagnostic or prognostic biomarkers for HCC.

FRI-324 - Chemerin protein in hepatocellular carcinomas is related to disease severity in European patients

FRI-324 - Chemerin protein in hepatocellular carcinomas is related to disease severity in European patients

Novel peptide binder to Glypican-3 for targeted radiopharmaceutical therapy of hepatocellular carcinoma.

e16131 Background: Glypican-3 (GPC3) is a membrane-associated heparan sulfate proteoglycan primarily involved in embryonic development, and is barely detectable in normal adult tissues. Significant upregulation of GPC3 protein in hepatocellular carcinomas (HCC) has been observed in multiple immunohistochemistry (IHC) studies with up to 75% positivity rate, and is associated with poor prognosis. GPC3 is not expressed in healthy or non-malignant liver tissue. Targeting GPC3 could fulfill an unmet medical need for HCC, a leading cause of cancer-related deaths worldwide for which efficacious therapies are lacking. The differential expression of GPC3 between tumor and normal tissues provides an opportunity for GPC3-targeted radiopharmaceutical therapy (RPT) to treat HCC. Methods: RAYZ-8009 is comprised of a novel macrocyclic peptide binder to GPC3, a linker, and chelator DOTA that can be complexed with different radioisotopes. The affinity of peptide binders to GPC3 was determined by surface plasma resonance (SPR), as well as a radioligand binding assay in human HCC cell line HepG2. The cross-species binding was assessed by radioligand binding using recombinant mouse, cynomolgus monkey, and human GPC3 proteins. Target-mediated internalization in HepG2 cells was measured using Microbeta at various time points. In vivo biodistribution with 177Lu, and anti-tumor efficacy studies using 225Ac were performed in HepG2 tumor-bearing athymic nude mice. Results: RAYZ-8009 showed high binding affinity to human GPC3 with a KD of 0.7 nM as determined by SPR. Binding affinity was maintained across mouse, cynomolgus monkey and human GPC3. Potent cellular binding was confirmed in GPC3+ HepG2 cells, and was independent of choice of isotope. 177Lu-RAYZ-8009 showed fast and efficient internalization with 42% internalized by 20 minutes in HepG2 cells. In vivo biodistribution of 177Lu-RAYZ-8009 showed tumor uptake of 19.8, 16.6, 16.4, and 8.8 %ID/g at 2, 24, 48, and 96 hours, respectively. Renal uptake was 16.1, 4.7, 1.6, and 0.7 %ID/g at the same timepoints, with tumor/kidney ratios of 1.3, 3.7, 11.3, and 15.0, respectively. Minimal uptake was observed in other normal tissues. Tumor-specific uptake and retention were also observed when tumors were implanted orthotopically with no uptake in non-malignant liver tissue. Furthermore, significant tumor growth inhibition and survival benefit were achieved with 225Ac-RAYZ-8009 in GPC3+ HCC xenografts. Conclusions: Preclinical pharmacodynamic, pharmacokinetic, biodistribution and efficacy data demonstrate the potential of RAYZ-8009 as a RPT agent for the treatment of patients with GPC3-positive HCC.

Roles of ribosomal proteins in hematologic disorders and cancers: a review

Abstract Ribosomes are important organelles for synthesizing proteins in cells. They are composed of ribosomal RNA and more than 80 ribosomal proteins. It is well known that an essential function of ribosomal proteins is to participate in protein translation. In addition, ribosomal proteins also perform extra-ribosomal functions, such as participating in DNA replication, transcription, and damage repair, regulating cell growth, proliferation, apoptosis, and transformation. In recent years, studies have shown that alterations in ribosomal protein synthesis or function can lead to various hematologic diseases, including Diamond-Blackfan anemia, 5q-syndrome, Shwachman-Diamond syndrome, and other blood system diseases. Moreover, abnormal expressions of specific ribosomal protein genes have been reported in many malignant tumors. In this review, we elaborated on the changes in ribosomal proteins in hepatocellular carcinoma and colorectal, prostate, gastric, esophageal, and other cancers and discussed the relationship between ribosomal proteins and the occurrence of hematologic disorders and cancers.

NamiRNA-mediated high expression of KNSTRN correlates with poor prognosis and immune infiltration in hepatocellular carcinoma.

Mutations of kinetochore-localized astrin/sperm-associated antigen 5 (KNSTRN) can interfere with chromatid cohesion, increase aneuploidy in tumours, and enhance tumourigenesis. However, the role of the KNSTRN-binding protein in hepatocellular carcinoma (HCC) remains unclear. Using The Cancer Genome Atlas databases, we investigated the potential oncogenic functions of KNSTRN in HCC along with R and various computational tools. Detailed results revealed that elevated expression of KNSTRN was considerably associated with poor overall survival (HR = 1.48, 95% CI: 1.05-2.09, p = 0.027) and progress-free interval (HR = 1.41, 95% CI: 1.05-1.89, p = 0.021) in HCC. Gene ontology/Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis showed that KNSTRN is closely related to organelle fission, chromosomal region, tubulin binding, and cell cycle signalling pathway. TIMER database analysis showed the correlations between KNSTRN expression and tumour-infiltrating immune cells, biomarkers of immune cells, and immune checkpoint expression. Moreover, the KNSTRN level was significantly positively associated with immunosuppressive cells in the tumour microenvironment, including regulatory T-cells, myeloid-derived suppressor cells, and cancer-associated fibrocytes. Finally, a possible nuclear activating miRNA (NamiRNA)-enhancer network of hsa-miR-107, which activates the KNSTRN expression in liver hepatocellular carcinoma, was constructed by correlation analysis. NamiRNA-mediated upregulation of KNSTRN correlated with poor prognosis and tumour immune infiltration in HCC. KNSTRN could serve as an effective biomarker for the diagnosis and prognosis of HCC and support the development of novel therapeutic strategies.

SMYD3 associates with the NuRD (MTA1/2) complex to regulate transcription and promote proliferation and invasiveness in hepatocellular carcinoma cells

BackgroundSMYD3, a member of the SET and MYND domain-containing (SMYD) family, is a histone methyltransferase (HMT) and transcription factor that plays an important role in transcriptional regulation in human carcinogenesis.ResultsUsing affinity purification and mass spectrometry assays to identify SMYD3-associated proteins in hepatocellular carcinoma (HCC) cells, we found several previously undiscovered SMYD3-interacting proteins, including the NuRD (MTA1/2) complex, the METTL family, and the CRL4B complex. Transcriptomic analysis of the consequences of knocking down SMYD3, MTA1, or MTA2 in HCC cells showed that SMYD3/NuRD complex targets a cohort of genes, some of which are critically involved in cell growth and migration. qChIP analyses showed that SMYD3 knockdown led to a significant reduction in the binding of MTA1 or MTA2 to the promoters of IGFBP4 and led to a significant decrease in H4K20me3 and a marked increase in H4Ac at the IGFBP4 promoter. In addition, we demonstrated that SMYD3 promotes cell proliferation, invasion, and tumorigenesis in vivo and in vitro and found that its expression is markedly upregulated in human liver cancer. Knockdown of MTA1 or MTA2 had the same effect as knockdown of SMYD3 on proliferation and invasion of hepatocellular carcinoma cells. Catalytic mutant SMYD3 could not rescue the phenotypic effects caused by knockdown of SMYD3. Inhibitors of SMYD3 effectively inhibited the proliferation and invasiveness of HCC cells.ConclusionsThese findings revealed that SMYD3 could transcriptionally repress a cohort of target genes expression by associating with the NuRD (MTA1/2) complex, thereby promoting the proliferation and invasiveness of HCC cells. Our results support the case for pursuing SMYD3 as a practical prognostic marker or therapeutic target against HCC.

Exploration and validation of the prognostic value of RNA-binding proteins in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. Increasing evidence suggests that the dysregulation of RNA-binding proteins (RBPs) is involved in the development of various cancers. However, there is a paucity of studies investigating the roles of RBPs in HCC. Data on HCC samples were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases (available at: www.ncbi.nlm.nih.gov/geo), and data regarding human RBPs were integrated from SONAR, XRNAX, and CARIC results. We identified modules associated with prognosis using weighted gene co-expression network analysis (WGCNA) and performed functional enrichment analysis. Univariate and least absolute shrinkage and selection operator (LASSO) regression analyses were used to identify prognostic RBPs and establish a prediction model. According to the median risk score, we separated patients into high- and low-risk groups and investigated the differences in immune cell infiltration, somatic mutations, and gene set enrichment. Univariate and multivariate regression analyses were used to identify prognostic factors for HCC. A nomogram was constructed, and its performance was evaluated with calibration curves. Sixteen RBPs (MEX3A, TTK, MRPL53, IQGAP3, PFN2, IMPDH1, TCOF1, DYNC1LI1, EIF2B4, NOL10, GNL2, EIF1B, PSMD1, AHSA1, SEC61A1, and YBX1) were identified as prognostic genes, and a prognostic model was established. Survival analysis indicated that the model had good predictive performance and that a high-risk score was significantly related to a poor prognosis. Additionally, there were significant differences in immune cell infiltration, somatic mutations, and gene set enrichment between the high- and low-risk groups. Univariate and multivariate regression analyses indicated that the RBP-based signature was an independent prognostic factor for HCC. The nomogram based on 16 RBPs performed well in predicting the overall survival of HCC patients. The RBP-based signature is an independent prognostic factor for HCC, and this study could provide an innovative method for analyzing prognostic biomarkers and therapeutic targets for HCC.