Several microRNAs could predict survival in patients with hepatitis B-related liver cancer

Anti-Osteoarthritis Mechanism of the Nrf2 Signaling Pathway

Osteoarthritis (OA) is a chronic degenerative disease and the primary pathogenic consequence of OA is inflammation, which can affect a variety of tissues including the synovial membrane, articular cartilage, and subchondral bone. The development of the intra-articular microenvironment can be significantly influenced by the shift of synovial macrophages between pro-inflammatory and anti-inflammatory phenotypes. By regulating macrophage inflammatory responses, the NF-κB signaling route is essential in the therapy of OA; whereas, the nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway appears to manage the relationship between oxidative stress and inflammation. Additionally, it has been demonstrated that under oxidative stress and inflammation, there is a significant interaction between transcriptional pathways involving Nrf2 and NF-κB. Studying how Nrf2 signaling affects inflammation and cellular metabolism may help us understand how to treat OA by reprogramming macrophage behavior because Nrf2 signaling is thought to affect cellular metabolism. The candidates for treating OA by promoting an anti-inflammatory mechanism by activating Nrf2 are also reviewed in this paper.

Dysregulated microRNAs as a biomarker for diagnosis and prognosis of hepatitis B virus-associated hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a malignancy with a high incidence and fatality rate worldwide. Hepatitis B virus (HBV) infection is one of the most important risk factors for its occurrence and development. Early detection of HBV-associated HCC (HBV-HCC) can improve clinical decision-making and patient outcomes. Biomarkers are extremely helpful, not only for early diagnosis, but also for the development of therapeutics. MicroRNAs (miRNAs), a subset of non-coding RNAs approximately 22 nucleotides in length, have increasingly attracted scientists' attention due to their potential utility as biomarkers for cancer detection and therapy. HBV profoundly impacts the expression of miRNAs potentially involved in the development of hepatocarcinogenesis. In this review, we summarize the current progress on the role of miRNAs in the diagnosis and treatment of HBV-HCC. From a molecular standpoint, we discuss the mechanism by which HBV regulates miRNAs and investigate the exact effect of miRNAs on the promotion of HCC. In the near future, miRNA-based diagnostic, prognostic, and therapeutic applications will make their way into the clinical routine.

Significance of logistic regression scoring model based on natural killer cell-mediated cytotoxic pathway in the diagnosis of colon cancer

Background

The poor clinical accuracy to predict the survival of colon cancer patients is associated with a high incidence rate and a poor 3-year survival rate. This study aimed to identify the poor prognostic biomarkers of colon cancer from natural killer cell-mediated cytotoxic pathway (NKCP), and establish a logistical regression scoring model to predict its prognosis.

Methods

Based on the expressions and methylations of NKCP-related genes (NRGs) and the clinical information, dimensionality reduction screening was performed to establish a logistic regression scoring model to predict survival and prognosis. Risk score, clinical stage, and ULBP2 were used to establish a logistic regression scoring model to classify the 3-year survival period and compare with each other. Comparison of survival, tumor mutation burden (TMB), estimation of immune invasion, and prediction of chemotherapeutic drug IC50 were performed between low- and high-risk score groups.

Results

This study found that ULBP2 was significantly overexpressed in colon cancer tissues and colon cancer cell lines. The logistic regression scoring model was established to include six statistically significant features: S = 1.70 × stage - 9.32 × cg06543087 + 6.19 × cg25848557 + 1.29 × IFNA1 + 0.048 × age + 4.37 × cg21370856 - 8.93, which was used to calculate risk score of each sample. The risk scores, clinical stage, and ULBP2 were classified into three-year survival, the 3-year prediction accuracy based on 10-fold cross-validation was 80.17%, 67.24, and 59.48%, respectively. The survival time of low-risk score group was better than that of the high-risk score group. Moreover, compared to high-risk score group, low-risk score group had lower TMB [2.20/MB (log10) vs. 2.34/MB (log10)], higher infiltration score of M0 macrophages (0.17 vs. 0.14), and lower mean IC50 value of oxaliplatin (3.65 vs 3.78) (p < 0.05).

Conclusions

The significantly upregulated ULBP2 was a poor prognostic biomarker of colon cancer. The risk score based on the six-feature logistic regression model can effectively predict the 3-year survival time. High-risk score group demonstrated a poorer prognosis, higher TMB, lower M0 macrophage infiltration score, and higher IC50 value of oxaliplatin. The six-feature logistic scoring model has certain clinical significance in colon cancer.

Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle

Background

Genotypic information produced from single nucleotide polymorphism (SNP) arrays has routinely been used to identify genomic regions associated with complex traits in beef and dairy cattle. Herein, we assembled a dataset consisting of 15,815 Red Angus beef cattle distributed across the continental U.S. and a union set of 836,118 imputed SNPs to conduct genome-wide association analyses (GWAA) for growth traits using univariate linear mixed models (LMM); including birth weight, weaning weight, and yearling weight. Genomic relationship matrix heritability estimates were produced for all growth traits, and genotype-by-environment (GxE) interactions were investigated.

Results

Moderate to high heritabilities with small standard errors were estimated for birth weight (0.51 ± 0.01), weaning weight (0.25 ± 0.01), and yearling weight (0.42 ± 0.01). GWAA revealed 12 pleiotropic QTL (BTA6, BTA14, BTA20) influencing Red Angus birth weight, weaning weight, and yearling weight which met a nominal significance threshold (P ≤ 1e-05) for polygenic traits using 836K imputed SNPs. Moreover, positional candidate genes associated with Red Angus growth traits in this study (i.e., LCORL, LOC782905, NCAPG, HERC6, FAM184B, SLIT2, MMRN1, KCNIP4, CCSER1, GRID2, ARRDC3, PLAG1, IMPAD1, NSMAF, PENK, LOC112449660, MOS, SH3PXD2B, STC2, CPEB4) were also previously associated with feed efficiency, growth, and carcass traits in beef cattle. Collectively, 14 significant GxE interactions were also detected, but were less consistent among the investigated traits at a nominal significance threshold (P ≤ 1e-05); with one pleiotropic GxE interaction detected on BTA28 (24 Mb) for Red Angus weaning weight and yearling weight.

Conclusions

Sixteen well-supported QTL regions detected from the GWAA and GxE GWAA for growth traits (birth weight, weaning weight, yearling weight) in U.S. Red Angus cattle were found to be pleiotropic. Twelve of these pleiotropic QTL were also identified in previous studies focusing on feed efficiency and growth traits in multiple beef breeds and/or their composites. In agreement with other beef cattle GxE studies our results implicate the role of vasodilation, metabolism, and the nervous system in the genetic sensitivity to environmental stress.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08667-6.

The Role, Significance, and Association of MicroRNA-10a/b in Physiology of Cancer

MicroRNAs (miRNAs) are small non-coding RNAs that regulate the translation of mRNA and protein, mainly at the posttranscriptional level. Global expression profiling of miRNAs has demonstrated a broad spectrum of aberrations that correlated with several diseases, and miRNA- 10a and miRNA-10b were the first examined miRNAs to be involved in abnormal activities upon dysregulation, including many types of cancers and progressive diseases. It is expected that the same miRNAs behave inconsistently within different types of cancer. This review aims to provide a set of information about our updated understanding of miRNA-10a and miRNA-10b and their clinical significance, molecular targets, current research gaps, and possible future applications of such potent regulators.

Comprehensive Analysis Identified ASF1B as an Independent Prognostic Factor for HBV-Infected Hepatocellular Carcinoma

Purpose

Hepatitis B (HBV)-infected hepatocellular carcinoma is one of the most common cancers, and it has high incidence and mortality rates worldwide. The incidence of hepatocellular carcinoma has been increasing in recent years, and existing treatment modalities do not significantly improve prognosis. Therefore, it is important to find a biomarker that can accurately predict prognosis.

Methods

This study was analyzed using the The Cancer Genome Atlas (TCGA) database and validated by the International Cancer Genome Consortium (ICGC) database. The STRING database was used to construct a gene co-expression network and visualize its functional clustering using Cytoscape. A prognostic signature model was constructed to observe high and low risk with prognosis, and independent prognostic factors for HBV-infected hepatocellular carcinoma were identified by Cox regression analysis. The independent prognostic factors were then analyzed for expression and survival, and their pathway enrichment was analyzed using gene set enrichment analysis (GSEA).

Results

805 differentially expressed genes (DEGs) were obtained by differential analysis. Protein–protein interaction (PPI) showed that DEGs were mostly clustered in functional modules, such as cellular matrix response, cell differentiation, and tissue development. Prognostic characterization models showed that the high-risk group was associated with poor prognosis, while Cox regression analysis identified ASF1B as the only independent prognostic factor. As verified by expression and prognosis, ASF1B was highly expressed in HBV-infected hepatocellular carcinoma and led to a poor prognosis. GSEA showed that high ASF1B expression was involved in cell cycle-related signaling pathways.

Conclusion

Bioinformatic analysis identified ASF1B as an independent prognostic factor in HBV-infected hepatocellular carcinoma, and its high expression led to a poor prognosis. Furthermore, it may promote hepatocellular carcinoma progression by affecting cell cycle-related signaling pathways.

Regulatory mechanisms and therapeutic targeting of vasculogenic mimicry in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a typical hyper-vascular solid tumor; aberrantly rich in tumor vascular network contributes to its malignancy. Conventional anti-angiogenic therapies seem promising but transitory and incomplete efficacy on HCC. Vasculogenic mimicry (VM) is one of functional microcirculation patterns independent of endothelial vessels which describes the plasticity of highly aggressive tumor cells to form vasculogenic-like networks providing sufficient blood supply for tumor growth and metastasis. As a pivotal alternative mechanism for tumor vascularization when tumor cells undergo lack of oxygen and nutrients, VM has an association with the malignant phenotype and poor clinical outcome for HCC, and may challenge the classic anti-angiogenic treatment of HCC. Current studies have contributed numerous findings illustrating the underlying molecular mechanisms and signaling pathways supporting VM in HCC. In this review, we summarize the correlation between epithelial-mesenchymal transition (EMT), cancer stem cells (CSCs) and VM, the role of hypoxia and extracellular matrix remodeling in VM, the involvement of adjacent non-cancerous cells, cytokines and growth factors in VM, as well as the regulatory influence of non-coding RNAs on VM in HCC. Moreover, we discuss the clinical significance of VM in practice and the potential therapeutic strategies targeting VM for HCC. A better understanding of the mechanism underlying VM formation in HCC may optimize anti-angiogenic treatment modalities for HCC.

Biology and Clinical Application of Regulatory RNAs in Hepatocellular Carcinoma

Most of the human genome consists of DNA genes that are translated into RNAs but not into proteins. These RNA molecules are named noncoding RNAs (ncRNA). While in the past it was thought that ncRNAs would be redundant without relevant functions, it is now well established that ncRNAs identify a class of regulatory molecules that finely tune cell homeostasis and are deregulated in disease states, including hepatocellular carcinoma (HCC). Of note, the number of ncRNAs within a cell increases progressively, with the complexity of the species indicating their essential role in the maintenance of regulatory networks that affect the intricacy of the organism. ncRNAs have been demonstrated to mediate HCC development and progression by affecting intrinsic cancer cell signaling and crosstalk between malignant cells and the microenvironment. Moreover, ncRNAs hold promise as clinical biomarkers, but further evidence is warranted before their translation and integration within clinical practice.

An Integrating Immune-Related Signature to Improve Prognosis of Hepatocellular Carcinoma

Growing evidence suggests that the superiority of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) could act as biomarkers for cancer prognosis. However, the prognostic marker for hepatocellular carcinoma with high accuracy and sensitivity is still lacking. In this research, a retrospective, cohort-based study of genome-wide RNA-seq data of patients with hepatocellular carcinoma was carried out, and two protein-coding genes (GTPBP4, TREM-1) and one lncRNA (LINC00426) were sorted out to construct an integrative signature to predict the prognosis of patients. The results show that both the AUC and the C-index of this model perform well in TCGA validation dataset, cross-platform GEO validation dataset, and different subsets divided by gender, stage, and grade. The expression pattern and functional analysis show that all three genes contained in the model are associated with immune infiltration, cell proliferation, invasion, and metastasis, providing further confirmation of this model. In summary, the proposed model can effectively distinguish the high- and low-risk groups of hepatocellular carcinoma patients and is expected to shed light on the treatment of hepatocellular carcinoma and greatly improve the patients' prognosis.

Long intergenic noncoding RNA01134 accelerates hepatocellular carcinoma progression by sponging microRNA-4784 and downregulating structure specific recognition protein 1

Dysregulation of long noncoding RNAs (lncRNAs) has been suggested to foster the carcinogenesis of hepatocellular carcinoma (HCC). To date, the role of long intergenic noncoding RNA01134 (LINC01134) in HCC have never been researched yet. Herein, we found that LINC01134 was highly expressed in HCC tissues in comparison with the matched normal liver tissues and increased LINC01134 expression correlated with shorter overall survival of patients with HCC. Additionally, we demonstrated LINC01134 downregulation significantly suppressed the proliferation ability and colony formation capacity of HCC cells. Furthermore, we revealed that LINC01134 functioned as a competitive endogenous RNA (ceRNA) for miR-4784 to upregulate structure-specific recognition protein 1 (SSRP1) in HCC cells. Meanwhile, miR-4784 inhibitor or restoration of SSRP1 could markedly attenuate the inhibitory effect of LINC01134 downregulation on HCC cells. Taken together, LINC01134 may promote the carcinogenesis of HCC at least partly via the miR-4784/SSRP1 axis. Therefore, LINC01134/miR-4784/SSRP1 axis should be developed as the promising therapeutic target for HCC.

Dysregulated microRNAs in Hepatitis B Virus-Related Hepatocellular Carcinoma: Potential as Biomarkers and Therapeutic Targets

MicroRNAs (miRNAs) are non-coding small RNAs that can function as gene regulators and are involved in tumorigenesis. We review the commonly dysregulated miRNAs in liver tumor tissues and plasma/serum of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) patients. The frequently reported up-regulated miRNAs in liver tumor tissues include miR-18a, miR-21, miR-221, miR-222, and miR-224, whereas down-regulated miRNAs include miR-26a, miR-101, miR-122, miR-125b, miR-145, miR-199a, miR-199b, miR-200a, and miR-223. For a subset of these miRNAs (up-regulated miR-222 and miR-224, down-regulated miR-26a and miR-125b), the pattern of dysregulated circulating miRNAs in plasma/serum is mirrored in tumor tissue based on multiple independent studies. Dysregulated miRNAs target oncogenes or tumor suppressor genes involved in hepatocarcinogenesis. Normalization of dysregulated miRNAs by up- or down-regulation has been shown to inhibit HCC cell proliferation or sensitize liver cancer cells to chemotherapeutic treatment. miRNAs hold as yet unrealized potential as biomarkers for early detection of HCC and as precision therapeutic targets, but further studies in diverse populations and across all stages of HCC are needed.

The prognostic and diagnostic values of MicroRNA-10b in gastric cancer: A comprehensive study based on meta-analysis and TCGA database

We conducted a study to evaluate the prognostic and diagnostic values of microRNA-10b (miR-10b) in gastric cancer (GC) based on meta-analysis and TCGA database. Relevant studies were searched in English and Chinese database and meta-analysis was conducted on Stata 12.0. The expression value of miR-10b and clinical parameters of GC patients were downloaded from TCGA database, and relevant analyses were conducted on SPSS. High expression of miR-10b was linked with unfavorable overall survival (OS) in GC (HR = 1.572, 95% CI: 1.240-1.992, P < .001). However, the meta-analysis was significant for patients in early stage, but not for patients in advanced stage. The expression of miR-10b-3p was significantly lower in cancer tissue compared with adjacent tissue (P < .001). Meanwhile, the area under the ROC curve (AUC) value was 0.652 (0.562-0.742), P = .001. Disease-free survival analysis showed increasing miR-10b-5p was correlated with worse survival outcome (HR = 2.366, 95% CI: 1.414-3.959, P = .001). In conclusion, miR-10b acts as a tumor suppressor with prognostic and diagnostic values for GC.

Two predictive precision medicine tools for hepatocellular carcinoma

Background

Hepatocellular carcinoma (HCC) is a serious threat to public health due to its poor prognosis. The current study aimed to develop and validate a prognostic nomogram to predict the overall survival of HCC patients.

Methods

The model cohort consisted of 24,991 mRNA expression data points from 348 HCC patients. The least absolute shrinkage and selection operator method (LASSO) Cox regression model was used to evaluate the prognostic mRNA biomarkers for the overall survival of HCC patients.

Results

Using multivariate Cox proportional regression analyses, a prognostic nomogram (named Eight-mRNA prognostic nomogram) was constructed based on the expression data of N4BP3, -ADRA2B, E2F8, MAPT, PZP, HOXD9, COL15A1, and -NDST3. The C-index of the Eight-mRNA prognostic nomogram was 0.765 (95% CI 0.724-0.806) for the overall survival in the model cohort. The Harrell's concordance-index of the Eight-mRNA prognostic nomogram was 0.715 (95% CI 0.658-0.772) in the validation cohort. The survival curves demonstrated that the HCC patients in the high risk group had a significantly poorer overall survival than the patients in the low risk group.

Conclusion

In the current study, we have developed two convenient and efficient predictive precision medicine tools for hepatocellular carcinoma. These two predictive precision medicine tools are helpful for predicting the individual mortality risk probability and improving the personalized comprehensive treatments for HCC patients. The Smart Cancer Predictive System can be used by clicking the following URL: https://zhangzhiqiao2.shinyapps.io/Smart_cancer_predictive_system_HCC_2/. The Gene Survival Analysis Screen System is available at the following URL: https://zhangzhiqiao5.shinyapps.io/Gene_Survival_Analysis_A1001/.

Anti-angiogenesis triggers exosomes release from endothelial cells to promote tumor vasculogenesis

Although anti-angiogenic therapies (AATs) have some effects against multiple malignancies, they are limited by subsequent tumor vasculogenesis and progression. To investigate the mechanisms by which tumor vasculogenesis and progression following AATs, we transfected microRNA (miR)-9 into human umbilical vein endothelial cells (HUVECs) to mimic the tumor-associated endothelial cells in hepatocellular carcinoma and simulated the AATs in vitro and in vivo. We found that administration of the angiogenesis inhibitor vandetanib completely abolished miR-9-induced angiogenesis and promoted autophagy in HUVECs, but induced the release of vascular endothelial growth factor (VEGF)-enriched exosomes. These VEGF-enriched exosomes significantly promoted the formation of endothelial vessels and vasculogenic mimicry in hepatocellular carcinoma and its progression in mice. Anti-autophagic therapy is proposed to improve the efficacy of AATs. However, similar effects by AATs were observed with the application of anti-autophagy by 3-methyladenine. Our results revealed that tumor vasculogenesis and progression after AATs and anti-autophagic therapies were due to the cross-talk between endothelial and tumor cells via VEGF-enriched exosomes.

Abnormal expression of miR-4784 in chondrocytes of osteoarthritis and associations with chondrocyte hyperplasia

The aim of the present study was to assess the expression of microRNA (miRNA)-4784 in the chondrocytes of early osteoarthritis (OA) and to determine the effect of double-stranded (ds)-miRNA-4784 transfection on chondrocyte function. Following the construction of an OA rabbit model, normal chondrocytes (normal control group), OA chondrocytes obtained 4 weeks after modeling (OA at week 4 group) and 8 weeks after modeling (OA at week 8 group) were used. The relative expression of miRNA-4784 in each group was detected using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Western blotting was performed to measure the expression of type II collagen (Col2a1) and matrix metalloproteinase (MMP)-3 in each group with or without ds-miRNA-4784 transfection. The results revealed that the levels of miR-4784 in groups OA at week 4 and 8 were significantly lower than that of normal control group (P<0.05). It was also demonstrated that Col2a1 mRNA expression levels in groups OA at week 4 and 8 were 49 and 38% of that in the normal control group, respectively. Furthermore, MMP-3 mRNA expression levels increased by 3.12- and 3.95-fold in groups OA at week 4 and 8, respectively, compared with those in the normal control group (P<0.01). Following transfection with ds-miRNA-4784, Col2a1 mRNA expression levels increased by 63 and 126% compared with the levels prior to treatment in groups OA at week 4 and 8, respectively (P<0.01). The expression levels of MMP-3 mRNA in groups OA at week 4 and 8 decreased following transfection compared with the levels prior to treatment. Col2a1 and MMP-3 protein expression exhibited similar patterns to the mRNA expression. In summary, the results of the present study suggest that miRNA-4784 expression is significantly reduced in early stage OA chondrocytes. Transfection with ds-miRNA-4784 promotes the expression of Col2a1 and inhibits the MMP-3 expression in chondrocytes.

Prospect of Circular RNA in Hepatocellular Carcinoma: A Novel Potential Biomarker and Therapeutic Target

CircRNA, a kind of tissue specific and covalently closed circular non-coding RNA is very abundant in eukaryocyte. Generally, circRNA is generated by back-splicing of protein-coding genes' pre-mRNA. Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. Due to the characteristics of poor prognosis and high recurrence, the pathogenesis of HCC is highly concerned by researchers worldwide. Recent studies demonstrated that numerous circRNAs were differentially expressed in HCC tissues and normal liver tissues, which is closely related with the development and prognosis of HCC. However, the mechanism of circRNA in HCC remains unclear. In this review, we summarized the abnormal expressions of circRNAs in HCC, discussed its role, and potential mechanisms, and tried to explore the prospective values of circRNA in the diagnosis, therapy, and prognosis of HCC.

Circular RNA circMTO1 acts as the sponge of microRNA-9 to suppress hepatocellular carcinoma progression

Noncoding RNAs play important roles in cancer biology, providing potential targets for cancer intervention. As a new class of endogenous noncoding RNAs, circular RNAs (circRNAs) have been recently identified in cell development and function, and certain types of pathological responses, generally acting as a microRNA (miRNA) sponge to regulate gene expression. Identifying the deregulated circRNAs and their roles in cancer has attracted much attention. However, the expression profile and function of circRNAs in human hepatocellular carcinoma (HCC) remain to be investigated. Here, we analyzed the expression profile of human circRNAs in HCC tissues and identified circMTO1 (mitochondrial translation optimization 1 homologue; hsa_circRNA_0007874/hsa_circRNA_104135) as one circRNA significantly down-regulated in HCC tissues. HCC patients with low circMTO1 expression had shortened survival. By using a biotin-labeled circMTO1 probe to perform RNA in vivo precipitation in HCC cells, we identified miR-9 as the circMTO1-associated miRNA. Furthermore, silencing of circMTO1 in HCC could down-regulate p21, the target of oncogenic miR-9, resulting in the promotion of HCC cell proliferation and invasion. In addition, the tumor-promoting effect of circMTO1 silencing was blocked by miR9 inhibitor. Intratumoral administration of cholesterol-conjugated circMTO1 small interfering RNA promoted tumor growth in HCC-bearing mice in vivo.

CONCLUSION

circMTO1 suppresses HCC progression by acting as the sponge of oncogenic miR-9 to promote p21 expression, suggesting that circMTO1 is a potential target in HCC treatment. The decrease of circMTO1 in HCC tissues may serve as a prognosis predictor for poor survival of patients. (Hepatology 2017;66:1151-1164).