XIAP, commonly targeted by tumor suppressive miR-3607-5p and miR-3607-3p, promotes proliferation and inhibits apoptosis in hepatocellular carcinoma

Identification of a hypoxia-suppressed lncRNA RAMP2-AS1 in breast cancer

Hypoxia is a critical feature of solid tumors and exerts crucial roles in cancers, including breast cancer. However, the detailed relationship between lncRNA-miRNA-mRNA triple network and hypoxia in breast cancer is still indistinct. In this study, a series of in silico analyses and online databases or tools were employed to establish a hypoxia-related lncRNA-miRNA-mRNA network in breast cancer based on competing endogenous RNA mechanism at single-cell resolution. RAMP2-AS1 was, eventually, identified as the most potential lncRNA, which was significantly negatively associated with hypoxia in breast cancer. Compared with normal controls, RAMP2-AS1 was markedly downregulated in breast cancer. Moreover, survival analysis revealed favorable prognostic values of RAMP2-AS1 in total or in specific clinicopathological breast cancer patients. Next, miR-660-5p, miR-2277-5p and miR-1301-3p, upregulated and possessed poor prognostic values in breast cancer, were identified as three potential downstream miRNAs of RAMP2-AS1. Then, the most potential downstream hypoxia-related genes (ATM and MYH11) of RAMP2-AS1/miRNA axis in breast cancer were screened out. Intriguingly, in vitro experiments confirmed that RAMP2-AS1 was a hypoxia-suppressed lncRNA and miR-660-5p/ATM was a potential downstream axis of RAMP2-AS1 in breast cancer. Collectively, our current data elucidated a key hypoxia-suppressed lncRNA RAMP2-AS1 and its possible miRNA-mRNA regulatory mechanism in breast cancer.

Integrated analysis reveals a potential cuproptosis-related ceRNA axis SNHG17/miR-29a-3p/GCSH in prostate adenocarcinoma

Cuproptosis is a novel form of programmed cell death. The role and mechanism of cuproptosis-related genes in prostate adenocarcinoma have not been fully understood. In this study, a series of bioinformatic analyses were performed. Consequently, glycine cleavage system protein H with high expression and unfavorable prognosis was regarded as the most potential cuproptosis-related gene in prostate adenocarcinoma. Moreover, glycine cleavage system protein H might be a promising indicator for predicting leuprolide sensitivity in prostate adenocarcinoma and three potential drugs targeting glycine cleavage system protein H were identified. Enrichment analysis revealed that glycine cleavage system protein H-correlated genes were significantly enriched in tricarboxylic acid cycle-related pathways. Subsequently, small nucleolar RNA host gene 17/miR-29a-3p axis was found to partially account for overexpression of glycine cleavage system protein H in prostate adenocarcinoma. Collectively, the current study elucidated a potential cuproptosis-related competing endogenous RNA axis small nucleolar RNA host gene 17/miR-29a-3p/glycine cleavage system protein H in prostate adenocarcinoma.

In silico whole-transcriptome analysis reveals a potential hsa_circ_0000375-miR-424-5p-TPM2/SRPX/SRGAP1 regulatory network related to liver metastasis of colorectal cancer

Liver metastasis is the main lethal cause of colorectal cancer (CRC). The knowledge of role and mechanism of circular RNA (circRNA) in liver metastasis of CRC is still inadequate. In this study, whole-transcriptome analysis was performed using three datasets (GSE147597, GSE147602 and GSE147603). A total of 14 potential circRNAs were identified, after which their structural patterns and binding miRNAs were obtained. Next, 45 differentially expressed miRNAs (DEmiRNAs) between CRC without and with liver metastasis were acquired, consisting 38 upregulated and 7 downregulated miRNAs. After conducting intersection analysis, expression validation and correlation analysis, miR-761 and miR-424-5p were selected as the most potential miRNAs linked to liver metastasis of CRC. Subsequently, the target genes of miR-761 or miR-424-5p were predicted and differentially expressed genes (DEGs) between CRC without and with liver metastasis were obtained. 257 genes that were commonly appeared in predicted genes and DEGs were significantly enriched in "epithelial-to-mesenchymal transition" and "signaling by Robo receptor". Among these enriched genes, only TPM2, SRPX and SRGAP1 were significantly negatively correlated with miR-424-5p and were positively linked to hsa_circ_0000375 in CRC without or with liver metastasis. Collectively, the current findings elucidated a potential hsa_circ_0000375-miR-424-5p-TPM2/SRPX/SRGAP1 network contributing to liver metastasis of CRC.

Necroptosis-related signatures identify two distinct hepatocellular carcinoma subtypes: Implications for predicting drug sensitivity and prognosis

Background

Necroptosis is associated with oncogenesis, tumor immunity and progression. This research aims to investigate the association of necroptosis-related genes with drug sensitivity and prognosis in hepatocellular carcinoma (HCC).

Methods

Based on necroptosis-related signatures, HCC patients retrieved from the TCGA database were categorized. Survival outcomes, mutation profile, immune microenvironment, and drug sensitivity between HCC subtypes were further compared. Then, LASSO analysis was performed to construct a necroptosis-related prognostic signature, which was further evaluated using another independent cohort.

Results

A total of 371 patients with HCC could be categorized into two necroptosis-related subtypes. About 36% of patients were allocated to subtype A, with worse survival, more mutant TP53, and a lower likelihood of immunotherapy response. In contrast, patients in subtype B had a favorable prognosis, with lower expression of immunosuppressive signatures but a lower abundance of B and CD8⁺ T-cell infiltration. The prognostic risk score calculated using the expression levels of nine genes involved in the necroptosis pathway (MLKL, FADD, XIAP, USP22, UHRF1, CASP8, RIPK3, ZBP1, and FAS) showed a significant association with tumor stage, histologic grade, and Child‒Pugh score. Additionally, the risk score model was proven to be accurate in both the training and independent external validation cohorts and performed better than the TNM staging system and three well-recognized risk score models.

Conclusions

Based on necroptosis-related signatures, we identified two HCC subtypes with distinctive immune microenvironments, mutation profiles, drug sensitivities, and survival outcomes. A novel well-performing prognostic model was further constructed.

Comprehensive analysis reveals the involvement of hsa_circ_0037858/miR-5000-3p/FMR1 axis in malignant metastasis of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is a heterogenous tumor with high metastatic potential. Circular RNAs (circRNAs) play key roles in cancer initiation and progression. However, the knowledge of circRNA in ccRCC metastasis is still inadequate. In this study, a series of in silico analyses and experimental validation were employed. The differentially expressed circRNAs (DECs) between ccRCC and normal or metastatic ccRCC tissues were screened out using GEO2R. Hsa_circ_0037858 was identified as the most potential circRNA related to ccRCC metastasis, which was significantly downregulated in ccRCC compared with normal and was also markedly decreased in metastatic ccRCC compared with primary ccRCC. The structural pattern of hsa_circ_0037858 presented several microRNA response elements and four binding miRNAs of hsa_circ_0037858, consisting of miR-3064-5p, miR-6504-5p, miR-345-5p and miR-5000-3p, were predicted using CSCD and starBase. Among them, miR-5000-3p with high expression and statistical diagnostic value was considered as the most potential binding miRNA of hsa_circ_0037858. Then, protein-protein interaction analysis revealed a close linkage among the target genes of miR-5000-3p and the top 20 hub genes among them were identified. Based on node degree, MYC, RHOA, NCL, FMR1 and AGO1 were ranked as the top 5 hub genes. FMR1 was identified as the most potential downstream gene of hsa_circ_0037858/miR-5000-3p axis according to expression, prognosis and correlation analysis. Moreover, hsa_circ_0037858 suppressed in vitro metastasis and enhanced FMR1 expression in ccRCC, which could be markedly reversed by introduction of miR-5000-3p overexpression. Collectively, we elucidated a potential hsa_circ_0037858/miR-5000-3p/FMR1 axis involved in ccRCC metastasis.

Identification of multi-omics biomarkers and construction of the novel prognostic model for hepatocellular carcinoma

Genome changes play a crucial role in carcinogenesis, and many biomarkers can be used as effective prognostic indicators in various tumors. Although previous studies have constructed many predictive models for hepatocellular carcinoma (HCC) based on molecular signatures, the performance is unsatisfactory. Because multi-omics data can more comprehensively reflect the biological phenomenon of disease, we hope to build a more accurate predictive model by multi-omics analysis. We use the TCGA to identify crucial biomarkers and construct prognostic models through difference analysis, univariate Cox, and LASSO/stepwise Cox analysis. The performances of predictive models were evaluated and validated through survival analysis, Harrell’s concordance index (C-index), receiver operating characteristic (ROC) curve, and decision curve analysis (DCA). Multiple mRNAs, lncRNAs, miRNAs, CNV genes, and SNPs were significantly associated with the prognosis of HCC. We constructed five single-omic models, and the mRNA and lncRNA models showed good performance with c-indexes over 0.70. The multi-omics model presented a robust predictive ability with a c-index over 0.77. This study identified many biomarkers that may help study underlying carcinogenesis mechanisms in HCC. In addition, we constructed multiple single-omic models and an integrated multi-omics model that may provide practical and reliable guides for prognosis assessment.

Prognostic MicroRNA Panel for HCV-Associated HCC: Integrating Computational Biology and Clinical Validation

Early detection of hepatocellular carcinoma (HCC) will reduce morbidity and mortality rates of this widely spread disease. Dysregulation in microRNA (miRNA) expression is associated with HCC progression. The objective is to identify a panel of differentially expressed miRNAs (DE-miRNAs) to enhance HCC early prediction in hepatitis C virus (HCV) infected patients. Candidate miRNAs were selected using a bioinformatic analysis of microarray and RNA-sequencing datasets, resulting in nine DE-miRNAs (miR-142, miR-150, miR-183, miR-199a, miR-215, miR-217, miR-224, miR-424, and miR-3607). Their expressions were validated in the serum of 44 healthy individuals, 62 non-cirrhotic HCV patients, 67 cirrhotic-HCV, and 72 HCV-associated-HCC patients using real-time PCR (qPCR). There was a significant increase in serum concentrations of the nine-candidate miRNAs in HCC and HCV patients relative to healthy individuals. MiR-424, miR-199a, miR-142, and miR-224 expressions were significantly altered in HCC compared to non-cirrhotic patients. A panel of five miRNAs improved sensitivity and specificity of HCC detection to 100% and 95.12% relative to healthy controls. Distinguishing HCC from HCV-treated patients was achieved by 70.8% sensitivity and 61.9% specificity using the combined panel, compared to alpha-fetoprotein (51.4% sensitivity and 60.67% specificity). These preliminary data show that the novel miRNAs panel (miR-150, miR-199a, miR-224, miR-424, and miR-3607) could serve as a potential non-invasive biomarker for HCC early prediction in chronic HCV patients. Further prospective studies on a larger cohort of patients should be conducted to assess the potential prognostic ability of the miRNAs panel.

miR-10b-5p-mediated upregulation of PIEZO1 predicts poor prognosis and links to purine metabolism in breast cancer

BACKGROUND

Increasing evidence has reported the critical roles of PIEZO1 in organism. However, the knowledge of PIEZO1 in human cancers is still inadequate.

METHODS

In silico analyses and experimental validation were performed to analyze PIEZO1's expression, prognostic values and potential upstream/downstream mechanism in breast cancer.

RESULTS

PIEZO1 was significantly overexpressed in human breast cancer cell lines and tissue samples. PIEZO1 expression was statistically positively associated with malignant progression and short survival of breast cancer. miR-10b-5p downregulation was partially responsible for PIEZO1 upregulation in breast cancer. Further exploration revealed that PIEZO1 might exert its function by regulating purine metabolism (especially GUK1, POLD1 and APRT) in breast cancer.

CONCLUSIONS

Collectively, the current study elucidated an important role of PIEZO1 in breast cancer and providing key clues for identifying PIEZO1 as a therapeutic target and prognostic biomarker in breast cancer.