RESUMEN
Clear-cell renal-cell carcinoma (ccRCC) is a silent-development pathology with a high rate of metastasis in patients. The activity of coding genes in metastatic progression is well known. New studies evaluate the association with non-coding genes, such as competitive endogenous RNA (ceRNA). This study aims to build a ceRNA network and a gene signature for ccRCC associated with metastatic development and analyze their biological functions. Using data from The Cancer Genome Atlas (TCGA), we constructed the ceRNA network with differentially expressed genes, assembled nine preliminary gene signatures from eight feature selection techniques, and evaluated the classification metrics to choose a final signature. After that, we performed a genomic analysis, a risk analysis, and a functional annotation analysis. We present an 11-gene signature: SNHG15, AF117829.1, hsa-miR-130a-3p, hsa-mir-381-3p, BTBD11, INSR, HECW2, RFLNB, PTTG1, HMMR, and RASD1. It was possible to assess the generalization of the signature using an external dataset from the International Cancer Genome Consortium (ICGC-RECA), which showed an Area Under the Curve of 81.5%. The genomic analysis identified the signature participants on chromosomes with highly mutated regions. The hsa-miR-130a-3p, AF117829.1, hsa-miR-381-3p, and PTTG1 were significantly related to the patient's survival and metastatic development. Additionally, functional annotation resulted in relevant pathways for tumor development and cell cycle control, such as RNA polymerase II transcription regulation and cell control. The gene signature analysis within the ceRNA network, with literature evidence, suggests that the lncRNAs act as "sponges" upon the microRNAs (miRNAs). Therefore, this gene signature presents coding and non-coding genes and could act as potential biomarkers for a better understanding of ccRCC.
Asunto(s)
Carcinoma de Células Renales , Regulación Neoplásica de la Expresión Génica , Redes Reguladoras de Genes , Neoplasias Renales , Aprendizaje Automático , Humanos , Carcinoma de Células Renales/genética , Carcinoma de Células Renales/patología , Neoplasias Renales/genética , Neoplasias Renales/patología , Biomarcadores de Tumor/genética , Metástasis de la Neoplasia/genética , MicroARNs/genética , Perfilación de la Expresión Génica/métodos , Transcriptoma , ARN Endógeno CompetitivoRESUMEN
Colorectal cancer (CRC) represents the second deadliest malignancy worldwide. Around 75% of CRC patients exhibit high levels of chromosome instability that result in the accumulation of somatic copy number alterations. These alterations are associated with the amplification of oncogenes and deletion of tumor-ppressor genes and contribute to the tumoral phenotype in different malignancies. Even though this relationship is well known, much remains to be investigated regarding the effect of said alterations in long non-coding RNAs (lncRNAs) and, in turn, the impact these alterations have on the tumor phenotype. The present study aimed to evaluate the role of differentially expressed lncRNAs coded in regions with copy number alterations in colorectal cancer patient samples. We downloaded RNA-seq files of the Colorectal Adenocarcinoma Project from the The Cancer Genome Atlas (TCGA) repository (285 sequenced tumor tissues and 41 non-tumor tissues), evaluated differential expression, and mapped them over genome sequencing data with regions presenting copy number alterations. We obtained 78 differentially expressed (LFC > 1|< -1, padj < 0.05) lncRNAs, 410 miRNAs, and 5028 mRNAs and constructed a competing endogenous RNA (ceRNA) network, predicting significant lncRNA-miRNA-mRNA interactions. Said network consisted of 30 lncRNAs, 19 miRNAs, and 77 mRNAs. To understand the role that our ceRNA network played, we performed KEGG and GO analysis and found several oncogenic and anti-oncogenic processes enriched by the molecular players in our network. Finally, to evaluate the clinical relevance of the lncRNA expression, we performed survival analysis and found that C5orf64, HOTAIR, and RRN3P3 correlated with overall patient survival. Our results showed that lncRNAs coded in regions affected by SCNAs form a complex gene regulatory network in CCR.
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INTRODUCTION: As ceRNA network of long non-coding RNA (lncRNA)-microRNA (miR)-messenger RNAs (mRNA) can be predicted on the basis of bioinformatics tools, we are now one step closer to deeper understanding carcinogenic mechanisms. In this study, we clarified the mechanistic understanding of JHDM1D-AS1-miR-940-ARTN ceRNA network in the development of breast cancer (BC). MATERIALS AND METHODS: The lncRNA-miRNA-mRNA interaction of interest was predicted by in silico analysis and identified by conducting RNA immunoprecipitation, RNA pull-down and luciferase assays. The expression patterns of JHDM1D-AS1, miR-940 and ARTN in BC cells were altered by lentivirus infection and plasmid transfection for functional assays on the biological properties of BC cells. Finally, the tumorigenic and metastatic abilities of BC cells were assessed in vivo. RESULTS: JHDM1D-AS1 was highly expressed, while miR-940 was poorly expressed in BC tissues and cells. JHDM1D-AS1 could competitively bind to miR-940, whereby promoting the malignant behaviors of BC cells. Furthermore, ARTN was identified as a target gene of miR-940. Through targeting ARTN, miR-940 exerted a tumor-suppressive role. In vivo experiments further confirmed that JHDM1D-AS1 enhanced the tumorigenesis and metastasis through up-regulation of ARTN. CONCLUSIONS: Taken together, our study demonstrated the involvement of ceRNA network JHDM1D-AS1-miR-940-ARTN in the progression of BC, which highlighted promising therapeutic targets for BC treatment.
Asunto(s)
Neoplasias de la Mama , MicroARNs , ARN Largo no Codificante , Humanos , Femenino , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , Proliferación Celular/genética , MicroARNs/genética , MicroARNs/metabolismo , Neoplasias de la Mama/patología , Transformación Celular Neoplásica/genética , Carcinogénesis/genética , ARN Mensajero/genética , Regulación Neoplásica de la Expresión Génica , Línea Celular TumoralRESUMEN
BACKGROUND: Acute myeloid leukemia (AML) is a hematological malignancy with high molecular and clinical heterogeneity, and is the most common type of acute leukemia in adults. Due to limited treatment options, AML is prone to relapse and has a poor prognosis. Excision repair cross-complementing 3 (ERCC3) is an important member of nucleotide excision repair (NER) that is overexpressed in types of solid cancers and potentially regarded as a prognostic factor. However, its role in AML remains unclear. The purpose of this study was to explore ERCC3 expression and functions in AML. METHODS: The Cancer Genome Atlas (TCGA) and GEO (Gene Expression Omnibus) were used to test the accuracy of ERCC3 expression levels for AML diagnosis. Using online databases and R packages, we also explored the signaling pathway, epigenetic regulation, infiltration of immune cells, clinical prognostic value, and ceRNA network in AML. RESULTS: Our results revealed that ERCC3 expression was increased in AML and that high ERCC3 expression had good value for disease-free survival and overall survival in AML patients who underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT). We found that ERCC3 and co-expressed genes were mainly involved in chemical carcinogenesis/reactive oxygen species, ubiquitin-mediated protein degradation and oxidative phosphorylation. In addition, almost all the m6A-related coding genes (except GF2BP1) were positively associated with ERCC3 expression. We also constructed a ceRNA regulatory network containing ERCC3 in AML and identified 6 pairs of ceRNA networks, indicating that ERCC3 expression is regulated by a noncoding RNA system. CONCLUSION: This study demonstrated that ERCC3 was overexpressed in AML and that high ERCC3 expression can be considered a biomarker conducive to allo-HSCT in AML patients.