MicroRNA‑mRNA integrated analysis based on a case of well‑differentiated thyroid cancer with both metastasis and metastatic recurrence

Abstract

The incidence of well-differentiated thyroid cancer (WDTC) is rapidly increasing. Poor survival follows distant metastasis (DM) and recurrence. In the present study, we aimed to analyze the expression alterations in different stages of WDTC and the regulatory mechanism of DM and the recurrence of DM. A male patient diagnosed with follicular thyroid cancer and distant metastasis in the eleventh thoracic vertebrae received total thyroidectomy and the removal of a metastatic lesion. A local relapse was found in the vertebrae after four-time iodine-131 treatment. We performed mRNA and microRNA microarray on the paracancerous, cancerous, metastatic and metastatic recurrent tissue. In combination with the data of The Cancer Genome Atlas (TCGA), we used bioinformatics approaches to analyze the common alterations and microRNA-mRNA interactions among the processes of tumorigenesis and metastasis. Metastatic lesions and recurrent lesions were used to investigate the molecular mechanism of tumor evolution and recurrence in this case. A total of four mRNAs and two microRNAs were newly found to be related to patient survival in WDTC. The microRNA-mRNA interactions were predicted for the overlapped mRNAs and microRNAs. Lineage deregulation of genes, such as C-X-C motif chemokine receptor 4 (CXCR4) and thyroglobulin (TG) were found from the tumorigenic stage to the metastatic stage. The ribosome pathway was highly enriched in the bone metastasis compared with the cancerous tissue. The downstreaming effects of p53 were impaired in the recurrent lesion due to deregulation of several functional genes. The integrated analysis with TCGA data indicated several prognostic markers and regulatory networks for potential treatment. Our results also provided possible molecular mechanisms in which the ribosome and p53 pathways may respectively contribute to bone metastasis and local recurrence of metastasis MicroRNA-mRNA integrated analysis based on a case of well-differentiated thyroid cancer with both metastasis and metastatic recurrence

Dual Regulatory Mechanisms of Expression and Mutation Involving Metabolism-Related Genes FDFT1 and UQCR5 during CLM

“…To explore the functions of proteins that are dysregulated in CLM, we used DAVID (Database for Annotation, Visualization and Integrated Discovery) analysis software to classify the gene ontology of the 2,170 significantly altered proteins in MT tissues 19 (Figures S3A–S3C). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed proteins 20 revealed that metabolic pathways were altered in the MT samples, with 323 significantly differentially expressed proteins (14.88%) involved in metabolic pathways (Figure S3D), which suggests that metabolism-related pathways may play important roles in the liver metastasis of CRC 21, 22, 23, 24Figure 1Differently Expressed Protein and mRNA-Protein Correlation Analysis(A) Numbers of differently expressed proteins (≥2-fold difference; p < 0.05 with a FDR q value < 0.05) between the 44 CRC and paired PN samples, and the 23 MT and 21 NM samples.…”

Profiling and Integrated Analysis of Differentially Expressed MicroRNAs as Novel Biomarkers of Hepatocellular Carcinoma

“…STRING (version: 11.0; ) was used to analyze the interaction relationships between differential proteins ( 17 ). The species was set to human and the import gene set was set to all degrees.…”

“…Protein-Protein Interaction (PPI) Network and Module Analysis of Dif-mRNAs STRING (version: 11.0; https://www.string-db.org/) was used to analyze the interaction relationships between differential proteins (17). The species was set to human and the import gene set was set to all degrees.…”

Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL

“…The interaction between DEG-encoded proteins was analyzed by STRING (version 10.0; https://string-db.org/cgi/input.pl ) database. 57 The input gene set was set as all DEGs, and the species was set as human. To get the most closely related interaction pairs, we set the parameter PPI score to 0.99 (high confidence).…”