Retracted : Deep integrative analysis of microRNA‐mRNA regulatory networks for biomarker and target discovery in chondrosarcoma

microRNAs and bone tumours: Role of tiny molecules in the development and progression of chondrosarcoma, of giant cell tumour of bone and of Ewing's sarcoma

The increasing interest on microRNAs (miRNAs), small non-coding RNA molecules containing about 22 nucleotides, about their biological functions led researchers to discover that they are actively involved in several biological processes. In the last decades, miRNAs become one of the most topic of cancer research. miRNAs, thanks to their function, are the perfect molecules to modulate multiple signaling pathways and gene expression in cancer, with the consequent capacity to modulate cancerous processes, such as cellular proliferation, invasion, metastasis and chemoresistance in various tumours. In the last years, several studies have demonstrated the role of miRNAs in their pathophysiology, but little we know about the underlying mechanism that lead to bone tumours like chondrosarcoma (COS), giant cell tumour of bone (GCTB) and Ewing sarcoma (EWS) to still be highly aggressive and resistant tumours. An exploration of the role of miRNAs in the biology of them will permit to researchers to find new molecular mechanisms that can be used to develop new and more effective therapies against these bone tumours. Here we present a comprehensive study of the latest discoveries which have been performed in relation to the role of miRNAs in the neoplastic processes which characterize COS, EWS and GCTB, demonstrating how these tiny molecules can act as tumour promoters or as tumour suppressors and how they can be used for improving therapeutic approaches.

The role of microRNAs in the osteogenic and chondrogenic differentiation of mesenchymal stem cells and bone pathologies

Mesenchymal stem cells (MSCs) have been identified in many adult tissues. MSCs can regenerate through cell division or differentiate into adipocytes, osteoblasts and chondrocytes. As a result, MSCs have become an important source of cells in tissue engineering and regenerative medicine for bone tissue and cartilage. Several epigenetic factors are believed to play a role in MSCs differentiation. Among these, microRNA (miRNA) regulation is involved in the fine modulation of gene expression during osteogenic/chondrogenic differentiation. It has been reported that miRNAs are involved in bone homeostasis by modulating osteoblast gene expression. In addition, countless evidence has demonstrated that miRNAs dysregulation is involved in the development of osteoporosis and bone fractures. The deregulation of miRNAs expression has also been associated with several malignancies including bone cancer. In this context, bone-associated circulating miRNAs may be useful biomarkers for determining the predisposition, onset and development of osteoporosis, as well as in clinical applications to improve the diagnosis, follow-up and treatment of cancer and metastases. Overall, this review will provide an overview of how miRNAs activities participate in osteogenic/chondrogenic differentiation, while addressing the role of miRNA regulatory effects on target genes. Finally, the role of miRNAs in pathologies and therapies will be presented.

Circulating extracellular vesicle-encapsulated microRNA as screening biomarkers for intraductal papillary mucinous neoplasm

Since intraductal papillary mucinous neoplasms (IPMNs) occasionally contain pancreatic malignancies, it is vital to develop a screening program that can detect IPMNs in the general population and that can identify IPMNs with high malignant potential. The present study investigated whether microRNAs (miRNAs/miRs) in the blood may be diagnostic markers for IPMN screening. Initially, extracellular vesicle-encapsulated miRNAs (EV-miRNAs) in the serum with altered expression between IPMN, IPMN-derived carcinoma (IPMC) and control samples, were identified using microarray analysis. To validate the microarray results, the expression levels of selected EV-miRNAs were detected. Briefly, serum EV-miRNAs were extracted from 38 patients with IPMN (11 patients with IPMC and 27 patients with benign IPMN) and 21 non-tumor controls. The results of the microarray analysis revealed that the expression levels of EV-miR-22-3p, EV-miR-4539 and EV-miR-6132 were higher in the IPMN and IPMC serum samples compared with those in the control samples. With regards to discriminating IPMNs from controls, only miR-4539 exhibited a significant difference (P=0.004). In the comparison between IPMN and IPMC, carcinogenic antigen 19-9 (CA19-9) and EV-miR-6132 exhibited significant differences (P=0.01 and P=0.007, respectively). Receiver operating characteristic (ROC) curve analysis demonstrated that EV-miR-4539 could discriminate patients with IPMNs from control patients, with an area under the curve (AUC) of 0.72. Additionally, ROC analysis indicated that the markers could discriminate patients with IPMC from benign IPMN, with AUC values of 0.77 for EV-miR-6132 and 0.74 for CA19-9. In conclusion, the present study suggested that EV-miRNAs may be used as diagnostic markers for the detection of IPMNs in the general population as well as for identifying IPMNs with high malignant potential.

The miR-143/145 Cluster, a Novel Diagnostic Biomarker in Chondrosarcoma, Acts as a Tumor Suppressor and Directly Inhibits Fascin-1

Chondrosarcoma is the second most frequent bone sarcoma. Due to the inherent chemotherapy and radiotherapy resistance and absence of known therapeutic targets, clinical management is limited to surgical resection. Consequently, patients with advanced disease face a poor prognosis. Hence, elucidating regulatory networks governing chondrosarcoma pathogenesis is vital for development of effective therapeutic strategies. Here, miRNA and mRNA next generation sequencing of different subtypes of human chondrogenic tumors in combination with in silico bioinformatics tools were performed with the aim to identify key molecular factors. We identified miR-143/145 cluster levels to inversely correlate with tumor grade. This deregulation was echoed in the miRNA plasma levels of patients and we provided the first evidence that circulating miR-145 is a potential noninvasive diagnostic biomarker and can be valuable as an indicator to improve the currently challenging diagnosis of cartilaginous bone tumors. Additionally, artificial upregulation of both miRNAs impelled a potent tumor suppressor effect in vitro and in vivo in an orthotopic xenograft mouse model. A combined in silico/sequencing approach revealed FSCN1 as a direct target of miR-143/145, and its depletion phenotypically resembled miR-143/145 upregulation in vitro. Last, FSCN1 is a malignancy-promoting factor associated with aggressive chondrosarcoma progression. Our findings underscore miR-143/145/FSCN1 as important players in chondrosarcoma and may potentially open new avenues for specific therapeutic intervention options. © 2020 American Society for Bone and Mineral Research.

Comprehensive analysis of transcriptome data for identifying biomarkers and therapeutic targets in head and neck squamous cell carcinoma

Background

Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancy worldwide. Accumulating evidences have highlighted the importance of transcriptome data during HNSCC tumorigenesis. The aim of this study was to identify significant genes as effective biomarkers for HNSCC and constructed miRNA-mRNA regulatory network for a more comprehensive understanding of the underlying molecular mechanisms.

Methods

A total of four independent microarrays conducted on HNSCC samples were downloaded from the Gene Expression Omnibus (GEO) and analyzed through R software. FunRich was applied to predict potential transcription factors and targeted genes of miRNAs. Protein-protein interaction (PPI) network and miRNA-mRNA regulatory network were constructed in Cytoscape. Additionally, the database for annotation, visualization, and integrated discovery (DAVID) was utilized to perform GO and KEGG pathway enrichment analyses. Validation of gene expression levels was conducted by online databases and qPCR experiments.

Results

A total of 35 and 193 differentially expressed miRNAs (DEMs) and mRNAs (DEGs) were screened out by the limma package in R. The interactive network of the overlapping DEGs presented three significant modules and ten hub genes (FN1, MMP3, SPP1, STAT1, LOX, CXCL5, CXCL11, ISG15, IFIT3, and RSAD2). Predicted target genes of DEMs were visualized in Cytoscape and six miRNA-mRNA regulatory pairs were identified. Further validation demonstrated the upregulation of SLC16A1 and COL4A1 in HNSCC.

Conclusions

We performed an integrated and comprehensive bioinformatics analysis of miRNAs and mRNAs in HNSCC, contributing to explore the underlying regulatory mechanisms and to identify genetic biomarkers and therapeutic targets for HNSCC.