A Novel Panel of 80 RNA Biomarkers with Differential Expression in Multiple Human Solid Tumors against Healthy Blood Samples

Abstract

The aim of this study was to identify genes with higher expression in solid tumor cells by comparing human tumor biopsies with healthy blood samples using both in silico statistical analysis and experimental validations. This approach resulted in a novel panel of 80 RNA biomarkers with high discrimination power to detect circulating tumor cells in blood samples. To identify the 80 RNA biomarkers, Affymetrix HG-U133 plus 2.0 microarrays datasets were used to compare breast tumor tissue biopsies and breast cancer cell lines with blood samples from patients with conditions other than cancer. A total of 859 samples were analyzed at the discovery stage, consisting of 417 mammary tumors, 41 breast lines, and 401 control samples. To confirm this discovery, external datasets of eight types of tumors were used, and experimental validation studies (NanoString n-counter gene expression assay) were performed, totaling 5028 samples analyzed. In these analyses, the 80 biomarkers showed higher expression in all solid tumors analyzed relative to healthy blood samples. Experimental validation studies using NanoString assay confirmed the results were not dependent of the gene expression platform. A panel of 80 RNA biomarkers was described here, with the potential to detect solid tumor cells present in the blood of multiple tumor types.

Clinical applications of liquid biopsy in HPV‐negative and HPV‐positive head and neck squamous cell carcinoma: advances and challenges

“…The first description of CTCs was in 1869 by Ashworth [ 70 ], where some cells present in the blood were described as similar to those of the primary tumor. Despite their primary origin, CTCs have characteristics that facilitate the metastatic mechanism, such as mesenchymal epithelial transition properties and immune evasion [ 71 ].…”

“…Due to the rare representation in the circulation, other methods are adopted for CTCs enrichment and validation. The CTCs identification is traditionally based on epithelial markers, with epithelial cell adhesion molecule (EPCAM) being the universal marker; however, its expression is diverse in different tumors and their subtypes [ 71 ]. The presence of CTCs in the bone marrow (BM) from HNSCC patients was revealed in 1995 with the labeling of the anti-cytokeratin monoclonal antibody (A45-B/B3) directed to the cytokeratins (CKs) 8, 18, and 19 [ 72 ].…”

Current Applications and Discoveries Related to the Membrane Components of Circulating Tumor Cells and Extracellular Vesicles

“…One key change during EMT is the “cadherin switch” from E-cadherin to N-cadherin, which is associated with a mesenchymal phenotype [ 56 , 57 ]. Moreover, metastasis-initiator CTCs are characterized by high phenotypic plasticity, leading to the re-expression of some epithelial markers that facilitate metastatic tumor initiation in a distant organ [ 58 , 59 ]. In the bloodstream, platelets interact with CTCs and release transforming growth factor-β that promotes EMT [ 60 ].…”