FIMED: Flexible management of biomedical data.

BACKGROUND AND OBJECTIVES: In the last decade, clinical trial management systems have become an essential support tool for data management and analysis in clinical research. However, these clinical tools have design limitations, since they are currently not able to cover the needs of adaptation to the continuous changes in the practice of the trials due to the heterogeneous and dynamic nature of the clinical research data. These systems are usually proprietary solutions provided by vendors for specific tasks. In this work, we propose FIMED, a software solution for the flexible management of clinical data from multiple trials, moving towards personalized medicine, which can contribute positively by improving clinical researchers quality and ease in clinical trials. METHODS: This tool allows a dynamic and incremental design of patients' profiles in the context of clinical trials, providing a flexible user interface that hides the complexity of using databases. Clinical researchers will be able to define personalized data schemas according to their needs and clinical study specifications. Thus, FIMED allows the incorporation of separate clinical data analysis from multiple trials. RESULTS: The efficiency of the software has been demonstrated by a real-world use case for a clinical assay in Melanoma disease, which has been indeed anonymized to provide a user demonstration. FIMED currently provides three data analysis and visualization components, guaranteeing a clinical exploration for gene expression data: heatmap visualization, clusterheatmap visualization, as well as gene regulatory network inference and visualization. An instance of this tool is freely available on the web at https://khaos.uma.es/fimed. It can be accessed with a demo user account, "researcher", using the password "demo". CONCLUSION: This paper shows FIMED as a flexible and user-friendly way of managing multidimensional clinical research data. Hence, without loss of generality, FIMED is flexible enough to be used in the context of any other disease where clinical data and assays are involved.

Stem-Mesenchymal Signature Cell Genes Detected in Heterogeneous Circulating Melanoma Cells Correlate With Disease Stage in Melanoma Patients.

During the process of metastasis, cancer cells dissociate from primary tumors, migrate to distal sites, and finally colonize, eventually leading to the formation of metastatic tumors. These cancer cells, defined circulating tumor cells (CTCs) spreading through the blood stream, may develop metastatic lesions or remain dormant. Some emerging clinical evidence supports that some tumor cells may possess metastatic properties already in the earlier stages of tumorigenesis. Because the initiation and progression of vertical growth in human melanoma is fundamental to the notion of tumor virulence and progression, we decided to immune-magnetic collect and molecularly characterize circulating melanoma cells (CMCs) from melanoma patients AJCC staged = pT1b (i.e., transition from radial to vertical phase). CMCs are phenotypically and molecularly heterogeneous, thus we performed a "home-made Liquid-Biopsy," by targeting the melanoma-associated-antigen, MCAM/MUC18/CD146, and/or the melanoma-initiating marker, ABCB5. We assessed a biomarker qualitative expression panel, contemplating the angiogenic-potential, melanoma-initiating and melanoma-differentiation drivers, cell-cell adhesion molecules, matrix-metallo-proteinases, which was performed on three enriched subpopulations from a total of 61 blood-samples from 21 melanoma patients. At first, a significant differential expression of the specific transcripts was documented between and within the CMC fractions enriched with MCAM-, ABCB5-, and both MCAM/ABCB5-coated beads, when analyzing two distinct groups: early AJCC- (stage I-II) and advanced- staged patients (stage II-IV). Moreover, in the early-AJCC staged-group, we could distinguish "endothelial," CD45-MCAM+ enriched-, "stem" S-CMCs, CD45-ABCB5+ enriched- and a third hybrid bi-phenotypic CD45-MCAM+/ABCB5+ enriched-fractions, due to three distinct gene-expression profiles. In particular, the endothelial-CMCs were characterized by positive expression of genes involved in migration and invasion, whilst the stem CMC-fraction only expressed stem and differentiation markers. The third subpopulation isolated based on concurrent MCAM and ABCB5 protein expression showed an invasive phenotype. All three distinct CMCs sub-populations, exhibited a primitive, "stem-mesenchymal" profile suggesting a highly aggressive and metastasizing phenotype. This study confirms the phenotypic and molecular heterogeneity observed in melanoma and highlights those putative genes involved in early melanoma spreading and disease progression.

Minimal Residual Disease in Melanoma:molecular characterization of in transit cutaneous metastases and Circulating Melanoma Cells recognizes an expression panel potentially related to disease progression.

Isolating circulating melanoma cells (CMCs) represents a powerful method to monitor minimal residual disease. We documented that MCAM/MUC18/CD146 expression is strongly associated with disease progression. ABCB5 is melanoma-stem antigen with self-renewal, proliferation, differentiation, tumorigenicity capabilities. These findings supported us to improve CMC detection, investigating MCAM/MUC18/CD146 and ABCB5 as enrichment targets in MM progression. Moreover, we decided to compare possible molecular diversity of these CMC fractions with metastatic tissue expression, collecting concomitantly cutaneous in transit metastases (CTM). We enriched CMCs from eight melanoma patients staged ≥pT1b AJCC, who developed CTMs at baseline or during follow up. We assessed a gene expression panel comprising ABCB5, the differentiation markers (Tyrosinase, MART1), angiogenic factors (VEGF, bFGF), the cell-cell adhesion molecules (MCAM/MUC18/CD146 5'-portion, Long, and Short isoforms, E-Cadherin, N-Cadherin, VE-Cadherin) and matrix-metallo-proteinases (MMP2 and MMP9) via high-sensitive RT-PCR. Preliminary findings defined three distinct sub-populations: "endothelial" CD45-CD146+CMCs, "stem" CD45-ABCB5+CMCs and a "hybrid- stem-endothelial"- CD45-MCAM+ABCB5+CMCs. The expression panel documented that - almost high expression found in CTMs - like in 73.5% of CMCs resulted positive for at least one transcript at baseline, showing gene-expression variability. Longitudinal monitoring documented shut-down of all gene-expressions in "endothelial"- and "hybrid stem-endothelial"-subsets, whilst persistency or acquisition of MCAM/MUC18/CD146, VE-CADH and MMPs was documented in disease-progression status.Conversely, a drastic expression shut-down was documented when patients achieved clinical remission. The "stem"- CMCs fraction" showed quite lower gene expression frequencies. MCAM/MUC18/CD146 and ABCB5 as melanoma-specific-targets are effective in the selection of highly primitive CMCs and highlights those putative genes associated with disease spreading progression.