Internet-based profiler system as integrative framework to support translational research

BACKGROUND: Translational research requires taking basic science observations and developing them into clinically useful tests and therapeutics. We have developed a process to develop molecular biomarkers for diagnosis and prognosis by integrating tissue microarray (TMA) technology and an internet-database tool, Profiler. TMA technology allows investigators to study hundreds of patient samples on a single glass slide resulting in the conservation of tissue and the reduction in inter-experimental variability. The Profiler system allows investigator to reliably track, store, and evaluate TMA experiments. Here within we describe the process that has evolved through an empirical basis over the past 5 years at two academic institutions. RESULTS: The generic design of this system makes it compatible with multiple organ system (e.g., prostate, breast, lung, renal, and hematopoietic system,). Studies and folders are restricted to authorized users as required. Over the past 5 years, investigators at 2 academic institutions have scanned 656 TMA experiments and collected 63,311 digital images of these tissue samples. 68 pathologists from 12 major user groups have accessed the system. Two groups directly link clinical data from over 500 patients for immediate access and the remaining groups choose to maintain clinical and pathology data on separate systems. Profiler currently has 170 K data points such as staining intensity, tumor grade, and nuclear size. Due to the relational database structure, analysis can be easily performed on single or multiple TMA experimental results. The TMA module of Profiler can maintain images acquired from multiple systems. CONCLUSION: We have developed a robust process to develop molecular biomarkers using TMA technology and an internet-based database system to track all steps of this process. This system is extendable to other types of molecular data as separate modules and is freely available to academic institutions for licensing

The funhouse mirror: the I in personalised healthcare

Precision Medicine is driven by the idea that the rapidly increasing range of relatively cheap and efficient self-tracking devices make it feasible to collect multiple kinds of phenotypic data. Advocates of N = 1 research emphasize the countless opportunities personal data provide for optimizing individual health. At the same time, using biomarker data for lifestyle interventions has shown to entail complex challenges. In this paper, we argue that researchers in the field of precision medicine need to address the performative dimension of collecting data. We propose the fun-house mirror as a metaphor for the use of personal health data; each health data source yields a particular type of image that can be regarded as a ‘data mirror’ that is by definition specific and skewed. This requires competence on the part of individuals to adequately interpret the images thus provided

Understanding skeletal muscle adaptation in health and chronic disease: a multi-omics based systems biology perspective

Mammalian skeletal muscle has a major impact on whole-body metabolic homeostasis. Hence, maintenance of a metabolically active muscle mass is key for optimal health. Notably, both muscle function and mass are profoundly negatively affected by environmental factors such as chronic smoking and physical inactivity. RNA abundance integrates genetic, epigenetic and environmental influences. Therefore, while true understanding of physiological adaptation likely require the integration between multi-level datasets, the transcriptome represents a powerful investigative tool in determining the underlying molecular mechanisms behind complex phenotypic traits. The overarching aim of this thesis was to evaluate, using omics-based systems biology approaches, the global regulation of RNAs during exogenous modulation of mammalian muscle phenotype in order to characterize local homeostatic processes as well as identify robust biomarker signatures. The first part of this thesis deals with smoke-induced peripheral muscle wasting. Initially, biological domain knowledge is used to validate a pre-clinical smoking model. Then, specific cytokines are statistically linked to limb muscle energy metabolism; a testable hypothesis supported by both animal and human data. The second part deals with the development of ‘molecular predictors’ of endurance training adaptability. Two complex clinically relevant traits are considered, namely whole-body insulin sensitivity and plasma triglyceride content. Promisingly, quantitative multi-gene predictors of response to training for both traits of interest were developed

The use of induced pluripotent stem cells (iPSCs) and mesenchymal stem cells (MSCs) to study the genetic basis of human diseases

Objectives: The aim of this thesis was to evaluate the potential of new technologies, including two stem cell technologies, mesenchymal stem cells (MSCs) and induced pluripotent stem cells (iPSCs), to understand the molecular basis of human diseases. These technologies were evaluated for their ability to restore diabetes-induced defects in wound tissue repair (MSCs) and to generate mature neutrophils after in vitro differentiation of iPSCs. The latter used iPSCs from a patient with abnormal function due to impaired WASp (Wiskott Aldrich syndrome protein) signalling. Other techniques evaluated were differentiation of the myeloid cell line, PLB-985 (expressing exogenous genes) into mature neutrophils and new advances in metabolomics, to identify altered neutrophil function in human diseases. Methods: The potential of MSCs and oral vitamin C to generate factors that could promote healing of diabetic wounds, was measured by RT-PCR for eight genes associated with either angiogenesis or extracellular matrix production, after incubation under normoglycaemic and hyperglycaemic conditions with and without vitamin C. The angiogenic effects of the MSC secretome on wound healing was measured using a tubular formation assay (in vitro) and a nude mice diabetic wound model (in vivo). The bilateral full-skin thickness wounds were created in an in vivo wound model using diabetic nude mice. Oral vitamin C (1.5 g/L) was administered in combination with topical MSC treatment (MSCs 1x 106 cells per wound). Diabetic wound models were divided into five groups; control (CON; n=6), diabetes (DM; n=12), diabetes treated with MSCs (DM+MSCs; n=12), diabetes treated with VitC (DM+VitC; n=6), and diabetes treated with MSCs and VitC (DM+MSCs+VitC; n=12). The capillary density was measured under in vivo fluorescent microscopy, and the tissue VEGF levels were measured. WAS dermal fibroblasts were reprogrammed using retrovirus transfection, and the corrected-WAS-iPSCs were differentiated into the neutrophil-like cells via the formation of iPS-sacs (the sac-like structure containing haematopoietic progenitor cells derived from iPSCs). Neutrophil (from WAS patients and healthy controls) chemotaxis was measured using transwell migration towards N-formylmethionine-leucyl-phenylalanine (fMLP). PLB-985 and KCL-22 cells were differentiated into neutrophil-like cells using RPMI-1640 media containing N,N-dimethyl formamide, sodium pyruvate, all-trans retinoic acid, human AB serum and dimethyl sulfoxide (with penicillin/streptomycin). Morphology was assessed by cytospin. PLB-985 cells were transduced with enhanced green fluorescent protein (EGFP)-tagged Myeloid Cell Leukaemia-1 (Mcl-1), sub-cloned into a pLVX-TetOne-Puro system. 1H NMR metabolomics was carried out using protocols optimised for neutrophils as part of this thesis. An intracellular metabolite extraction method was developed to minimise the loss of neutrophil metabolites and to avoid contaminants arising during the extraction procedure. The NMR analyses were also optimised to identify neutrophil metabolites and allow the comparison from resting and activated states and in health and disease (rheumatoid arthritis patients). Results: Upregulation of angiogenic genes, vascular endothelial growth factor-α (mVEGF-α) and platelet-derived growth factor-BB (mPDGF-BB), in response to TGF-β1 in MSCs was lower following incubation under hyperglycemia (compared to normoglycaemic controls), but vitamin C treatment re-sensitised the MSC response to TGF-β1. A diabetic mouse model showed that administration of oral vitamin C, as an adjunct to MSC therapy, resulted in accelerated wound healing that was associated with increased capillary density. Preliminary experiments with WAS neutrophils showed significantly lower rates of chemotaxis towards fMLP compared to healthy controls. iPSCs from WAS fibroblasts were cultured and differentiated into neutrophil-like cells. The efficiency of both PLB-985 and KCL-22 cells to differentiation into neutrophil-like cells was evaluated and PLB-985 cells differentiated more efficiently into neutrophil-like cells than the KCL-22 cells. PLB-985 cells, transfected with Mcl-1:EGFP in pLVX-TetOne-Puro system were generated. Nuclear magnetic resonance (NMR) metabolomics identified metabolites and pathways altered during in vitro activation with PMA (including metabolites of NADPH synthesis and inhibitors of reactive oxygen species (ROS)) and in vivo activation in rheumatoid arthritis identified metabolites of the ketosis pathway, citrullination pathway and tryptophan metabolism. Conclusions: A number of technologies have been evaluated to study the molecular basis of human disease, including metabolic (diabetes mellitus) and genetic (WAS) diseases. Vitamin C modulated the secretome of MSCs, increasing angiogenesis and accelerating wound healing, providing a potential new approach for designing adjuncts to existing therapies. Neutrophils from WAS patients demonstrated chemotactic defects, and the potential of WAS-iPSCs to differentiate into neutrophil-like cells was demonstrated. The approach could be applied in further studies to study genetic defects of leukocyte function. PLB-985 cells transduced with EGFP-tagged Mcl-1 in an inducible expression vector, was developed as a cell-line model of neutrophil differentiation, to facilitate further studies into the role of the Mcl-1 gene in regulating neutrophil survival. Protocols for human neutrophil metabolomics, using 1H NMR spectroscopy were developed and applied to the study of in vitro and in vivo activated neutrophils. The results demonstrated the potential of metabolomics for future studies of human diseases