Genomics and proteomics in stem cell research: the road ahead

An integrated network analysis approach to identify potential key genes, transcription factors, and microRNAs regulating human hematopoietic stem cell aging

Hematopoietic stem cells (HSCs) undergo functional deterioration with increasing age that causes loss of their self-renewal and regenerative potential. Despite various efforts, significant success in identifying molecular regulators of HSC aging has not been achieved, one prime reason being the non-availability of appropriate human HSC samples. To demonstrate the scope of integrating and re-analyzing the HSC transcriptomics data available, we used existing tools and databases to structure a sequential data analysis pipeline to predict potential candidate genes, transcription factors, and microRNAs simultaneously. This sequential approach comprises (i) collecting matched young and aged mice HSC sample datasets, (ii) identifying differentially expressed genes, (iii) identifying human homologs of differentially expressed genes, (iv) inferring gene co-expression network modules, and (v) inferring the microRNA-transcription factor-gene regulatory network. Systems-level analyses of HSC interaction networks provided various insights based on which several candidates were predicted. For example, 16 HSC aging-related candidate genes were predicted (e.g., CD38, BRCA1, AGTR1, GSTM1, etc.) from GCN analysis. Following this, the shortest path distance-based analyses of the regulatory network predicted several novel candidate miRNAs and TFs. Among these, miR-124-3p was a common regulator in candidate gene modules, while TFs MYC and SP1 were identified to regulate various candidate genes. Based on the regulatory interactions among candidate genes, TFs, and miRNAs, a potential regulation model of biological processes in each of the candidate modules was predicted, which provided systems-level insights into the molecular complexity of each module to regulate HSC aging.

A proteomic study of mesenchymal stem cells from equine umbilical cord

To the best of our knowledge, this is the first study describing the proteome of equine umbilical cord intervascular matrix mesenchymal stem cells (UCIM-MSCs) in a global and functional manner. The aim of this work was to analyze the proteome of previously characterized UCIM-MSCs to determine protein abundance and classify the identified proteins according to Gene Ontology (GO) terms. Protein classification analysis according to biological process, molecular function and cellular component was performed using the PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System, which revealed enrichment for 42 biological processes, 23 molecular functions and 18 cellular components. Protein abundance was estimated according to the emPAI method (Exponential Modified Protein Abundance Index). The two most abundant proteins in the proteome of UCIM-MSCs were the cytoskeletal proteins actin and vimentin, which have important roles in cell stability and motility. Additionally, we identified 14 cell surface antigens. Three of them, CD44, CD90 and CD105, had been previously validated by flow cytometry. In the present study, we also identified important information about the biological properties of UCIM-MSCs such as differentiation potential, low immunogenicity (low MHC-II expression) and chromosomal stability, which reinforces their use for cell therapy. Together with the proteomic findings, this information allowed us to infer the functional relevance of several activities related to primary metabolic processes, protein synthesis, production of vesicle coats, vesicle-mediated transport and antioxidant activity. In addition, the identification of different cell surface markers may help establish an immunophenotypic panel suitable for the characterization of MSCs from equine fetal membranes.

Transcriptomics and proteomics in stem cell research

Stem cells are capable of self-renewal and differentiation, and the processes regulating these events are among the most comprehensively investigated topics in life sciences. In particular, the molecular mechanisms of the self-renewal, proliferation, and differentiation of stem cells have been extensively examined. Multi-omics integrative analysis, such as transcriptomics combined with proteomics, is one of the most promising approaches to the systemic investigation of stem cell biology. We reviewed the available information on stem cells by examining published results using transcriptomic and proteomic characterization of the different stem cell processes. Comprehensive understanding of these important processes can only be achieved using a systemic methodology, and employing such method will strengthen the study on stem cell biology and promote the clinical applications of stem cells.

Expression of surface markers and myogenic potential of rat bone marrow- and adipose-derived stem cells: a comparative study

In recent years, examination and comparison of the biological characteristics of bone marrow- and adipose-derived mesenchymal stem cells (MSCs) from various perspectives have come into the focus of stem cell research, as these cells should be well characterized in order to utilize them in future cellular therapies. Therefore, in the present study, surface protein markers and the skeletal myogenic differentiation potential of rat bone marrow- and adipose-derived MSCs were examined. The expression of CD44, CD45, CD73, and CD90 on bone marrow- and adipose-derived MSCs was characterized using flow cytometry. Subsequently, the stem cells were differentiated into myogenic lineages, and the expression of the skeletal myogenic markers MyoD1, Myog, and Myh2 was studied in cells using real time polymerase chain reaction and immunofluorescence. Our results reveal that the pattern of CD marker expression differs between these 2 types of MSCs to some extent, whereas no significant difference was observed with respect to their myogenic differentiation potential. Therefore, we concluded that despite the differences observed in the biological features of these 2 types of MSCs, their myogenic potential appears to be similar, and that adipose-derived stem cells may be useful in skeletal muscle tissue engineering, due to their easy isolation and capacity for rapid expansion in a short time span.

Improving the outcomes: developing cancer therapeutics

Oncology therapeutics are less likely to reach the market than other therapeutics, at a higher cost, and only approximately one in ten cancer drugs in clinical development actually reach the market. To improve, there need to be new approaches to oncology research and development, based on understanding cancer biology and improving preclinical models and clinical trials, such as more use of biomarkers and evaluation of other targets including cancer stem cells and use of combination therapies. Biomarkers can be used to make early go/no-go decisions in drug development and can speed up drug development by selecting patients who will benefit and excluding patients likely to experience severe side effects, but they need validation before use. New approaches to preclinical and clinical trials can also speed up and improve the development of cancer therapeutics.