Stem cell therapy has a place for future application in the treatment of degenerative diseases. Regardless of the origin of the stem cell, when placed within a milieu of inflammatory mediator, they will show varied functions. This review focuses on human mesenchymal stem cells (MSCs) and discusses neuronal replacement using multi- and inter-disciplinary approaches. We caution the enthusiasm of scientists since there is always the potential for tumor formation, even for adult stem cells. The review places RE-1 silencing transcription factor (REST) gene as central to the understanding of stem cell behavior in the microenvironment of tissue injury. REST is relevant in the development of dopaminergic and peptidergic neurons from MSCs. Premature downregulation of REST by the pro-inflammatory mediator, IL-1alpha, can prematurely lead to the expression of neurotransmitters, which in turn, could develop rapid crosstalk with immune cells. In-depth inter- and multi-disciplinary research will lead to rapid and safe translation of MSCs to patients. An understanding of the changes induced in MSCs by cytokines and other mediators will establish future application of MSCs and other stem cells for safe and effective treatments. This study also alludes to the potential of personalized medicine through engineering and mathematics.