Regulatory interactions maintaining self-renewal of human embryonic stem cells as revealed through a systems analysis of PI3K/AKT pathway.

MOTIVATION: Maintenance of the self-renewal state in human embryonic stem cells (hESCs) is the foremost critical step for regenerative therapy applications. The insulin-mediated PI3K/AKT pathway is well appreciated as being the central pathway supporting hESC self-renewal; however, the regulatory interactions in the pathway that maintain cell state are not yet known. Identification of these regulatory pathway components will be critical for designing targeted interventions to facilitate a completely defined platform for hESC propagation and differentiation. Here, we have developed a systems analysis approach to identify regulatory components that control PI3K/AKT pathway in self-renewing hESCs. RESULTS: A detailed mathematical model was adopted to explain the complex regulatory interactions in the PI3K/AKT pathway. We evaluated globally sensitive processes of the pathway in a computationally efficient manner by replacing the detailed model by a surrogate meta-model. Our mathematical analysis, supported by experimental validation, reveals that negative regulators of the molecules IRS1 and PIP3 primarily govern the steady state of the pathway in hESCs. Among the regulators, negative feedback via IRS1 reduces the sensitivity of various reactions associated with direct trunk of the pathway and also constraints the propagation of parameter uncertainty to the levels of post receptor signaling molecules. Furthermore, our results suggest that inhibition of negative feedback can significantly increase p-AKT levels and thereby, better support hESC self-renewal. Our integrated mathematical modeling and experimental workflow demonstrates the significant advantage of computationally efficient meta-model approaches to detect sensitive targets from signaling pathways. AVAILABILITY AND IMPLEMENTATION: FORTRAN codes for the PI3K/AKT pathway and the RS-HDMR implementation are available from the authors upon request.

Dynamical modeling reveals RNA decay mediates the effect of matrix stiffness on aged muscle stem cell fate.

Loss of muscle stem cell (MuSC) self-renewal with aging reflects a combination of influences from the intracellular (e.g., post-transcriptional modifications) and extracellular (e.g., matrix stiffness) environment. Whereas conventional single cell analyses have revealed valuable insights into factors contributing to impaired self-renewal with age, most are limited by static measurements that fail to capture nonlinear dynamics. Using bioengineered matrices mimicking the stiffness of young and old muscle, we showed that while young MuSCs were unaffected by aged matrices, old MuSCs were phenotypically rejuvenated by young matrices. Dynamical modeling of RNA velocity vector fields in silico revealed that soft matrices promoted a self-renewing state in old MuSCs by attenuating RNA decay. Vector field perturbations demonstrated that the effects of matrix stiffness on MuSC self-renewal could be circumvented by fine-tuning the expression of the RNA decay machinery. These results demonstrate that post-transcriptional dynamics dictate the negative effect of aged matrices on MuSC self-renewal.

The biphasic and age-dependent impact of klotho on hallmarks of aging and skeletal muscle function.

Aging is accompanied by disrupted information flow, resulting from accumulation of molecular mistakes. These mistakes ultimately give rise to debilitating disorders including skeletal muscle wasting, or sarcopenia. To derive a global metric of growing 'disorderliness' of aging muscle, we employed a statistical physics approach to estimate the state parameter, entropy, as a function of genes associated with hallmarks of aging. Escalating network entropy reached an inflection point at old age, while structural and functional alterations progressed into oldest-old age. To probe the potential for restoration of molecular 'order' and reversal of the sarcopenic phenotype, we systemically overexpressed the longevity protein, Klotho, via AAV. Klotho overexpression modulated genes representing all hallmarks of aging in old and oldest-old mice, but pathway enrichment revealed directions of changes were, for many genes, age-dependent. Functional improvements were also age-dependent. Klotho improved strength in old mice, but failed to induce benefits beyond the entropic tipping point.

Endothelial cells mediate islet-specific maturation of human embryonic stem cell-derived pancreatic progenitor cells.

It is well recognized that in vitro differentiation of embryonic stem cells (ESC) can be best achieved by closely recapitulating the in vivo developmental niche. Thus, implementation of directed differentiation strategies has yielded encouraging results in the area of pancreatic islet differentiation. These strategies have concentrated on direct addition of chemical signals, however, other aspect of the developmental niche are yet to be explored. During development, pancreatic progenitor (PP) cells grow as an epithelial sheet, which aggregates with endothelial cells (ECs) during the final stages of maturation. Several findings suggest that the interactions with EC play a role in pancreatic development. In this study, we recapitulated this phenomenon in an in vitro environment by maturing the human ESC (hESC)-derived PP cells in close contact with ECs. We find that co-culture with different ECs (but not fibroblast) alone results in pancreatic islet-specific differentiation of hESC-derived PP cells even in the absence of additional chemical induction. The differentiated cells responded to exogenous glucose levels by enhanced C-peptide synthesis. The co-culture system aligned well with endocrine development as determined by comprehensive analysis of involved signaling pathways. By recapitulating cell-cell interaction aspects of the developmental niche we achieved a differentiation model that aligns closely with islet organogenesis.

Mechanisms of action of hESC-secreted proteins that enhance human and mouse myogenesis.

Adult stem cells grow poorly in vitro compared to embryonic stem cells, and in vivo stem cell maintenance and proliferation by tissue niches progressively deteriorates with age. We previously reported that factors produced by human embryonic stem cells (hESCs) support a robust regenerative capacity for adult and old mouse muscle stem/progenitor cells. Here we extend these findings to human muscle progenitors and investigate underlying molecular mechanisms. Our results demonstrate that hESC-conditioned medium enhanced the proliferation of mouse and human muscle progenitors. Furthermore, hESC-produced factors activated MAPK and Notch signaling in human myogenic progenitors, and Delta/Notch-1 activation was dependent on MAPK/pERK. The Wnt, TGF-ß and BMP/pSmad1,5,8 pathways were unresponsive to hESC-produced factors, but BMP signaling was dependent on intact MAPK/pERK. c-Myc, p57, and p18 were key effectors of the enhanced myogenesis promoted by the hECS factors. To define some of the active ingredients of the hESC-secretome which may have therapeutic potential, a comparative proteomic antibody array analysis was performed and identified several putative proteins, including FGF2, 6 and 19 which as ligands for MAPK signaling, were investigated in more detail. These studies emphasize that a "youthful" signaling of multiple signaling pathways is responsible for the pro-regenerative activity of the hESC factors.