Cellular reprogramming: Mathematics meets medicine

Abstract

Generating needed cell types using cellular reprogramming is a promising strategy for restoring tissue function in injury or disease. A common method for reprogramming is addition of one or more transcription factors that confer a new function or identity. Advancements in transcription factor selection and delivery have culminated in successful grafting of autologous reprogrammed cells, an early demonstration of their clinical utility. Though cellular reprogramming has been successful in a number of settings, identification of appropriate transcription factors for a particular transformation has been challenging. Computational methods enable more sophisticated prediction of relevant transcription factors for reprogramming by leveraging gene expression data of initial and target cell types, and are built on mathematical frameworks ranging from information theory to control theory. This review highlights the utility and impact of these mathematical frameworks in the field of cellular reprogramming. This article is categorized under: Reproductive System Diseases > Reproductive System Diseases>Genetics/Genomics/Epigenetics Reproductive System Diseases > Reproductive System Diseases>Stem Cells and Development Reproductive System Diseases > Reproductive System Diseases>Computational Models.

Keywords: Control Theory; Reprogramming; Transcription Factors.

Figure 1:

(A) Cellular differentiation in developmental biology. During normal development, concentration gradients of morphogens (red spheres) lead to differing levels of transcription factor (dimeric green spheres) activation in a distance-dependent manner. This leads to differing transcription profiles of cells as a function of spatial location, allowing for body patterning. (B,C) Re-imagining of Waddington’s epigenetic landscape. Waddington’s original model (B) best describes the process of cellular differentiation and presents an intuitive illustration of non-specialized cell types traversing down peaks and settling in valleys once specialized. In a re-imagined version of Waddington’s landscape (C), the essence of cellular reprogramming is captured, where a cell is unimpeded by the gravity of a hierarchical model and can flow between any potency, germ layer, and cell state. The common center of the concentric circles represents the totipotent state while the subsequent inverted circles represent decreasing levels of cellular potency moving outwards. Here, direct reprogramming is analogous to ‘direct conversion’ or ‘transdifferentiation’, and refers to a change in cell fate that does not incorporate a pluripotent or progenitor state.

Figure 2:

Medical applications of cellular reprogramming. Dermal fibroblasts can be acquired via a minimally invasive punch biopsy, and subsequently differentiated into a desired cell type via the addition of select TFs. Finally, autologous cultured cells of the desired type can be reintroduced into the patient without concern for graft rejection.

Figure 3:

Timeline of key experimental and computational cellular reprogramming advancements.

Figure 4:

Data-guided control overview. (A) Summary of control equation variables. (B) Each box represents a topological domain containing several genes. The blue connections represent the edges of the network and are determined from time series RNA-seq data. The small green plots at each node represent the expression of each domain changing over time. The red arrows indicate additional regulation imposed by exogenous TFs. (C) Conceptual illustration of determining TFs to push a cell state from one basin to another. Figure reproduced with permission from Ronquist et al. 2017.

Figure 5:

Transcription factor delivery. (A) Transduction of a TF-encoding gene by a DNA integrating virus such as a lentivirus. The virus first binds to the host membrane and fuses its viral envelope with the eukaryotic phospholipid membrane to enter the cell. Nucleic acids are released in the cytosol, where RNA-dependent DNA polymerase creates double stranded DNA. Viral DNA is integrated into the host genome. Host cells then express virally-delivered genes, which are translated into functional proteins. (B) Introduction of mRNA coding for a TF by a non-integrating virus such as a Sendai virus. As above, the virus docks, fuses with the cell membrane, and releases nucleic acids into the cytosol. RNA-dependent RNA polymerase then generates positive sense RNA, which is translated to functional protein. (C) Delivery of modified mRNA via a lipid nanoparticle. First, the lipid particle-embeded peptides bind target cell receptors and trigger receptor-mediated endocytosis. Next, the endosome is acidified by H⁺ pumps. The acidified endosome and lipid nanoparticle are destabilized, releasing mRNA into the cytosol. Free mRNA is translated to functional protein. (D) Bacterial type-III secretion system as a TF delivery mechanism. First, a bacterial DNA plasmid is expressed and protein is produced. Next, the bacterial T3SS delivers the protein to the eukaryotic cell through a molecular needle.