IOP Reports on Progress in Physics Reports on Progress in Physics Rep. Prog. Phys. Rep. Prog. Phys. 78 (2015) 036602 (51pp) doi:10.1088/0034-4885/78/3/036602 78 Review Article 2015 The unforeseen challenge: from © 2015 IOP Publishing Ltd genotype-to-phenotype in cell populations ROP Erez Braun 036602 Department of Physics and Network Biology Research Laboratories, Technion, Haifa 32000, Israel E-mail: [email protected] Received 27 June 2014, revised 4 December 2014 E Braun Accepted for publication 18 December 2014 Published 26 February 2015 Printed in the UK Abstract Biological cells present a paradox, in that they show simultaneous stability and fexibility, ROP allowing them to adapt to new environments and to evolve over time. The emergence of stable cell states depends on genotype-to-phenotype associations, which essentially refect the organization of gene regulatory modes. The view taken here is that cell-state organization is a dynamical 10.1088/0034-4885/78/3/036602 process in which the molecular disorder manifests itself in a macroscopic order. The genome does not determine the ordered cell state; rather, it participates in this process by providing a set of constraints on the spectrum of regulatory modes, analogous to boundary conditions in physical 0034-4885 dynamical systems. We have developed an experimental framework, in which cell populations are exposed to unforeseen challenges; novel perturbations they had not encountered before along their 3 evolutionary history. This approach allows an unbiased view of cell dynamics, uncovering the potential of cells to evolve and develop adapted stable states. In the last decade, our experiments have revealed a coherent set of observations within this framework, painting a picture of the living cell that in many ways is not aligned with the conventional one. Of particular importance here, is our fnding that adaptation of cell-state organization is essentially an effcient exploratory dynamical process rather than one founded on random mutations. Based on our framework, a set of concepts underlying cell-state organization—exploration evolving by global, non-specifc, dynamics of gene activity—is presented here. These concepts have signifcant consequences for our understanding of the emergence and stabilization of a cell phenotype in diverse biological contexts. Their implications are discussed for three major areas of biological inquiry: evolution, cell differentiation and cancer. There is currently no unifed theoretical framework encompassing the emergence of order, a stable state, in the living cell. Hopefully, the integrated picture described here will provide a modest contribution towards a physics theory of the cell. Keywords: cell-state organization, adaptation, population dynamics, evolution, cell differentiation, cancer (Some fgures may appear in colour only in the online journal) Contents 1.3. Genome rewiring of yeast cells ...............................6 1.4. Main phenomena observed .....................................8 1. Cell-state organization: a phenomenological 1.4.1. Fast inherited adaptation ..............................8 approach ..................................................................2 1.4.2. Global gene expression response ...............12 1.1. The nature of living cells ........................................2 1.4.3. Metastable population states ......................14 1.2. An experimental framework: genome rewiring 1.4.4. The generality of adaptation to a and cell adaptation to unforeseen challenges ..........4 rewiring challenge ......................................17 0034-4885/15/036602+51$33.00 1 © 2015 IOP Publishing Ltd Printed in the UK Rep. Prog. Phys. 78 (2015) 036602 Review Article 1.5. Summary of main experimental results ................19 of characteristics with fexibility that allows them to adapt 1.5.1. Perturbations of regulatory modes .............19 to novel and severe challenges. Indeed, the development of a 1.5.2. Inherited adaptation to an unforeseen multicellular organism from the single-cell zygote, crucially challenge ....................................................19 depends on the process of cell differentiation; the stabiliza- 1.5.3. Multiple trajectories in adaptation— tion within a lineage of specifc cell states (types)—neuron, genetics-physiology interrelations .............19 muscle, skin etc, at precise times and locations, forming the 1.5.4. From local perturbation to global body-plan and functional tissues. This developmental pro- reorganization of gene regulation ..............19 cess is highly reproducible and robust; so much so, that it 1.5.5. Slow collective population modes ............ 20 is almost natural to regard development as an execution of a 1.5.6. Universal distributions of protein program, much like a computer program. However, the simul- content ....................................................... 20 taneous existence of these seemingly contradicting capabili- 1.5.7. Metastable growth-rate phenotypes .......... 20 ties, robustness and fexibility, is an essential property that 1.6. Implications: main lessons from our yeast enables evolution [1–3]. The roots of the organism’s ability experiments .......................................................... 20 to evolve—the hallmark of the living world—to large extent 1.6.1. Two types of responses ............................. 20 may be traced to the level of the cell and manifested in cell 1.6.2. Adaptation ................................................. 21 plasticity, its ability to react to internal or external cues and 1.6.3. Epigenetics ................................................ 21 constraints. Thus, the organization of cell states in develop- 1.6.4. Gene activity phase-space ......................... 21 ment and the emergence of novel phenotypes in evolution are 1.6.5. Levels of organization ............................... 21 tightly connected complementary characteristics of the living 1.6.6. Relevant and irrelevant variables .............. 22 cell and their coexistence is one of the greatest mysteries in 1.6.7. Population dynamics beyond genetics ...... 22 biology. 2. Refections on the biology of cell-state organization .... 23 The issue of an emergent order—stable cell states—in 2.1. Evolution .............................................................. 23 essence is that of the genotype-to-phenotype associations. 2.1.1. Evolution of developmental systems ........ 23 The genotype of a cell is its genetic makeup while the pheno- 2.1.2. Gene recruitment ...................................... 24 type encompasses its traits, such as morphology and function. 2.1.3. Degeneracy ............................................... 25 Genotype and phenotype represent two separate cellular enti- 2.1.4. Canalization .............................................. 25 ties; while the former is the structure of the genome—the DNA 2.1.5. Population dynamics ................................. 28 sequence, the latter is the determination of the form, growth 2.2. Cell differentiation ............................................... 34 and interactions with the external world of the cell. The phe- 2.2.1. Stem-cells and differentiation ................... 35 notype is a central concept in the description of a biological 2.2.2. Trans-differentiation and system. In principle, it can be any observable property of the reprogramming ......................................... 36 living organism. However, in the context of the present article, 2.3. Cancer .................................................................. 38 we reserve this term to the composite of observables related to 2.3.1. The nature of the phenomenon ................. 38 the growth, morphology, metabolism and functionality of the 2.3.2. Cancer—a process of organization ........... 39 cell. The establishment of a phenotype, given a certain geno- 2.3.3. The classical picture and its alternatives .... 40 type, depends on the protein makeup of the cell. The set of 2.3.4. Cancer as an adaptation process ............... 42 expressed proteins, a subset of the entire genome potential, 2.3.5. The role of the microenvironment ............ 42 and their concentrations, are determined by regulatory sys- 3. Summary and outlook ................................................... 43 tems at many levels. Thus, the emerging phenotype depends on the spectrum of regulatory modes—temporal profles of expressed genes. However, a snapshot of the molecular con- What was life, really? It was the existence of what… It tent of a cell and the structure of its underlying interactions do was not matter, it was not spirit. It was something in not capture the spectrum of regulatory profles (the intermo- between the two, a phenomenon borne by matter, like lecular correlations and the stability of temporal modes) that the rainbow above a waterfall, like a fame. defne the relevant observables that determine the phenotype. Thomas Mann, The Magic Mountain, 19241 As shown below, the protein content of each isolated gene is by itself not such a relevant observable. Therefore, inquiring into the genotype-to-phenotype associations requires a shift in 1. Cell-state organization: a phenomenological focus from structure to dynamics, from the molecular stuff of approach the cell to its temporal organization. The prevailing approach of modern molecular biology for 1.1. The nature of living cells studying the living cell relies on several tenets. First, a bio- Living cells, under specifc conditions, exhibit well defned