Maximiliano Portal - Cell Plasticity and Epigenetics

Genesis and propagation of epigenetic states underlying drug tolerance

It is generally accepted that tumours are subjected to a myriad of evolutionary constraints at their niche of origin and further within the ecosystems encountered while invading novel tissues1,2. Thus, evolutionary forces shape cancer development on many levels, as progression of the disease is often correlated with the appearance of somatic mutations and the selection of genetic traits that eventually become beneficial to neoplastic growth and often prejudicial to the host. Indeed, often-acquired mutations alter growth control systems and obliterate cell death programs, ultimately granting mutated cells with replicative immortality at the expense of genetic instability. However, due to the variable nature of the selective pressure in a particular niche, stable somatic mutations arise only after recurrent encounters with a challenging force. This suggests that, though under heavy evolutionary constraints, genetic changes driving adaptation do not occur immediately and highlights the biological relevance of cancer cell plasticity during neoplastic evolution3.

A striking example that brings forward the plasticity of cancer cells is their resilience when confronted with therapeutic paradigms. Indeed it is acknowledged that, in response to sustained treatment, cancer cells may acquire genetic mutations that permanently block the tumouricidal action of the administered drug. However, in other settings, the emergence of fully drug-resistant clones cannot be explained by genetic mechanisms and results from cells that escape the initial death challenge by “adapting” to the pernicious agent. In the latter scenario, the traits granting adaptation to treatment are reversible in nature and are readily inherited through several cell divisions. This particularity strongly suggests the existence of a non-genetically encoded “temporal memory” underlying the acquisition of “drug-tolerant” phenotypes and represents an exquisite example of the transfer of non-genetic information through cell division4-6.

Under this premises, we have developed a solid cellular model to study the mechanisms underlying the inheritance of non-genetically encoded “drug-resistant” states. Our model is based on the drug-induced activation of a cell death pathway, which in several cancer-derived cell lines prompts cell death while concomitantly generates a resistant subpopulation. Notably, the resistant subpopulation resume growth in the presence of the death-triggering agent and following the removal of the drug, regain drug-sensitivity but only after a defined number of cell divisions. Thus suggesting that the drug-tolerant phenotype is sustained by cell plasticity rather than driven by stable genetic changes. The short-lived, dynamic and reversible nature of the “induced resistant phenotype” makes this system the ideal choice to study epigenetic inheritance.

The main objective of this PhD project is to further explore/establish an experimental/computational framework to study epigenetic inheritance in cancer relevant settings. In particular, the student will generate from a single non-transformed “parental” cell line a battery of cellular models were the introduction of oncogenic factors (H-RAS(G12V), BRAF(V600E) or MYC) drive cellular transformation. These cell lines will be used to analyze the generation and propagation of the innate/acquired resistant phenotype at a single cell level. In particular, we will explore dynamic changes in the expression, intracellular localization and segregation of non-coding RNAs and its link with epigenetic events supporting drug resistance7-12.

The successful candidate will benefit extensively from training in molecular and cellular biology, cancer cell biology, epigenetics and non-coding RNA biology. The student is expected to generate new biological insights into the mechanism underlying epigenetic information transfer through cell division and its potential role on the acquisition of drugresistance in cancer settings.

References

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  2. Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 144, 646-674, doi:10.1016/j.cell.2011.02.013 (2011).
  3. Trerotola, M., Relli, V., Simeone, P. & Alberti, S. Epigenetic inheritance and the missing heritability. Hum Genomics 9, 17, doi:10.1186/s40246-015-0041-3 (2015).
  4. Brock, A., Chang, H. & Huang, S. Non-genetic heterogeneity--a mutation-independent driving force for the somatic evolution of tumours. Nat Rev Genet 10, 336-342, doi:10.1038/nrg2556 (2009).
  5. Pisco, A. O. et al. Non-Darwinian dynamics in therapy-induced cancer drug resistance. Nat Commun 4, 2467, doi:10.1038/ncomms3467 (2013).
  6. Pisco, A. O. & Huang, S. Non-genetic cancer cell plasticity and therapy-induced stemness in tumour relapse: 'What does not kill me strengthens me'. Br J Cancer 112, 1725-1732, doi:10.1038/bjc.2015.146 (2015).
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  8. Chandler, V. L. & Stam, M. Chromatin conversations: mechanisms and implications of paramutation. Nat Rev Genet 5, 532-544, doi:10.1038/nrg1378 (2004).
  9. Suter, C. M. & Martin, D. I. Paramutation: the tip of an epigenetic iceberg? Trends Genet 26, 9-14, doi:10.1016/j.tig.2009.11.003 (2010).
  10. Macara, I. G. & Mili, S. Polarity and differential inheritance--universal attributes of life? Cell 135, 801-812, doi:10.1016/j.cell.2008.11.006 (2008).
  11. Lambert, J. D. & Nagy, L. M. Asymmetric inheritance of centrosomally localized mRNAs during embryonic cleavages. Nature 420, 682-686, doi:10.1038/nature01241 (2002).
  12. Xie, J., Wooten, M., Tran, V. & Chen, X. Breaking Symmetry - Asymmetric Histone Inheritance in Stem Cells. Trends Cell Biol 27, 527-540, doi:10.1016/j.tcb.2017.02.001 (2017).