Dr. David Vilchez

Research Area: Protein homeostasis regulation in stem cells and ageing

Website: http://www.vilchezlab.com/

1. Research Background:

By 2050, the global population over the age of 80 will triple. Thus, research for improving the quality of life at older age can be of enormous benefit for our ever-aging society. To address this challenge, we propose an innovative approach based on a combination of stem cell research with genetic experiments in C. elegans. Mechanisms that promote protein homeostasis (proteostasis) slow down aging and decrease the incidence of age-related diseases. Since human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) replicate continuously in the absence of senescence, we hypothesize that they can provide a novel paradigm to study proteostasis and its demise in aging. We have found that hESCs exhibit increased proteasome activity. Moreover, we have uncovered that the proteasome subunit RPN-6 is required for this activity and sufficient to extend healtshpan in C. elegans. However, the mechanisms by which the proteasome regulates hESC/iPSC function remain unknown. Our first aim is to define how the proteasome regulates not only hESC/iPSC identity but also aging and the onset of age-related diseases. Moreover, one of the next challenges is to define how other proteostasis pathways impinge upon hESC/iPSC function. We hypothesize that, in addition to the proteasome, hESCs/iPSCs differentially regulate other subcellular stress response pathways designed to protect them from disequilibrium in the folding and degradation of their proteome. We will perform a comprehensive study of proteostasis of hESCs and mimic this network in somatic cells to alleviate age-related diseases. Finally, we propose to determine whether loss of proteostasis promotes somatic stem cell (SC) exhaustion, which is one of the most obvious characteristics of the aging process and contributes to tissue degeneration. By using in vitro and in vivo models, we will examine whether sustained proteostasis delays neural SC exhaustion. Our research will have an impact in several fields such as stem cell research, neurogenesis, proteostasis, aging and age-related diseases.

2. Research questions addresses by the group:

We seek to probe the requirements of proteostasis in hESC/iPSCs, healthspan and regenerative potential by addressing the following questions:

  • Aim 1:
    What are the mechanisms by which proteasome activity regulates hESC/iPSC function and organismal aging?
  • Aim 2:
    Do hESCs/iPSCs have increased proteome surveillance mechanisms? Can these mechanisms be adapted to slow down aging and age-related diseases?
  • Aim 3:
    Can sustained increased proteasome activity ameliorate age-associated NSC exhaustion?

3. Possible projects:

  • Defining the ubiquitin proteasome-system of pluripotent stem cells for disease intervention
    Alterations in the ubiquitin/proteasome-system (UPS) hasten neurodegeneration of Alzheimer’s (AD), Parkinson’s (PD), Huntington’s (HD) and amyotrophic lateral sclerosis (ALS) disease models. The UPS is a key node of the proteostasis network to terminate aberrant disease-related proteins. Notably, iPSCs from patients do not present inclusions of disease-related aggregation-prone proteins. Here we propose to assess whether the intrinsic UPS of hESCs/iPSCs suppresses aggregation of disease-related proteins. In addition, we aim to mimic the UPS network of iPSCs in somatic cells (e.g., C. elegans, neurons derived from distinct patient-iPSCs) to examine whether intervention of these mechanisms can ameliorate proteostatic deficiencies and delay disease-related changes.
  • Identifying novel mechanisms for disease intervention by defining protein homeostasis of stem cells.
    Besides the proteasome system, we have found that hESCs/iPSCs also differentially regulate subcellular stress response pathways designed to protect the cell from disequilibrium in the folding and degradation of disease-related proteins. Our goal is to determine whether these mechanisms impinge upon proteostasis, pluripotency and neurogenesis of hESCs/iPSCs. Finally, by using iPSC-derived neurons and C. elegans, we will assess whether intervention of these mechanisms ameliorates proteostatic deficiencies in disease models.

4. Applied Methods and model organisms:

  • hESC culturing and differentiation into distinct lineages (including specific neuronal types such as striatum neurons and motorneurons)
  • iPSC from Huntington’s (HD) and amyotrophic lateral sclerosis (ALS) patients
  • Organoids from hESCs/iPSCs
  • C. elegans
  • HD and ALS C. elegans models
  • RNAi
  • CRISPR/Cas9
  • Proteomics
  • Co-Immunoprecipitation
  • Western blot
  • Quantitative PCR
  • RNA sequencing
  • ChIP-sequencing
  • Ribosome profiling

5. Desirable skills and qualifications:

We seek enthusiastic and highly motivated students interested in stem cell and aging research. Experience in stem cell research or C. elegans is welcome but not necessary. If you are motivated and eager to learn, it will be easy to get familiarized with all the techniques in the lab.

6. References:

Top 15 project-related publications from the lab:

  1. D. Irmak, A. Fatima, R. Gutierrez-Garcia, M. Rinschen, P. Wagle, J. Altmüller, L. Arrigoni, B. Hummel, C. Klein, C.K. Frese, R. Sawarkar, A. Rada-Iglesias, D. Vilchez. Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations. Human Molecular Genetics.https://doi.org/10.1093/hmg/ddy304
  2. S. Koyuncu, I. Saez, H.J. Lee, R. Gutierrez-Garcia, W. Pokrzywa, A. Fatima, T. Hoppe, D. Vilchez (2018). The ubiquitin ligase UBR5 suppresses proteostasis collapse in immortal pluripotent stem cells from Huntington’s disease patients. Nature Communications9: 2886.
  3. I. Saez, S. Koyuncu, R. Gutierrez-Garcia, C. Dieterich, D. Vilchez (2018). Modulation of human embryonic stem cell identity by the ubiquitin-proteasome system. Scientific Reports 8: 4092.
  4. H.J. Lee, D. Bartsch, C. Schindler, J.M. Moresco, J.R. Yates III, C. Dieterich, L. Kurian, D. Vilchez (2017). A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells. Nature Communications 8: 1456.
  5. A. Noormohammadi, G. Calculli, R. Gutierrez-Garcia, A. Khodokarami, S. Koyuncu and D. Vilchez (2017). Mechanisms of protein homeostasis (proteostasis) mantain stem cell identity in mammalian pluripotent stem cells. Cellular and Molecular Life Sciences 75(2), 275-290.
  6. S. Koyuncu, A. Fatima, R. Gutierrez-Garcia and D. Vilchez (2017).Proteostasis of huntingtin in health and disease. International Journal of Molecular Sciences 18(7), E1568.
  7. A. Noormohammadi, A. Khodakarami, R. Gutierrez-Garcia, H.J. Lee, S. Koyuncu, T. König, C. Schindler, I. Saez, A. Fatima, C. Dieterich, D. Vilchez (2016). Somatic increase of CCT8 mimics proteostasis of human pluripotent stem cells and extends C. elegans lifespan. Nature Communications 7: 13649.
  8. H.J. Lee, R. Gutierrez-Garcia, D. Vilchez (2016). Embryonic stem cells: A novel approach to study proteostasis? FEBS Journal 284(3), 391-398.
  9. D. Vilchez, I. Saez andA. Dillin (2014).The role of protein clearance mechanisms in organismal ageing and age-related diseases. Nature Communications 5: 5659.
  10. A. Khodakarami, I. Saez, J. Mels and D. Vilchez (2015).Mediation of organismal aging and somatic proteostasis by the germline. Frontiers in Molecular Biosciences 2(3): 1-7
  11. I. Saez and D. Vilchez (2014).The mechanistic links between proteasome activity, aging and age-related diseases. Current Genomics 15(1): 38-51.
  12. D. Vilchez#, M. Simic# and A. Dillin (2014). Proteostasis and aging of stem cells. Trends in Cell Biology24(3): 161-170. #These authors contributed equally to this work.
  13. D. Vilchez, L. Boyer, M. Lutz, C. Merkwirth, I. Morantte, C. Tse, B. Spencer, L. Page, E. Masliah, W.T. Berggren, F.H. Gage and A. Dillin (2013). FOXO4 is necessary for neural differentiation of human embryonic stem cells. Aging Cell 12(3): 518-522.
  14. D. Vilchez, I. Morantte, Z. Liu, P.M. Douglas, C. Merkwirth, A.P. Rodrigues, G. Manning and A. Dillin (2012). RPN-6 determines C. elegans longevity under proteotoxic stress conditions. Nature489(7415): 263-268.
  15. D. Vilchez, L. Boyer, I. Morantte, M. Lutz, C. Merkwirth, D. Joyce, B. Spencer, L. Page, E. Masliah, F.H. Gage and A. Dillin (2012). Increased proteasome activity in human embryonic stem cells is regulated by PSMD11. Nature489(7415): 304-308.