Institute of Cell Biology

Research

Prof. Dr. Olivier Pertz

Cellular Dynamics lab

 

We use a multidisciplinary approach to study single-cell, spatio-temporal signaling dynamics that regulate cell morphogenesis and cell fate decisions.

https://www.pertzlab.net
Please visit our lab webpage for more details

Research

We study the spatio-temporal signaling events that regulate cell morphogenesis and cell fate decisions. The main hypothesis relevant to our research is that these signaling events are highly dynamic, are precisely regulated in time and space, and can be highly heterogeneous within distinct cells of a population. An important current limitation in our field is that this spatio-temporal resolution of signaling is missed in classic biochemical methods that average populations of thousands of cells, or that rely on the analysis of static, steady-states. To address these challenges, we devise novel quantitative approaches to measure/manipulate signaling dynamics at biologically relevant time/length scales. This includes: 1. Designing and using genetically-encoded biosensors that report on signaling dynamics in single living cells; 2. Microfabrication techniques that mimic geometric features of extracellular environments and induce in vivo relevant cellular behaviors, or allow us to dynamically perturb our cellular systems; 3. Computer vision/statistical image analysis methods to quantify the complex datasets we generate; 4. Mathematical modeling approaches to provide biological insight into these complex cellular systems. We specifically use these technologies to study Rho GTPase signaling regulating cell migration and neuronal differentiation, receptor tyrosine kinase signaling regulating cell fate decisions, and the process of local mRNA translation. Our multidisciplinary approach is likely to provide novel insights that will allow us to tackle a variety of pathologies including nervous system regeneration, neurodegeneration, metastatic cancer or drug resistance. Our approach might also allow us to efficiently manipulate stem cell fate.

Team

Pertz lab

Staff Scientists

Post Docs

PhD students

Master students

Technicians

Publications

Jump to: 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2010

2024

Pulfer, Alain; Pizzagalli, Diego Ulisse; Gagliardi, Paolo Armando; Hinderling, Lucien; Lopez, Paul; Zayats, Romaniya; Carrillo-Barberà, Pau; Antonello, Paola; Palomino-Segura, Miguel; Grädel, Benjamin; Nicolai, Mariaclaudia; Giusti, Alessandro; Thelen, Marcus; Gambardella, Luca Maria; Murooka, Thomas T; Pertz, Olivier; Krause, Rolf; Gonzalez, Santiago Fernandez (2024). Transformer-based spatial-temporal detection of apoptotic cell death in live-cell imaging. eLife, 12 eLife Sciences Publications 10.7554/eLife.90502

2023

Gagliardi, Paolo Armando; Grädel, Benjamin; Jacques, Marc-Antoine; Hinderling, Lucien; Ender, Pascal; Cohen, Andrew R; Kastberger, Gerald; Pertz, Olivier; Dobrzynski, Maciej (2023). Automatic detection of spatio-temporal signaling patterns in cell collectives. The Journal of cell biology, 222(10) Rockefeller Institute Press 10.1083/jcb.202207048

Nałęcz-Jawecki, Paweł; Gagliardi, Paolo Armando; Kochańczyk, Marek; Dessauges, Coralie; Pertz, Olivier; Lipniacki, Tomasz (2023). The MAPK/ERK channel capacity exceeds 6 bit/hour. PLoS computational biology, 19(5), e1011155. Public Library of Science 10.1371/journal.pcbi.1011155

2022

Hell, Tanja; Dobrzyński, Maciej; Gröflin, Fabian; Reinhardt, Jakob K; Dürr, Lara; Pertz, Olivier; Hamburger, Matthias; Garo, Eliane (2022). Flavonoids from Ericameria nauseosa inhibiting PI3K/AKT pathway in human melanoma cells. Biomedicine & pharmacotherapy, 156(113754), p. 113754. Elsevier 10.1016/j.biopha.2022.113754

Dürr, Lara; Reinhardt, Jakob K; Dobrzyński, Maciej; Hell, Tanja; Smieško, Martin; Pertz, Olivier; Hamburger, Matthias; Garo, Eliane (2022). A Dimerosesquiterpene and Sesquiterpene Lactones from Artemisia argyi Inhibiting Oncogenic PI3K/AKT Signaling in Melanoma Cells. Journal of natural products, 85(11), pp. 2557-2569. American Chemical Society 10.1021/acs.jnatprod.2c00471

Ender, Pascal; Gagliardi, Paolo Armando; Dobrzyński, Maciej; Frismantiene, Agne; Dessauges, Coralie; Höhener, Thomas; Jacques, Marc-Antoine; Cohen, Andrew R; Pertz, Olivier (2022). Spatiotemporal control of ERK pulse frequency coordinates fate decisions during mammary acinar morphogenesis. Developmental cell, 57(18), 2153-2167.e6. Elsevier 10.1016/j.devcel.2022.08.008

Höhener, Thomas Christoph; Landolt, Alex Erich; Dessauges, Coralie; Hinderling, Lucien; Gagliardi, Paolo Armando; Pertz, Olivier (2022). LITOS: a versatile LED illumination tool for optogenetic stimulation. Scientific reports, 12(1), p. 13139. Springer Nature 10.1038/s41598-022-17312-x

Dessauges, Coralie; Mikelson, Jan; Dobrzyński, Maciej; Jacques, Marc-Antoine; Frismantiene, Agne; Gagliardi, Paolo Armando; Khammash, Mustafa; Pertz, Olivier (2022). Optogenetic actuator - ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics. Molecular systems biology, 18(6), e10670. EMBO Press 10.15252/msb.202110670

Dürr, Lara; Hell, Tanja; Dobrzyński, Maciej; Mattei, Alberto; John, Anika; Augsburger, Nathanja; Bradanini, Gloria; Reinhardt, Jakob K; Rossberg, Florian; Drobnjakovic, Milos; Gupta, Mahabir P; Hamburger, Matthias; Pertz, Olivier; Garo, Eliane (2022). High-Content Screening Pipeline for Natural Products Targeting Oncogenic Signaling in Melanoma. Journal of natural products, 85(4), pp. 1006-1017. American Chemical Society 10.1021/acs.jnatprod.1c01154

Dobrzyński, Maciej; Jacques, Marc-Antoine; Pertz, Olivier (2022). Mining of Single-Cell Signaling Time-Series for Dynamic Phenotypes with Clustering. Methods in molecular biology, 2488, pp. 183-206. Springer 10.1007/978-1-0716-2277-3_13

2021

Loewith, Robbie; Roux, Aurélien; Pertz, Olivier (2021). Chemical-Biology-derived in vivo Sensors: Past, Present, and Future. CHIMIA, 75(12), pp. 1017-1021. Schweizerische Chemische Gesellschaft 10.2533/chimia.2021.1017

Gagliardi, Paolo Armando; Dobrzyński, Maciej; Jacques, Marc-Antoine; Dessauges, Coralie; Ender, Pascal; Blum, Yannick; Hughes, Robert M; Cohen, Andrew R; Pertz, Olivier (2021). Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival. Developmental cell, 56(12), 1712-1726.e6. Elsevier 10.1016/j.devcel.2021.05.007

Jacques, Marc-Antoine; Dobrzyński, Maciej; Gagliardi, Paolo Armando; Sznitman, Raphael; Pertz, Olivier (2021). CODEX, a neural network approach to explore signaling dynamics landscapes. Molecular systems biology, 17(4), e10026. EMBO Press 10.15252/msb.202010026

Mattei, Alberto (2021). Exploring Signaling Mechanisms regulating genetic and non-genetic Drug Resistance in Melanoma (Unpublished). (Dissertation, Institute of Cell Biology, Faculty of Science)

2020

Müller, Paul M; Rademacher, Juliane; Bagshaw, Richard D; Wortmann, Celina; Barth, Carolin; van Unen, Jakobus; Alp, Keziban M; Giudice, Girolamo; Eccles, Rebecca L; Heinrich, Louise E; Pascual-Vargas, Patricia; Sanchez-Castro, Marta; Brandenburg, Lennart; Mbamalu, Geraldine; Tucholska, Monika; Spatt, Lisa; Czajkowski, Maciej T; Welke, Robert-William; Zhang, Sunqu; Nguyen, Vivian; ... (2020). Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. Nature cell biology, 22(4), pp. 498-511. Springer Nature 10.1038/s41556-020-0488-x

2019

Blum, Yannick; Mikelson, Jan; Dobrzynski, Maciej; Ryu, Hyunryul; Jacques, Marc-Antoine; Jeon, Noo Li; Khammash, Mustafa; Pertz, Olivier (2019). Temporal perturbation of ERK dynamics reveals network architecture of FGF2/MAPK signaling. Molecular systems biology, 15(11), e8947. EMBO Press 10.15252/msb.20198947

Gagliardi, Paolo Armando; Pertz, Olivier (2019). Developmental Erk Signaling Illuminated. Developmental cell, 48(3), pp. 289-290. Elsevier 10.1016/j.devcel.2019.01.022

Bagonis, Maria; Fusco, Ludovico; Pertz, Olivier; Danuser, Gaudenz (2019). Automated profiling of growth cone heterogeneity defines relations between morphology and motility. Journal of cell biology, 218(1), pp. 350-379. Rockefeller Institute Press 10.1083/jcb.201711023

2018

Ryu, H; Chung, M; Pertz, Olivier; Jeon, NL (2018). Integrated Platform for Monitoring Single-cell MAPK Kinetics in Computer-controlled Temporal Stimulations. Scientific Reports, 8(1), p. 11126. Nature Publishing Group 10.1038/s41598-018-28873-1

Song, Jiyoung; Ryu, Hyunryul; Chung, Minhwan; Kim, Youngtaek; Blum, Yannick; Lee, Sung Sik; Pertz, Olivier; Jeon, Noo Li (2018). Microfluidic platform for single cell analysis under dynamic spatial and temporal stimulation. Biosensors & bioelectronics, 104, pp. 58-64. Elsevier 10.1016/j.bios.2017.12.038

2017

Kempf, Anissa; Boda, Enrica; Kwok, Jessica C F; Fritz, Rafael; Grande, Valentina; Kaelin, Andrea M; Ristic, Zorica; Schmandke, Andre; Schmandke, Antonio; Tews, Bjoern; Fawcett, James W; Pertz, Olivier; Buffo, Annalisa; Schwab, Martin E (2017). Control of Cell Shape, Neurite Outgrowth, and Migration by a Nogo-A/HSPG Interaction. Developmental cell, 43(1), 24-34.e5. Cell Press 10.1016/j.devcel.2017.08.014

Dessauges, Coralie; Pertz, Olivier (2017). Developmental ERK Signaling Goes Digital. Developmental cell, 42(5), pp. 443-444. Cell Press 10.1016/j.devcel.2017.08.023

Blum, Yannick; Fritz, Rafael D; Ryu, Hyunryul; Pertz, Olivier (2017). Measuring ERK Activity Dynamics in Single Living Cells Using FRET Biosensors. In: Jimenez, Gerardo (ed.) ERK signaling. Methods in molecular biology: Vol. 1487 (pp. 203-221). Springer 10.1007/978-1-4939-6424-6_15

2016

Nölke, Thilo; Schwan, Carsten; Lehmann, Friederike; Østevold, Kristine; Pertz, Olivier; Aktories, Klaus (2016). Septins guide microtubule protrusions induced by actin-depolymerizing toxins like Clostridium difficile transferase (CDT). Proceedings of the National Academy of Sciences of the United States of America - PNAS, 113(28), pp. 7870-7875. National Academy of Sciences NAS 10.1073/pnas.1522717113

Fusco, Ludovico; Lefort, Riwal; Smith, Kevin; Benmansour, Fethallah; Gonzalez, German; Barillari, Caterina; Rinn, Bernd; Fleuret, Francois; Fua, Pascal; Pertz, Olivier (2016). Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling. Journal of cell biology, 212(1), pp. 91-111. Rockefeller Institute Press 10.1083/jcb.201506018

Martin, Katrin; Reimann, Andreas; Fritz, Rafael D; Ryu, Hyunryul; Jeon, Noo Li; Pertz, Olivier (2016). Spatio-temporal co-ordination of RhoA, Rac1 and Cdc42 activation during prototypical edge protrusion and retraction dynamics. Scientific Reports, 6, p. 21901. Nature Publishing Group 10.1038/srep21901

Fritz, Rafael Dominik; Pertz, Olivier (2016). The dynamics of spatio-temporal Rho GTPase signaling: formation of signaling patterns. F1000Research, 5(749) F1000 Research Ltd 10.12688/f1000research.7370.1

2015

Ryu, Hyunryul; Chung, Minhwan; Dobrzyński, Maciej; Fey, Dirk; Blum, Yannick; Lee, Sung Sik; Peter, Matthias; Kholodenko, Boris N; Jeon, Noo Li; Pertz, Olivier (2015). Frequency modulation of ERK activation dynamics rewires cell fate. Molecular systems biology, 11(11), p. 838. EMBO Press 10.15252/msb.20156458

Fritz, Rafael Dominik; Menshykau, Denis; Martin, Katrin; Reimann, Andreas; Pontelli, Valeria; Pertz, Olivier (2015). SrGAP2-Dependent Integration of Membrane Geometry and Slit-Robo-Repulsive Cues Regulates Fibroblast Contact Inhibition of Locomotion. Developmental cell, 35(1), pp. 78-92. Cell Press 10.1016/j.devcel.2015.09.002

Moretti, Francesca; Rolando, Chiara; Winker, Moritz; Ivanek, Robert; Rodriguez, Javier; Von Kriegsheim, Alex; Taylor, Verdon; Bustin, Michael; Pertz, Olivier (2015). Growth Cone Localization of the mRNA Encoding the Chromatin Regulator HMGN5 Modulates Neurite Outgrowth. Molecular and cellular biology, 35(11), pp. 2035-2050. American Society for Microbiology 10.1128/MCB.00133-15

2014

Martin, Katrin; Vilela, Marco; Jeon, Noo Li; Danuser, Gaudenz; Pertz, Olivier (2014). A growth factor-induced, spatially organizing cytoskeletal module enables rapid and persistent fibroblast migration. Developmental cell, 30(6), pp. 701-716. Cell Press 10.1016/j.devcel.2014.07.022

Fengos, Georgios; Schmidt, Alexander; Martin, Katrin; Fluri, Erika; Aebersold, Ruedi; Iber, Dagmar; Pertz, Olivier (2014). Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome Science, 12, p. 23. BioMed Central 10.1186/1477-5956-12-23

2013

Fritz, Rafael D; Letzelter, Michel; Reimann, Andreas; Martin, Katrin; Fusco, Ludovico; Ritsma, Laila; Ponsioen, Bas; Fluri, Erika; Schulte-Merker, Stefan; van Rheenen, Jacco; Pertz, Olivier (2013). A versatile toolkit to produce sensitive FRET biosensors to visualize signaling in time and space. Science signaling, 6(285), rs12. American Association for the Advancement of Science 10.1126/scisignal.2004135

2012

Feltrin, Daniel; Fusco, Ludovico; Witte, Harald; Moretti, Francesca; Martin, Katrin; Letzelter, Michel; Fluri, Erika; Scheiffele, Peter; Pertz, Olivier (2012). Growth cone MKK7 mRNA targeting regulates MAP1b-dependent microtubule bundling to control neurite elongation. PLoS biology, 10(12), e1001439. Public Library of Science 10.1371/journal.pbio.1001439

2010

Pertz, Olivier (2010). Spatio-temporal Rho GTPase signaling - where are we now? Journal of cell science, 123(Pt 11), pp. 1841-1850. Company of Biologists Limited 10.1242/jcs.064345

Jang, Kyung-Jin; Kim, Min Sung; Feltrin, Daniel; Jeon, Noo Li; Suh, Kahp-Yang; Pertz, Olivier (2010). Two distinct filopodia populations at the growth cone allow to sense nanotopographical extracellular matrix cues to guide neurite outgrowth. PLoS ONE, 5(12), e15966. Public Library of Science 10.1371/journal.pone.0015966

Positions

While we have no funded position available right now, the Cellular Dynamics lab is always looking for highly motivated students and post-docs with an interest in signaling to the cytoskeleton, control of cell fate decisions, or local mRNA translation.

If interested, please submit a CV, statement of research interest, and names of  1-2 references in one pdf file to olivier.pertz@izb.unibe.ch.

We have currently advertised two master thesis positions for UniBE students.