Raphaëlle LUISIER

Short Biography

Raphaëlle Luisier is a Researcher at Idiap Research Institute, where she leads the Genomics and Health Informatics Group. Her expertises encompass genomics, bioinformatics, RNA biology, neuroscience, data science and data visualisation. She earned her Master of Science in Bioengineering and Biotechnology at the Swiss Federal Institute of Lausanne (EPFL, Switzerland) in 2009, and her PhD in Bioinformatics from the Basel University (Switzerland) in 2013, working with Erik Van Nimwegen (Basel University) and Rémi Terranova (Novartis Institute for Biomedical Research).

In her master thesis performed at the Queensland Institute of Technology, she developed mathematical and in vitro models of skin wound healing to elucidate the triggers and regulators of epidermal homeostasis; this project has been recognized by the annual award for the best MSc project in bioengineering and biotechnology at EPFL (2009). She then shifted her research focus to study principles of gene expression regulation in various systems. In her PhD work jointly performed at the Novartis Institute for Biomedical Research (NIBR) and at Basel University, she developed novel statistical methods which led to the identification of candidate early gene regulators involved in drug-induced liver tumorigenesis. This research provided new mechanistic insights into drug-mediated hepatocarcinogenesis and received an honourable mention at the 2015 Society of Toxicology meeting.

Before joining Idiap in November 2019, she was leading several collaborative projects on RNA metabolism in developing neurons and its impact on disease using high content genomic data at the Francis Crick Institute in London in Luscombe laboratory. In collaboration with Antonella Riccio laboratory (University College London), she demonstrated for the first time evidence for mechanisms underlying mRNA remodelling in axons, a new regulatory principle that will be crucial for the emerging field of transcriptomics. In collaboration with Rickie Patani laboratory (Francis Crick Institute), she made the breakthrough discovery of aberrant intron retention as the earliest detectable molecular event in ALS and revealed universal nuclear-to-cytoplasmic mislocalisation of the SFPQ protein encompassing the full spectrum of ALS. Importantly, these findings are potentially targetable disease mechanisms.

Research Synopsis

Raphaelle research interests have centered around developing computational models and statistical methods for interpreting complex data sets to address biological questions related to human disorders.

The mass generation of high-content genomic, imaging and digital data has brought rapid advances in our understanding of cell biology and human diseases, and offers promising avenues for the field of precision medicine. A major obstacle revolves around delivering meaningful information from these data, requiring the deployment of a variety of methods such as statistics, machine learning and data visualisation in tight collaboration with clinicians. The Genomics and Health Informatics Group develops statistical and machine-learning methods to integrate genomic, clinical, and imaging data aiming to accelerate the diagnosis and improve the understanding and treatment of complex diseases such as neurodegenerative disorders in collaboration with clinical neuroscientists.

The current lines of research include (A) the integration of longitudinal cellular imaging with genomic data to study how molecular biology shapes cellular morphology in neurodegenerative diseases; (B) the development of machine learning methods to integrate longitudinal digital data with genomics to study how individual differences in motor and cognitive behaviours emerge and how such differences may confer vulnerability to neurodegenerative diseases. In collaborating with clinicians and expert laboratories in molecular neuroscience and bioengineering, the group has access to unique high quality data including longitudinal RNA-sequencing (Stem Cell Research laboratory , Francis Crick Institute, London) and time-lapse cellular imaging (Neural Circuit Bioengineering group, Kings College, London) from motor neurone cultures obtained from healthy and sick donors.

Professional Experience

  • Researcher at Idiap Research Institute, Martigny, Switzerland (since November 2019)
  • Senior Research Fellow, Francis Crick Institute, London, UK (2014-2019)
  • Research Assistant, Basel University/ Novartis Institute of Biomedical Research, Switzerland, (2010-2013)
  • Research Assistant, Laboratory of Stem Cell Bioengineering (EPFL), (2009-2010; 9 months)
  • Undergraduate researcher, Queensland University of Technology (QUT), Australia, (2008-2009; 9 months)
  • Undergraduate MICS researcher, EPFL, (2008;2 months)

Education

  • 2013 Docteur ès Sciences (PhD) in Bioinformatics, Basel University, Switzerland
  • 2009 Master of Science in Biotechnology and Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland
  • 2007 Master of Science in Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland

Publications

These

  1. R Luisier. Towards a better understanding of early drug-induced regulatory mechanisms of liver tumorigenesis. PhD Thesis, Basel University, Switzerland, September, 2013.
  2. R Luisier. Mathematical modeling of the re-epithelialization of a 3 dimensional (3d) human skin equivalent. MSc Thesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland, August 2009.

Preprint

  1. C Andreassi*, R Luisier*, H Crerar, S Franke, NM Luscombe, G Cuda, M Gaspari and A Riccio. 3′ UTR cleavage of transcripts localized in axons of sympathetic neurons. BiorXiv. *These authors contributed equally.

Original papers

  1. GE Tyzack*, R Luisier*, DM Taha, J Neeves, M Modic, JS Mitchell, I Meyer, L Greensmith, J Newcombe, J Ule, NM Luscombe, R Patani. Widespread FUS mislocalization is a molecular hallmark of ALS Brain 142 (9), 2572-2580. 2019. *These authors contributed equally.
  2. R Luisier*, GE Tyzack*, CE Hall, JS Mitchell, H Devine, DM Taha, B Malik, I Meyer, L Greensmith, J Newcombe, J Ule, NM Luscombe, R Patani. Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS. Nature communications 9 (1). 2018. *These authors contributed equally.
  3. L Gabrysova, M Alvarez-Martinez, R Luisier, LS Cox, J Sodenkamp, C Hosking, D Pérez-Mazliah, C Whicher, Y Kannan, et.al. c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells. Nature immunology 19 (5), 497. 2018.
  4. CE Hall, Z Yao, M Choi, GE Tyzack, A Serio, R Luisier, J Harley, E Preza, C Arber, et al. Progressive motor neuron pathology and the role of astrocytes in a human stem cell model of VCP-related ALS. Cell reports 19 (9), 1739-1749. 2017.
  5. R Luisier, EB Unterberger, JI Goodman, M Schwarz, JG Moggs, R Terranova, E van Nimwegen. Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion. Nucleic acids research 42 (7), 4180-4195. 2014.
  6. R Luisier, H Lempiainen, N Scherbichler, A Braeuning, M Geissler, V Dubost, et al. Phenobarbital Induces Cell Cycle Transcriptional Responses in Mouse Liver Humanized for Constitutive Androstane and Pregnane X Receptors. Toxicological Sciences 139 (2), 501-511. 2014
  7. EB Unterberger, J Eichner, C Wrzodek, H Lempiainen, R Luisier, R Terranova, U Metzger, S Plummer, T Knorpp, A Braeuning, JG Moggs, MF Templin, V Honndorf, M Piotto, A Zell, M Schwarz. H-ras and b-catenin oncoproteins orchestrate metabolic programs in mouse liver tumors. International journal of cancer 135 (7), 1574-1585. 2014.
  8. H Lempiainen, R Luisier, A Muller, P Marc, D Heard, F Bolognani, P Moulin, P Couttet, O Grenet, J Marlowe, JG Moggs, R Terranova. Epigenomics? Impact for Drug Safety Sciences. Toxicology and Epigenetics, 365-385. 2012.
  9. H Lempiainen, P Couttet, F Bolognani, A Muller, V Dubost, R Luisier, et al. Identification of Dlk1-Dio3 imprinted gene cluster non-coding RNAs as novel candidate biomarkers for liver tumor promotion. Toxicological sciences 131 (2), 375-386. 2012.
  10. EP Dupont, R Luisier and MAM Gijs. NOA 63 as UV-curable material for fabrication of microfluidic channels with native hydrophilicity. Microelectronic engineering 87 (5-8), 1253-1255. 2010.

Awards

  • 2017 Advanced mobility post-doctoral fellowship, 12 months, Swiss National Science Foundation.
  • 2015 Marie Curie Intra European Postdoctoral Fellowship, 24 months, European Commission.
  • 2015 Early mobility post-doctoral fellowship, 18 months, Swiss National Science Foundation.
  • 2009 Annual award for the best MSc project in bioengineering and biotechnology, EPFL
  • 2009 Mention Excellence for the study in Bioengineering and Biotechnology, EPFL

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