Multi-omics for healthcare materials

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The group Multi-omics for healthcare materials focuses on the mapping of disease-associated cellular signaling networks in order to inform precise imunoengineering solutions. Activities of the group are centered on generating and analyzing biomedical multi-omics datasets that can assist development of new materials for personalized healthcare applications. 

Our research work aims to enable rational design of new materials by capitalizing on large-scale biomedical datasets. This involves development of new software tools, employment of advanced data analytics and modeling of material properties. Through collaborations with material scientists, we evaluate the efficiency of the in silico designed functionalized nanoparticles and other modified materials. Together with clinical and industrial partners, we seek to implement these new concepts into next generation healthcare solutions.

Group's background

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The group has a strong expertise in studying molecular mechanisms of disease development and mapping cellular processes that underlie cell identity and response to stimuli. We are experienced with analyzing genomic, transcriptomic and proteomic large-scale datasets and with using statistics to identify disease-associated and patient-specific processes. Our group is a member of the Swiss Institute of Bioinformatics.

Signaling in tumor microenvironment

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Complexity of tumor microenvironment. Image created with BioRender.com.
Recent research in nanomedicine has opened exciting possibilities for expanding cancer immunotherapy options. In particular, engineered nanoparticles that are taken up by immune cells and subsequently delivered to tumor microenvironment have shown highly promising results on mouse models. Our research focuses on the study of signaling pathways within cell types that compose tumor microenvironment and on characterization of a cross talk among these cells. In particular, we seek to identify specific signaling networks that could be amenable to immunomodulation by functionalized nanoparticles. Immunotherapy represents the most important discovery in cancer treatment, but only a small fraction of patients responds favorably to it. Better understanding of signaling events in tumor microenvironment could form essential foundations for new combinatorial treatments.

Signaling pathways in disease cells

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Cellular signal flow. Image created with BioRender.com.
Changes in cellular signaling pathway activities are at the root of cancer and many other diseases. In collaboration with clinical researchers and through analysis of multi-omics datasets, we investigate disease-specific alterations in signal propagation and map molecular mechanisms that underlie disease development. In addition, we employ biomedical datasets for the study of mechanisms of treatment resistance. We have ongoing projects on several tumor types, but we are interested in applying our expertise in large-scale data integration and network modeling to different diseases. In our research, we aim to attain a comprehensive insight into molecular basis of disease phenotypes. For this, we rely on the characterization of cellular processes at different layers of information flow, including protein structural changes, kinase phosphorylation events and alternative splicing regulation.

Nanoparticles as drug delivery systems

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Nanoparticles functionalized with biomolecules. Image created with BioRender.com.
The recent advent of mRNA and siRNA drugs into clinics has brought into limelight polymer-, metal- and lipid-based nanoparticles which serve as scaffolds for the delivery of these molecules. Importantly, nanoparticles’ physicochemical properties that define their optimal uptake and efficiency are specific for different human cells. Through data analysis and machine learning, we aim to define properties of individual nanoparticles that ensure they can be used as scaffolds for a targeted, safe and efficient delivery into a specific cell type. Combined with in-depth insights into cellular pathways, this allows a precise functionalization of material scaffolds and supports a design of personalized therapeutic approaches. Our current focus is on immune cells that naturally act as phagocytes and thus take up nanoparticles. These cells play an essential role in cancer, infectious and autoimmune diseases and we are eager to explore different opportunities for immunoengineering.

 

Lukas Häuser, PhD

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Student 

Lukas.Haeuser@empa.ch

Alma Mater: Heidelberg University 

 

Katharina Hast, PhD Student 

Katharina.Hast@empa.ch

Alma Mater: Friedrich-Alexander-Universität Nürnberg-Erlangen

 

Jonas Bossart, PhD Student 

Jonas.Bossart@empa.ch

Alma Mater: ETH

 

Tiberiu Totu, PhD Student 

Tiberiu.Totu@empa.ch

Alma Mater: EPFL

 

Alumni

Benoit Hohl, MSc Student 

Alma Mater: EPFL

 

Emile Bourban, MSc Student 

Alma Mater: EPFL

 

Feifei Xia, MSc Student 

feifei.xia@empa.ch

Alma Mater: UZH

 

Delia Cella, MSc Student 

delia.cella@empa.ch

Alma Mater: ETH

 T Totu#, J Bossart#, K Hast, C Li, M Rottmar, B Sobottka, G Yu, V Ayala-Nunez, M Buljan*: Delineation of signaling routes that underlie differences in macrophage phenotypic states. bioRxiv (2024) 

M Buljan*, A Banaei-Esfahani, P Blattmann, F Meier-Abt, W Shao, O Vitek, H Tang, R Aebersold*: A computational framework for the inference of protein complex remodeling from whole-proteome measurements. Nature Methods 20(3):1523-1529. (2023)

M Buljan*, P Wick: Tailoring design of nanomaterials and systems to individualize patient treatments. Chimia 76(3):236-241. (2022)

M Buljan, R Ciuffa, A van Drogen, A Vichalkovski, M Mehnert, G Rosenberger, S Lee, M Varjosalo, L Espona Pernas, V Spegg, B Snijder, R Aebersold*, M Gstaiger*: Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. Molecular cell 79(3):504-520. (2020)

M Buljan, P Blattmann, R Aebersold*, M Boutros*: Systematic characterization of pan-cancer mutation clusters. Molecular systems biology 14(3): e7974. (2018)

JK White, AK Gerdin, NA Karp, E Ryder, M Buljan, JN Bussell, J Salisbury, S Clare, NJ Ingham, C Podrini, R Houghton, J Estabel, JR Bottomley, DG Melvin, D Sunter, NC Adams, L Baker, C Barnes, R Beveridge, E Cambridge, D Carragher, P Chana, K Clarke, Y Hooks, N Igosheva, C Ismail, H Jackson, L Kane, R Lacey, DT Lafont, M Lucas, S Maguire, K McGill, RE McIntyre, S Messager, L Mottram, L Mulderrig, S Pearson, HJ Protheroe, LA Roberson, G Salsbury, M Sanderson, D Sanger, C Shannon, PC Thompson, E Tuck, VE Vancollie, L Brackenbury, W Bushell, R Cook, P Dalvi, D Gleeson, B Habib, M Hardy, K Liakath-Ali, E Miklejewska, S Price, D Sethi, E Trenchard, D von Schiller, S Vyas, AP West, J Woodward, E Wynn, A Evans, D Gannon, M Griffiths, S Holroyd, V Iyer, C Kipp, M Lewis, W Li, D Oakley, D Richardson, D Smedley, C Agu, J Bryant, L Delaney, NI Gueorguieva, H Tharagonnet, AJ Townsend, D Biggs, E Brown, A Collinson, CE Dumeau, E Grau, S Harrison, James Harrison, Catherine E Ingle, Helen Kundi, Alla Madich, Danielle Mayhew, T Metcalf, S Newman, J Pass, L Pearson, H Reynolds, C Sinclair, H Wardle-Jones, M Woods, L Alexander, T Brown, F Flack, C Frost, N Griggs, S Hrnciarova, A Kirton, J McDermott, C Rogerson, G White, P Zielezinski, T DiTommaso, A Edwards, E Heath, MA Mahajan, B Yalcin, D Tannahill, DW Logan, DG MacArthur, J Flint, VB Mahajan, SH Tsang, I Smyth, FM Watt, WC Skarnes, G Dougan, DJ Adams, R Ramirez-Solis, A Bradley, KP Steel: Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes. Cell 154(2):452-464. (2013

M Buljan*, G Chalancon, S Eustermann, GP Wagner, M Fuxreiter, A Bateman, MM Babu*: Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Molecular cell 46(6): 871-883. (2012

Open positions

Regardless of open calls, if you are interested to join the lab as a Master student, a PhD student or a Postdoctoral fellow and are eligible for an independent fellowship, please get in touch!


News

Nov 2023

We are very happy that Lukas Häuser is starting his PhD in the group.

Sep 2023

We are chairing a session on the Dynamics of immune processes at the Basel Computational Biology conference.

Feb 2023

A very warm welcome to Katharina Hast who is starting her PhD at Empa! 

Jun 2022

We are very grateful to Uniscientia foundation for supporting our research.

Oct 2021

Marija has joined the National Advisory Board of the Swiss Personalized Health Network

Oct 2021

A very warm welcome to Jonas Bossart and Tiberiu Totu who are starting their PhD in the group! 

Jan 2021

The group has now joined the Swiss Institute of Bioinformatics!