Spatial Omics for Regenerative Medicine

cBITE Department

Spatial Omics for Regenerative Medicine

In the Cillero lab, we employ an interdisciplinary and multimodal approach at the interface of proteomics, mass spectrometry imaging and molecular biology to develop new strategies for regenerative medicine. We apply novel spatial omics approaches to get a better insight into fundamental molecular changes behind the process of ageing. We focus on the characterization of new biomarkers for patient classification and targeted therapy in combination with fundamental and mechanistic research.

Our main research topics are:

  • Single cell (spatial) omics. Tissues are heterogenous and composed by different cell types interacting with an extracellular matrix. In situ molecular characterization is needed to understand cell behaviour and how tissues degenerate and regenerate.
  • Mass spectrometry standardization. We are interested in developing quality control standards for mass spectrometry imaging as well as high throughput proteomics and automation strategies for clinical applications.
  • Patient specific molecular signatures. We employ high throughout mass spectrometry to study patient specific molecular fingerprints for personalized medicine.
  • Biofilm formation. Bacterial infection is a complication when biomaterials are implanted in the body. We aim to get a more fundamental understanding of biofilm formation for the design of new biomaterials with antimicrobial properties.
  • Local drug delivery for tissue regeneration. We develop mass spectrometry imaging methods to get a better insight on drug metabolization, location and biological effects.
  • In vitro models. We use different in vitro models to study tissue degeneration and regeneration as well as drug efficacy. We employ bioreactors to mimic cell and tissue microenvironments in a controlled manner. Some examples are spheroids and tissue explants obtained from osteoarthritis human patients.

External members

The Cillero lab has a joint supervision of the following M4i researchers:

  • Christel Kuik (PhD student)
  • Isabel Vermeulen (PhD student)
  • Mirella Haartmans (PhD student)
  • Charles-Henrie van Assche (PhD student)
  • Mudita Vats (PhD student)
  • Lidia Molina Mill├ín (PhD student)
  • Bo Cao (PhD student)
  • Erik van Zetten (researcher)

Selected publications

  • Eveque-Mourroux MR, Emans PJ, Boonen A, Claes BSR, Bouwman FG, Heeren RMA, Cillero-Pastor B. Heterogeneity of Lipid and Protein Cartilage Profiles Associated with Human Osteoarthritis with or without Type 2 Diabetes Mellitus. J Proteome Res. 2021;20(5):2973-2982, https://doi.org/10.1021/acs.jproteome.1c00186
  • Mezger STP, Mingels AMA, Bekers O, Heeren RMA, Cillero-Pastor B. Mass Spectrometry Spatial-Omics on a Single Conductive Slide. Anal Chem. 2021;93(4):2527-2533, https://doi.org/10.1021/acs.analchem.0c04572
  • Chiaradia E, Pepe M, Sassi P, Mohren R, Orvietani PL, Paolantoni M, Tognoloni A, Sforna M, Eveque M, Tombolesi N, Cillero-Pastor B. Comparative label-free proteomic analysis of equine osteochondrotic chondrocytes. J Proteomics. 2020;228:103927, https://doi.org/10.1016/j.jprot.2020.103927
  • Eveque-Mourroux MR , Emans PJ , Zautsen RRM , Boonen A , Heeren RMA , Cillero-Pastor B . Spatially resolved endogenous improved metabolite detection in human osteoarthritis cartilage by matrix assisted laser desorption ionization mass spectrometry imaging. Analyst. 2019;144(20):5953-5958, https://doi.org/10.1039/c9an00944b
  • Bakker B, Eijkel GB, Heeren RMA, Karperien M, Post JN, Cillero-Pastor B. Oxygen-Dependent Lipid Profiles of Three-Dimensional Cultured Human Chondrocytes Revealed by MALDI-MSI. Anal Chem. 2017;89(17):9438-9444, https://doi.org/10.1021/acs.analchem.7b02265

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