Poster Presentation 29th Annual Lorne Proteomics Symposium 2024

Data-independent acquisition (DIA) using as high-field asymmetric waveform ion mobility spectrometer (FAIMS) of formalin-fixed paraffin embedded (FFPE) lung tissue to elucidate the proteomic changes in mucopolysaccharidosis (MPS) disease murine models (#132)

Yuen Tung Ngai 1 , Matthew Briggs 1 , Clifford Young 1 , Manuela Klingler-Hoffmann 1 , Parul Mittal 1 , Emma Parkinson-Lawrence 1 , Sandra Orgeig 1 , Peter Hoffmann 1
  1. Clinical & Health Sciences, University of South Australia, Adelaide, SA, Australia

Background

Mucopolysaccharidosis (MPS) diseases are recessive lysosomal storage disorders resulting from dysfunctional lysosomes. Specifically, enzyme dysfunction in MPS diseases result in the accumulation of glycosaminoglycans in lysosomes and impact downstream metabolism pathways. Distinct clinical signs include altered facial features and impaired cognitive development in MPS type I and significant neurological and skeletal pathologies in MPS type IIIA. Despite lung dysfunction not being a primary clinical feature in both MPS type I and IIIA, patients suffer from recurrent respiratory infections and dysfunctions, contributing to mortality.1-3

 
Methods
20 weeks old C57BL/6 MPS mice were used and lungs were inflated in situ with 4 % paraformaldehyde neutral buffer and processed as formalin-fixed paraffin embedded tissue. The sections were dewaxed, rehydrated and antigen retrieval was performed with citric acid. The tissues went through denaturation, reduction, alkylation, and tryptic digestion. The samples were cleaned up with zip tip and and proteomics data were acquired using a high-field asymmetric waveform ion mobility spectrometer (FAIMS) with data-independent acquisition (DIA). FAIMS-DIA was performed with Orbitrap Exploris™ 480 mass spectrometry (Thermo Scientific). Spectronaut™ was used to process the data.

 

Results
We were able to identify ~5600 proteins in each sample with 500 ng injection performed in triplicate. Results demonstrated the disease effects multiple pathways including metabolism and cellular functions, analysed with DAVID GO tool.

 

Conclusions
The DIA proteomics approach of organs of interest is beneficial for investigating rare diseases and to gain a deeper understanding of the disease. This approach could be applicable to many other disease models.

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  2. Paget, T.L., et al., Increased Alveolar Heparan Sulphate and Reduced Pulmonary Surfactant Amount and Function in the Mucopolysaccharidosis IIIA Mouse. Cells, 2021. 10(4).
  3. Chiang, J., et al., Tachypnea of infancy as the first sign of Sanfilippo syndrome. Pediatrics, 2014. 134(3): p. e884-8.
  4. Carter, C.L., et al., MALDI-MSI spatially maps N-glycan alterations to histologically distinct pulmonary pathologies following irradiation. Scientific Reports, 2020. 10(1): p. 11559.