Oral Presentation 26th Annual Lorne Proteomics Symposium 2021

Comprehensive proteomic profiling of blood extracellular vesicles via SWATH mass spectrometry: a new avenue for glioma tumour monitoring (#19)

Susannah Hallal 1 2 , Heng Wei 2 3 , Maggie Lee 2 3 , Hao-Wen Sim 4 5 6 , Brindha Shivalingam 1 2 , Michael Buckland 2 7 8 , Kimberley Alexander-Kaufman 1 2 7
  1. Neurosurgery Department, Chris O'Brien Lifehouse, Sydney, NSW, Australia
  2. BrainStorm Brain Cancer Research Group, Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
  3. Department of Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
  4. Department of Medical Oncology and NHMRC Clinical Trials Centre, Chris O'Brien Lifehouse, Sydney, NSW, Australia
  5. Central Clinical School, University of Sydney, Sydney, NSW, Australia
  6. The Kinghorn Cancer Centre, St Vincent’s Hospital, Sydney, NSW, Australia
  7. Neuropathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
  8. Pathology, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia

Diffuse gliomas (grades II-IV) are the most frequent and devastating primary brain tumours of adults. Currently, the clinical management for glioma patients involves a tissue biopsy for diagnostics and routine neuro-radiographic assessments, both of which have major limitations for accurate clinical assessment. With efforts to improve the clinical management of glioma, comes a growing trend to design minimally-invasive liquid biopsies (i.e. blood tests) that can routinely measure glioma-derived molecules in body fluids and allow for tumour evolution to be assessed in real-time. In this regard, extracellular vesicles (EVs; 30-1000 nm membranous particles) hold major promise as biomarker reservoirs. EVs encapsulate molecules that reflect the identity and molecular state of their cell-of-origin and their release is upregulated in neoplasia. EVs also cross the blood-brain-barrier into the circulation where they are stable and readily accessible. Despite their suitability as biomarkers, in-depth proteomic characterisation of circulating-EVs by traditional shot-gun proteomics has been hindered by the complexity of the blood and the co-isolation of highly abundant blood proteins. In this study, a data-independent acquisition (DIA) proteomics platform, sequential window acquisition of all theoretical fragment ion spectra (SWATH), was used in conjunction with a targeted data extraction strategy to achieve in-depth protein profiles of circulating-EVs from glioma patients. EVs were isolated by size exclusion chromatography from the plasma of pre-operative glioma II-IV patients and controls. Nanoparticle tracking and transmission electron microscopy confirmed the isolation of small-EV subtypes (< 200 nm). The plasma-EV peptides were sequenced by SWATH-MS, and the identities and quantities of the proteins were extracted using a custom spectral library comprised of 8662-protein species, developed using peptide samples from a range of glioma specimens, including cell lysates, tumour tissues and EVs. A total of 4054 proteins were identified in the plasma-EVs of all sample groups. Of these proteins, 463 changed significantly across the glioma and non-glioma cohorts (adj. p < 0.05), and included proteins previously reported to have significance in glioma-EVs. Principal component analysis showed excellent discrimination between the patient groups, with samples observed to cluster with their respective glioma subtype/grade. Using SWATH mass spectrometry we describe the most comprehensive proteomic plasma-EV profiles for glioma reported to-date, for which future studies using larger longitudinal cohorts could define a set of circulating-EV biomarkers, capable of stratifying glioma patients and detecting recurrence, progression and treatment resistance.