Oral Presentation NSW State Cancer Conference 2023

Immunospatial tumour immune microenvironment (isTIME) organisation is associated with recurrence in primary melanoma (#7)

Grace H Attrill 1 2 3 , Nicholas Canete 1 4 , Yuzhou Feng 5 6 , Eva R Shteinman 1 2 3 , Xinyu Bai 1 2 3 , Camelia Quek 1 2 3 , Tuba N Gide 1 2 3 , Felix Marsh-Wakefield 1 2 7 , Ellis Patrick 4 8 , Anna S Trigos 5 6 , Umaimainthan Palendira 1 2 3 , Georgina V Long 1 2 3 9 10 , Richard A Scolyer 1 2 3 11 12 , James S Wilmott 1 2 3 , Ismael A Vergara 1 2 3
  1. Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
  2. Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
  3. Melanoma Institute Australia, Wollstonecraft, NSW, Australia
  4. Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia
  5. Division of Cancer Research, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
  6. Sir Peter McCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
  7. Centenary Institute, University of Sydney, Sydney, NSW, Australia
  8. School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
  9. Mater Hospital, Sydney, NSW, Australia
  10. Royal North Shore Hospital, Sydney, NSW, Australia
  11. Royal Prince Alfred Hospital, Sydney, NSW, Australia
  12. NSW Health Pathology, Sydney, NSW, Australia

The complex spatial interactions of immune cell populations within the melanoma isTIME are associated with patient prognosis and immunotherapy response. Novel multiplex immunofluorescence (mIHC) and spatial analysis techniques enable comprehensive investigation of these interactions. This study aimed to determine immunospatial patterns associated with outcome in patients with primary melanoma. To achieve this, we developed an automated spatial analysis workflow for large patient cohorts.

Melanoma tissue from 46 patients with primary disease was stained for CD8+ T cells and the markers CD103, PD-1 and CD39, as well as NK cells, B cells, and Langerhans cells (LCs) using multiplex immunohistochemistry (mIHC). mIHC data was analysed with the SPIAT spatial analysis R package (1). Immune cell localisation within each tumour was quantified within the mIHC whole slide images and analysed to identify clusters of immune cell types, or neighbourhoods, present in tumours. These spatial relationships were assessed for their associations with patient outcomes.

A set of 1617 neighbourhoods were identified throughout the images using spatial analysis algorithms within SPIAT, and were grouped into 11 distinct ‘neighbourhood metaclusters’ (NMCs) based on their immune composition. NMCs containing high B cells, CD39+CD103+ CD8+ T cells, or LCs were associated with improved 5-year RFS outcomes in this cohort. Neighbourhood composition varied based on tissue location, with B cells, LCs and NK cells significantly increased in marginal and stromal neighbourhoods (p<0.0001). B cell aggregate (BCA) neighbourhoods indicative of early tertiary lymphoid structures (TLSs) based on their localisation, structure and immune composition were identified predominantly at the tumour margins and adjacent stroma. BCA composition was further compared based on patient outcomes, with BCAs harbouring increased CD103-PD-1+ CD8+ T cells associated with poor outcomes. In-depth pairwise analysis of immune phenotypes with melanoma cells found that increased B cell-melanoma and CD103+PD-1- CD8+ T cell-melanoma interaction was associated with improved outcomes.

In developing a cohort-wide isTIME spatial analytic approach and workflow, we identified multiple immunospatial associations with patient outcome in primary melanoma. Intratumoral immune diversity and immune cell neighbourhoods identified in this study indicate a co-ordinated anti-tumour immune response, contributing towards reduced melanoma recurrence and improved patient outcomes.

  1. Feng, Y., Yang, T., Zhu, J. et al. Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments. Nat Commun 14, 2697 (2023). https://doi.org/10.1038/s41467-023-37822-0