Poster Presentation Multi-Omics Conference 2024

Single-cell and spatial transcriptomics reveal interactions between hepatic stellate cells and tumour cells in metastatic uveal melanoma (#138)

Weitao Lin 1 2 , Elena Denisenko 1 , Nima Meshbah Ardakani 3 4 5 , Neha Pulyani 2 6 , Rui Hou 1 , Ya-Yu Liu 1 , Joakim Karlsson 1 7 , Aaron Beasley 2 6 , Manjot Singh 1 2 , Rodrigo Carlessi 8 , Roger Olofsson Bagge 7 9 10 , Andrew Woo 1 2 , Jonas Nilsson 1 7 , Alistair Forrest 1 , Elin Gray 2 6
  1. Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, WA, Australia
  2. Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
  3. Department of Anatomical Pathology, PathWest, QEII Medical Centre, Nedlands, WA, Australia
  4. School of Pathology and Laboratory Medicine, the University of Western Australia, Crawley, WA, Australia
  5. College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
  6. School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
  7. Sahlgrenska Centre for Cancer Research, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
  8. Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
  9. Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden
  10. Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden

Background: Uveal melanoma (UM) is the second most common melanoma subtype. While the primary tumour in the eye can be effectively managed by surgery or radiotherapy, metastatic disease ultimately develops in half of all patients. In early 2022, the U.S. Food and Drug Administration approved the first drug, tebentafusp, for metastatic UM. However, only patients expressing a specific human leukocyte antigen (HLA-A*02:01) have the potential to benefit, with a small improvement in survival, meaning effective treatments are limited to less than half of patients. Therefore, there is an urgent need to develop other effective treatments for metastatic UM. UM possesses a distinctive characteristic whereby a vast majority (90%) of metastases initially develop within the liver. A better understanding the UM dependence on the liver microenvironment could reveal new targets for the development of new treatments.

Methods: Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics analyses were applied to study the cell-to-cell communication networks between tumour cells and normal cells within UM liver metastases.

Results: Single-cell RNA-seq datasets of ten UM liver metastases were integrated using Seurat with twelve cell types annotated. Cell-to-cell communication networks using NATMI identified hepatic stellate cells as the most prevalent cell type signalling to tumour cells. CD44 receptor on tumour cells was observed to interact with ligands produced primarily by stellate cells such as COL1A1 and COL1A2, with NicheNet validating this interaction. Enrichment of stellate cells and tumour cells in the tumour nodule was confirmed by Visium spatial analysis in formalin-fixed paraffin-embedded metastatic UM samples. RNAscope multiplex fluorescent assay further confirmed the proximity of stellate cells and tumour cells together with the presence of COL1A1 and CD44 on archival UM metastases.

Conclusion: Our study highlights stellate cells as a key player in UM liver metastases and identified CD44 signalling as a targetable molecular pathway to treat UM.