Tumour Evolution And Microenvironment Interactions In 2d And 3d Space Chiakuei Mo1 by Chia-kuei Mo1, 2, 19, Jingxian Liu1, 2, 19, Siqi Chen1, 2, 20, Erik Storrs1, 2, 20, instant download after payment.

To study the spatial interactions among cancer and non-cancer cells1, we here examined a cohort of 131 tumour sections from 78 cases across 6 cancer types by Visium spatial transcriptomics (ST). This was combined with 48 matched singlenucleus RNA sequencing samples and 22 matched co-detection by indexing (CODEX) samples. To describe tumour structures and habitats, we defned ‘tumour microregions’ as spatially distinct cancer cell clusters separated by stromal components. They varied in size and density among cancer types, with the largest microregions observed in metastatic samples. We further grouped microregions with shared genetic alterations into ‘spatial subclones’. Thirty fve tumour sections exhibited subclonal structures. Spatial subclones with distinct copy number variations and mutations displayed diferential oncogenic activities. We identifed increased metabolic activity at the centre and increased antigen presentation along the leading edges of microregions. We also observed variable T cell infltrations within microregions and macrophages predominantly residing at tumour boundaries. We reconstructed 3D tumour structures by co-registering 48 serial ST sections from 16 samples, which provided insights into the spatial organization and heterogeneity of tumours. Additionally, using an unsupervised deep-learning algorithm and integrating ST and CODEX data, we identifed both immune hot and cold neighbourhoods and enhanced immune exhaustion markers surrounding the 3D subclones. These fndings contribute to the understanding of spatial tumour evolution through interactions with the local microenvironment in 2D and 3D space, providing valuable insights into tumour biology.