Abstract 5629: Spatial genomics and proteomics enable multimodal analyses of oral SCC clonal heterogeneity and interactions with tumor microenvironment
Authors: Kumar Raju , Ibrahim Rana , Cheikh Bassem Ben , Bailey Emma , Cottom Hannah , Braubach Oliver , Graham Trevor , Wang Jun , Sequeira Ines 
Published: April 2023

Cancer progression is an evolutionary process governed by the clonal evolution of the genetic mutations acquired during tumor growth, together with the co-evolution of the tumour ecosystem. The nature of cancer subclonal mutations and their effects on the tumour microenvironment are the major drivers of intratumor heterogeneity and contribute to cancer progression, metastasis, therapy resistance and disease recurrence. Therefore, a spatially resolved genetic and cellular profiling of tumors is crucial to investigate tumor architecture and cellular diversity. Oral squamous cell carcinoma (OSCC), a subset of head and neck cancer, accounts for 355,000 new cases annually worldwide and has a 5-year survival rate of only 50%. We recently conducted a multi-level analysis of OSCC genetic and microenvironment heterogeneity (Sequeira et al, 2020, NatComms). Computational analysis of tumour clonal dynamics from DNA sequencing data revealed that high genetic heterogeneity to be a feature of early-stage lesions that are likely to progress to more aggressive tumors (Williams et al 2018, NatGen; Sequeira et al, 2020, NatComms). These tools can be used to predict tumour behavior and for early diagnosis of aggressive lesions. The goal of this study is to elucidate the functional and spatial intratumor heterogeneity, tumor clonal dynamics and evolutionary landscape of human OSCC, and to study the interaction of tumour cells with the microenvironment, in particular the role of specific mutations in promoting epithelial-to-mesenchymal transition and tumor progression, using an interdisciplinary approach that combines spatial integrative genome analysis and deep single-cell phenotyping of tumor microenvironment. We performed whole-exome sequencing from multifocal OSCC tumor regions and matched metastasis, and used computational methods to investigate the tumor subclonal organization, construct phylogenetic trees for each tumor and assess the genetic diversity of the different tumour regions and metastasis. We then combined Single cell Spatial Phenotyping on the PhenoCycler platform (Akoya Biosciences) (Black et al, 2021, NatProtocols) with the subclonal genomic analysis to investigate how different mutational landscapes affect tumor microenvironment and metastasis, at unprecedented detail. Together, this multi-modal integrated spatial genomics and proteomics analysis of the tumor ecosystem highlights the importance of spatial cellular organization and provides a comprehensive human OSCC spatial atlas of tumour heterogeneity, providing a foundation for exploring cancer evolution, heterogeneity and progression.

Citation Format: Raju Kumar, Rana Ibrahim, Bassem Ben Cheikh, Emma Bailey, Hannah Cottom, Oliver Braubach, Trevor Graham, Jun Wang, Ines Sequeira. Spatial genomics and proteomics enable multimodal analyses of oral SCC clonal heterogeneity and interactions with tumor microenvironment. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5629.