Abstract 6830: Xenium in situ analysis and reproducibility study of multiple carcinomas for clinical studies

Abstract

Abstract 10x Genomics’ Xenium is the newest in situ spatial transcriptomics platform offering sub-cellular resolution in frozen and FFPE tissue sections for a deeper study of cellular mechanisms and interactions. Mapping RNA targets at high specificity with fully customizable assays and quick workflow, it uses rolling circle amplification and interpretation-ready data is available immediately after the run. At BioChain Institute, Inc. (BioChain), we are conducting validation studies for reproducibility of results with the Xenium platform using BioChain’s oncology biospecimen.FFPE tissues from BioChain’s repository were screened by our pathologist for tumor content above 30%. Four carcinoma tissues from Breast, Colon, Lung, and Kidney with high DV200 scores were selected. An array was constructed with these tissues to fit the Xenium slide’s imageable area. Two serial sections were used for the Xenium run per 10x Genomics’ protocol. The Off-the-shelf Human Multi-Tissue and Cancer Panel was used for targeting 377 genes. H&E staining and imaging was performed, and the image was integrated with the data on the Xenium platform. The results were found to be reproducible between two different operators. For example, in the breast section, over 96,000 cells were detected and median transcripts per cell were 70 in both the runs. There were 20 clusters representing different cell types/states, 99% transcripts were within cells, and ~85% of the transcripts were found to be high quality. Furthermore, we are analyzing the expression of unique tumor type and immune transcripts to map the heterogeneity of the tissues, as well as sensitivity, and standard deviation between the runs. The Xenium platform is a powerful tool for the sub-cellular spatial transcriptomics study of tissues with targeted gene panels. However, one of the four tissues used here failed to show enough transcripts. Further investigation is underway to examine the issue and conclude best practices thereafter. Our future studies will include accuracy and concordance validation with Xenium run on different days and Visium whole transcriptome assay post- Xenium. Citation Format: Elim Cheung, Baowen Zhang, Lutong Zhang, Tong Lu, Rikita Gakhar, Vidyodhaya Sundaram. Xenium in situ analysis and reproducibility study of multiple carcinomas for clinical studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6830.