Abstract 7417: SpatialCS: A tool to effectively integrate histological annotations and spatial transcriptomics analysis
Authors: Chu Yanshuo , Cho Kyung Serk , Khanduri Isha , Zhou Tieling , Jiang Jiahui , Liu Yunhe , Yan Xinmiao , Pei Guangsheng , Dai Yibo , Liu Yang , Wang Ruiping , Jadhav Akshaya S , Hernandez Sharia , Kadara Humam , Soto Luisa Maren Solis , Kopetz Scott , Maru Dipen Maheshbhai , Wang Linghua 
Published: March 2024

Spatial transcriptomics is revolutionizing our understanding of tumor ecosystems, providing insights into the spatial dimensions of cell locations, their organization, and interactions within tissues. A key challenge in this field is integrating histological annotations with spatial domains identified through unsupervised clustering methods like SpaGCN. This integration is crucial for accurate spatial domain identification and further analyses. However, clustering results often vary based on parameters such as resolution, leading to inconsistencies with histological annotations. This variation necessitates optimized parameter selection to achieve the best clustering outcomes.

We here introduce SpatialCS, a novel tool specifically designed to both visualize and quantify the alignment between histological annotations and the clustering results obtained from spatial transcriptomics data. SpatialCS employs a new index based on the asymmetric Wallace indices. This index penalizes spot pairs that are clustered together but do not share the same histology annotation type, with penalties scaled according to their transcriptional similarity. Additionally, we propose a purity index, derived by calculating the average transcriptional entropy of all clusters. This index serves as a measure of the homogeneity within each cluster. Furthermore, SpatialCS includes a unique visualization function. This function projects histological annotations onto the clustering results as outlines, making it easier to assess the consistency between histology annotations and clustering outcomes.

We have applied SpatialCS to Visium spatial transcriptomics data generated on four colorectal cancer liver metastases, each accompanied by comprehensive spot-level histological annotations in both tumor and normal compartments. The histologic annotations include but not limited to are tumor cells, tumor cell cluster subtypes, tumor stroma, tumor in the vessels, portal tract, individual bile ducts, portal vein and liver cell plates and non-neoplastic stroma. The application of SpatialCS has proven its effectiveness in identifying the most consistent clustering results, which were further confirmed by experienced pathologists. Notably, the output of SpatialCS offers helpful guidance for improving histological annotations. Together, SpatialCS not only provides a quantitative approach to evaluate the consistency between histological annotations and unsupervised clustering analysis but also showcases its potential to significantly enhance histological annotations.

Citation Format: Yanshuo Chu, Kyung Serk Cho, Isha Khanduri, Tieling Zhou, Jiahui Jiang, Yunhe Liu, Xinmiao Yan, Guangsheng Pei, Yibo Dai, Yang Liu, Ruiping Wang, Akshaya S Jadhav, Sharia Hernandez, Humam Kadara, Luisa Maren Solis Soto, Scott Kopetz, Dipen Maheshbhai Maru, Linghua Wang. SpatialCS: A tool to effectively integrate histological annotations and spatial transcriptomics analysis [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 7417.