Abstract 6775: Combination of spatial transcriptomics and multiplex IHC as valuable multi-omics tool for biomarker discovery
Authors: Kerstedt Nicole , Schoeppler Monika , Motamedi-Baniassad Bita , Hirt Antonia , Ploetzky Julia , Kastein Mirja , Thoms Laura , Khenkhar Malik , Juhl Hartmut , David Kerstin A. 
Published: April 2023

Colorectal cancer (CRC) is one of the most common cancers worldwide and shows heterogenous molecular subtypes making personalized medicine as well as identifying new targets highly important to provide individual patients with the most appropriate treatment.

To gain more insight into the visualization of potential molecules or pathways for targeting CRC we used a multi-omics approach for the simultaneous analysis of gene and protein expression within a sample. In this study we combined fluorescent multiplex immunohistochemistry (mIHC) for the detection of proteins (4-plex panel) with the Visium Spatial Transcriptomics technology (10x Genomics) that enables the detection of the whole transcriptome in the histological context.

A formalin-fixed paraffin-embedded (FFPE) tumor tissue sample from a patient diagnosed with CRC was selected according to our quality standards. For this multi-omics approach, serial sections were prepared. The first section was used for fluorescent mIHC staining visualizing the protein expression of Ki67 (proliferation marker), p53 and p21 (both tumor suppressor genes). The second section was stained for hematoxylin and eosin (H&E) to evaluate the tissue morphology. On the third section the Visium FFPE Spatial Gene Expression workflow was applied, and gene expression patterns were analyzed by using the software Space Ranger and Loupe Browser.

Our data showed on the one hand a good correlation of protein and gene expression of Ki67, p53 and p21 within the analyzed sample and on the other hand a clear difference of expression patterns between tumor cell areas and regions with corresponding normal mucosa cells. Moreover, by comparing Spatial Transcriptomics gene expression patterns of tumor cell and corresponding normal mucosa cell areas, we also identified genes that were linked to other cancer types and/or are still only poorly described in cancer, especially for CRC. Corresponding protein expression will be verified by chromogenic IHC in the next steps.

The combination of fluorescent mIHC and Spatial Transcriptomics has been shown to be a valuable approach not only to visualize already described relations as proof of principle, but more importantly to enable the discovery of new biomarkers or pathways predominantly linked to colorectal tumor tissue that may serve as new targets for cancer treatment.

Citation Format: Nicole Kerstedt, Monika Schoeppler, Bita Motamedi-Baniassad, Antonia Hirt, Julia Ploetzky, Mirja Kastein, Laura Thoms, Malik Khenkhar, Hartmut Juhl, Kerstin A. David. Combination of spatial transcriptomics and multiplex IHC as valuable multi-omics tool for biomarker discovery. [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 6775.