Abstract 866: Identification of survival-associated epithelial cell markers linked to TROP2 through single-cell and bulk sequencing analysis

Abstract

Abstract Introduction: Colorectal Cancer (CRC) is known for its aggressiveness and drug resistance. This has increased the interest in antibody-drug conjugates (ADCs) as a possible therapy. In this study, we aim to investigate the effects of the ADC target TROP2, on the level of epithelial cells and its correlation with survival outcomes in CRC patients. Methods: Single-cell RNA (scRNA) data was downloaded from Gene Expression Omnibus (GEO) for CRC patients and evaluated for TROP2 expression. Patients were grouped into low and high-TROP2 based on median TROP2 expression, and pseudo-bulk analysis was used to find the differentially expressed genes (DEGs). The DEGs were used to find the survival association in the TCGA-CRC cohort. A risk score was built using principal component analysis (PCA) on the TROP2-DEGs and cutoff point was chosen based on survival. Kaplan-Meier curve was used to compare overall survival (OS), progression-free survival (PFS), and disease-free survival (DFS) risk groups. Gene Set Variation Analysis (GSVA) was used to identify the enriched pathways between low- and high-TROP2 in GSE using pseudo-bulk by pooling epithelial cells of individual patients. Results: Of the 10424 cells of 15 different types for 9 CRC patients retrieved from GSE146771, TROP2 was significantly expressed by epithelial cells (n = 766) with mean expression of 1.64 (SD: 1.96, P-value: 0.003) using pseudo-bulk analysis. Three significant DEGs were obtained which are: KIF13B, UCHL3, and PLAC8. These were evaluated for survival association in resectable stages (I-III) CRC patients (n = 419) using PCA to group the patients into low-risk (n = 88) and high-risk (n = 331), using -1.4 as the cutoff point. High risk group showed a better survival with a 1-year survival probability of 94% compared to 90% in the low group and a 5-year survival probability of 74% vs. 46% in the low group. The Kaplan-Meier curve showed that OS, PFS & DFS were significantly better in the low-risk group (p-value = 0.004, 0, 04, and 0.024 respectively). TROP2 and PLAC8 were significantly associated with worse prognosis, whereas UCHL3 was associated with better prognosis (p-value = <0.001), however, KIF3B did not significantly affect the prognosis. APC gene mutation and TP53 were higher in the low-risk group (p-value = 0.004, 0.007 respectively). KRAS-signaling, IL-18-signaling, MET activation of PTK2-signaling were upregulated in high-TROP2 group, while MYC targets, MTORC1 signaling, DNA repair, reactive-oxygen-species signaling, and TCR-signaling were upregulated in low-TROP2. Conclusion: In this study we developed a TROP2-associated risk score that significantly predicted OS, PFS, and DFS in patients with resectable CRC by combining single-cell and bulk-RNA-seq datasets and showing predominant expression of TROP2 in epithelial cells. These findings support the development of TROP2 targeting therapeutics in this space. Citation Format: Noor Nedal Al-Bzour, Ayah Nedal Al-Bzour, Azhar Saeed, Lujia Chen, Anwaar Saeed. Identification of survival-associated epithelial cell markers linked to TROP2 through single-cell and bulk sequencing 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 866.