Identification and Validation of a Malignant Cell Subset Marker-Based Polygenic Risk Score in Stomach Adenocarcinoma Through Integrated Analysis of Bulk and Single-Cell RNA Sequencing Data.

Qiyuan Zou,Zuhuan Gan,Yufeng Lv,Shulan Liao,Zhonghui Liang

doi:10.3389/fcell.2021.720649

Abstract

Objectives: The aim of the present study was to construct a polygenic risk score (PRS) for poor survival among patients with stomach adenocarcinoma (STAD) based on expression of malignant cell markers.Methods: Integrated analyses of bulk and single-cell RNA sequencing (scRNA-seq) of STAD and normal stomach tissues were conducted to identify malignant and non-malignant markers. Analyses of the scRNA-seq profile from early STAD were used to explore intratumoral heterogeneity (ITH) of the malignant cell subpopulations. Dimension reduction, cell clustering, pseudotime, and gene set enrichment analyses were performed. The marker genes of each malignant tissue and cell clusters were screened to create a PRS using Cox regression analyses. Combined with the PRS and routine clinicopathological characteristics, a nomogram tool was generated to predict prognosis of patients with STAD. The prognostic power of the PRS was validated in two independent external datasets.Results: The malignant and non-malignant cells were identified according to 50 malignant and non-malignant cell markers. The malignant cells were divided into nine clusters with different marker genes and biological characteristics. Pseudotime analysis showed the potential differentiation trajectory of these nine malignant cell clusters and identified genes that affect cell differentiation. Ten malignant cell markers were selected to generate a PRS: RGS1, AADAC, NPC2, COL10A1, PRKCSH, RAMP1, PRR15L, TUBA1A, CXCR6, and UPP1. The PRS was associated with both overall and progression-free survival (PFS) and proved to be a prognostic factor independent of routine clinicopathological characteristics. PRS could successfully divide patients with STAD in three datasets into high- or low-risk groups. In addition, we combined PRS and the tumor clinicopathological characteristics into a nomogram tool to help predict the survival of patients with STAD.Conclusion: We revealed limited but significant intratumoral heterogeneity in STAD and proposed a malignant cell subset marker-based PRS through integrated analysis of bulk sequencing and scRNA-seq data.

Highlights

Stomach adenocarcinoma (STAD) is the most frequent histological type of stomach cancer and the fifth most common type of cancer
Despite intratumoral heterogeneity (ITH), patients with STAD are treated according to pathological staging and expression of certain cancer markers such as Hrb-b2 receptor tyrosine kinase
ITH is the problem that must be overcome in the treatment of acquired drug-resistant tumors

Summary

Introduction

Stomach adenocarcinoma (STAD) is the most frequent histological type of stomach cancer and the fifth most common type of cancer. Similar results were seen in studies from Singapore (Lei et al, 2013) and the Asian Cancer Research Group (Cristescu et al, 2015) These classification systems may lead to the development of specific therapies. Patients with EBV-positive or MSI–high STAD may not benefit from adjuvant chemotherapy (Ramos et al, 2020), but they may benefit from immune checkpoint inhibitors (Derks et al, 2016; Muro et al, 2016). These classification systems are based on data derived from bulk tissues, so they cannot capture intratumoral heterogeneity (ITH). Partial responses and secondary resistance indicate that some but not all subpopulations in a given tumor are sensitive to therapy

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