Single Cell RNA-Seq Identifies Immune-Related Prognostic Model and Key Signature-SPP1 in Pancreatic Ductal Adenocarcinoma

Kai Chen; Qi Wang; Xinxin Liu; Feng Wang; Yongsu Ma; Shupeng Zhang; Zhijiang Shao; Yinmo Yang; Xiaodong Tian

doi:10.3390/genes13101760

Single Cell RNA-Seq Identifies Immune-Related Prognostic Model and Key Signature-SPP1 in Pancreatic Ductal Adenocarcinoma

Genes (Basel). 2022 Sep 29;13(10):1760. doi: 10.3390/genes13101760.

Authors

Kai Chen¹, Qi Wang¹, Xinxin Liu¹, Feng Wang², Yongsu Ma¹, Shupeng Zhang³, Zhijiang Shao³, Yinmo Yang¹, Xiaodong Tian¹

Affiliations

¹ Department of General Surgery, Peking University First Hospital, Beijing 100034, China.
² Department of Endoscopy Center, Peking University First Hospital, Beijing 100034, China.
³ Department of General Surgery, Tianjin Fifth Centre Hospital, Tianjin 300450, China.

Abstract

There are no reliable biomarkers for early diagnosis or prognosis evaluation in pancreatic ductal adenocarcinoma (PDAC). Multiple scRNA-seq datasets for PDAC were retrieved from online databases and combined with scRNA-seq results from our previous study. The malignant ductal cells were identified through calculating copy number variation (CNV) scores. The robust markers of malignant ductal cells in PDAC were found. Five immune-related signatures, including SPP1, LINC00683, SNHG10, LINC00237, and CASC19, were used to develop a risk score formula to predict the overall survival of PDAC patients. We also constructed an easy-to-use nomogram, combining risk score, N stage, and margin status. The expression level of SPP1 was related to the prognosis and immune regulators. We found that SPP1 was mainly expressed in ductal cells and macrophages in PDAC. In conclusion, we constructed a promising prognostic model based on immune-related signatures for PDAC using scRNA-seq and TCGA_PAAD datasets.

Keywords: SPP1; ScRNA-seq; immune related signatures; pancreatic cancer; prognostic model.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biomarkers, Tumor / genetics
Biomarkers, Tumor / metabolism
Carcinoma, Pancreatic Ductal* / pathology
DNA Copy Number Variations
Gene Expression Regulation, Neoplastic
Humans
Osteopontin / metabolism
Pancreatic Neoplasms* / diagnosis
Pancreatic Neoplasms* / genetics
Pancreatic Neoplasms* / metabolism
Prognosis
RNA-Seq

Substances

Biomarkers, Tumor
SPP1 protein, human
Osteopontin

Grants and funding

This study was supported by The Natural Science Foundation of China (No. 82171722, 81871954) and Beijing Municipal Natural Science Foundation (No. 7212111).