PNOC Expressed by B Cells in Cholangiocarcinoma Was Survival Related and LAIR2 Could Be a T Cell Exhaustion Biomarker in Tumor Microenvironment: Characterization of Immune Microenvironment Combining Single-Cell and Bulk Sequencing Technology

Abstract

BackgroundCholangiocarcinoma was a highly malignant liver cancer with poor prognosis, and immune infiltration status was considered an important factor in response to immunotherapy. In this investigation, we tried to locate immune infiltration related genes of cholangiocarcinoma through combination of bulk-sequencing and single-cell sequencing technology.MethodsSingle sample gene set enrichment analysis was used to annotate immune infiltration status in datasets of TCGA CHOL, GSE32225, and GSE26566. Differentially expressed genes between high- and low-infiltrated groups in TCGA dataset were yielded and further compressed in other two datasets through backward stepwise regression in R environment. Single-cell sequencing data of GSE138709 was loaded by Seurat software and was used to examined the expression of infiltration-related gene set. Pathway changes in malignant cell populations were analyzed through scTPA web tool.ResultsThere were 43 genes differentially expressed between high- and low-immune infiltrated patients, and after further compression, PNOC and LAIR2 were significantly correlated with high immune infiltration status in cholangiocarcinoma. Through analysis of single-cell sequencing data, PNOC was mainly expressed by infiltrated B cells in tumor microenvironment, while LAIR2 was expressed by Treg cells and partial GZMB+ CD8 T cells, which were survival related and increased in tumor tissues. High B cell infiltration levels were related to better overall survival. Also, malignant cell populations demonstrated functionally different roles in tumor progression.ConclusionPNOC and LAIR2 were biomarkers for immune infiltration evaluation in cholangiocarcinoma. PNOC, expressed by B cells, could predict better survival of patients, while LAIR2 was a potential marker for exhaustive T cell populations, correlating with worse survival of patients.

The Functional Roles of Immune Cells in Primary Liver Cancer

“…Numbers of infiltrated B cells in CCA tissues are positively correlated with better overall survival. 75 High populations of infiltrating CD20 þ B cells, naïve B cells, IgM þ memory B cells, and isotype-switched memory B cells were associated with better survival, showing characteristics as prognostic factors for HCC patients. 76 Infiltration of CD20 þ or CD79a þ B cells in the tumor microenvironment was positively correlated with prolonged HCC patient survival.…”

Diversification and shared features of tumor‐binding antibody repertoires in tumor, sentinel lymph node and blood of three patients with breast cancer

“…Tumor‐45 exhibited markedly lower levels of CD19 and MS4A1 , but elevated expression of BLK and SPIB (both of which can also be expressed in plasmacytoid dendritic cells in addition to B cells 21,22 ). In addition, tumor 45 had high levels of TCL1A and PNOC , which are associated with improved prognosis in cancer 23,24 . Tumor 31, in contrast, showed comparatively low expression of B cell‐specific genes.…”

“…In addition, tumor 45 had high levels of TCL1A and PNOC, which are associated with improved prognosis in cancer. 23,24 Tumor 31, in contrast, showed comparatively low expression of B cell-specific genes. Gene transcripts for cytotoxic T cells, such as GZMA, GZMB, GZMH and CD8A, and gene transcripts for NK cells, mast cells and 25 neutrophils showed a trend of transcript abundance with patient 45 > patient 29 > patient 31, indicative of disparate immune cell composition and/or activity (Figure 1c).…”

Integrating Single-Cell RNA-seq to construct a Neutrophil prognostic model for predicting immune responses in non-small cell lung cancer

“…In order to evaluate the relationship between the prognostic risk model and immune in ltration, we used the single sample Gene Set Enrichment Analysis (ssGSEA) algorithm in R to calculate the degree of immune in ltration of 28 kinds of immune cells in the TCGA cohort to observe the relationship between prognostic risk and immune in ltration [21].…”