Integrated Multi-Omics Data Analysis Reveals Associations Between Glycosylation and Stemness in Hepatocellular Carcinoma

Abstract

BackgroundGlycosylation plays an essential role in driving the progression and treatment resistance of hepatocellular carcinoma (HCC). However, its function in regulating the acquisition and maintenance of the cancer stemness-like phenotype in HCC remains largely unknown. There is also very little known about how CAD and other potential glycosylation regulators may influence stemness. This study explores the relationship between glycosylation and stemness in HCC.MethodsGene set variance analysis (GSVA) was used to assess the TCGA pan-cancer enrichment in glycosylation-related pathways. Univariate, LASSO, and multivariate COX regression were then used to identify prognostic genes in the TCGA-LIHC and construct a prognostic signature. HCC patients were classified into high- and low-risk subgroups based on the signature. The relationship between gene expression profiles and stemness was confirmed using bulk and single-cell RNA-sequencing data. The role of CAD and other genes in regulating the stemness of HCC was also validated by RT-qPCR, CCK-8, and colony formation assay. Copy number variation (CNV), immune infiltration, and clinical features were further analyzed in different subgroups and subsequent gene expression profiles. Sensitive drugs were also screened.ResultsIn the pan-cancer analysis, HCC was shown to have specific glycosylation alterations. Five genes, CAD, SLC51B, LGALS3, B3GAT3, and MT3, identified from 572 glycosylation-related genes, were used to construct a gene signature and predict HCC patient survival in the TCGA cohort. The results demonstrated a significant positive correlation between patients in the high-risk group and both elevated gene expression and HCC dedifferentiation status. A significant reduction in the stemness-related markers, CD24, CD44, CD20, FOXM1, and EpCAM, was found after the knockdown of CAD and other genes in HepG2 and Huh7 cells. Frequent mutations increased CNVs, immune-suppressive responses, and poor prognosis were also associated with the high-risk profile. The ICGC-LIRI-JP cohort confirmed a similar relationship between glycosylation-related subtypes and stemness. Finally, 84 sensitive drugs were screened for abnormal glycosylation of HCC, and carfilzomib was most highly correlated with CAD.ConclusionsGlycosylation-related molecular subtypes are associated with HCC stemness and disease prognosis. These results provide new directions for further research on the relationship between glycosylation and stemness phenotypes.

Stemness analysis in hepatocellular carcinoma identifies an extracellular matrix gene–related signature associated with prognosis and therapy response

“…The results showed that the ECM-related signature was more accurate and robust than the stemness-related signature (p < 0.0001, Figure 2I). Also, the performance of the ECM-related signature was also better than other published stemness-related signatures (p < 0.0001, Figure 2J) (Zhang et al, 2020;Hong et al, 2021;Shen et al, 2021;Chen et al, 2022;Liu et al, 2022). We further explored the correlation between our prognostic model and ECM collagen or non-collagen genes.…”

Early phenotypic and soluble markers of T cell activity can distinguish sepsis associated HLH from sepsis in children

“…Whether a marked reduction in the CD4/CD8 ratio in SHLH patients is either governed by preferential apoptosis of CD4 T cells or excessive proliferation of activated CD8 T cells which is often reported in HLH patients; or both, needs further investigation. A number of studies have clearly demonstrated expansion of activated T cell population as a characteristic feature in HLH patients; more evidently in CD8 T cells 10,12,14 while in sepsis, suppressive T cell phenotypes or function was noticed 17,[19][20][21] . More recently, the diagnostic utility of CD38hi HLADR + activated T cells has also been reported in distinguishing active HLH from early sepsis in children 10 (Chaturvedi et al).…”

Identification of a novel matrix metalloproteinases-related prognostic signature in hepatocellular carcinoma

“…Regarding the remaining genes within the set of signature genes, carbamoyl phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD) play a crucial role as they encode CAD. These enzymes are essential for pyrimidine synthesis, new pyrimidine nucleotides, protein glycosylation, and the biosynthesis of phospholipids in mammals [ 38 , 39 ]. CAD is responsible for initiating the di-(UDP)-dependent glycosylation process, resulting in the production of UDP.…”