Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer

Chen, Erbao1; Yi, Jing2; Jiang, Jing3; Zou, Zhilin4; Mo, Yuqian5; Ren, Qingqi2; Lin, Zewei2; Lu, Yi1; Zhang, Jian1,6; Liu, Jikui2

2022-10-04

10.1186/s12885-022-10122-4

BMC CANCER   Impact Factor & Quartile

1471-2407

Background Fatty acid (FA) metabolism is considered the emerging cause of tumor development and metastasis, driving poor prognosis. Long non-coding RNAs (lncRNAs) are closely related to cancer progression and play important roles in FA metabolism. Thus, the discovery of FA metabolism-related lncRNA signatures to predict outcome and immunotherapy response is critical in improving the survival of patients with hepatocellular carcinoma (HCC). Methods FA metabolism scores and a FA metabolism-related lncRNA signature were constructed using a single-sample gene set enrichment analysis based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. "ConsensusClusterPlus" was used to screen molecular subtypes. Chi-squared test and Fisher's exact test were applied to explore the relationship between clinical, genomic mutation characteristics and subtypes. Transcription factor (TF) activity scores, cellular distributions, immune cell infiltration, and immunotherapy response were employed to investigate the functions of FA metabolism-related lncRNA signatures. FA metabolism microarray and western blot were performed to detect the biological function of candidate lncRNAs. Results A total of 70 lncRNAs that highly correlated with FA metabolism scores in two cohorts were used to construct two distinct clusters. Patients in cluster 2 had lower FA metabolism scores and worse survival than those in cluster 1. Patients in cluster 2 exhibited a high frequency of DNA damage, gene mutations, oncogenic signaling such as epithelial-to-mesenchymal transition, and a high degree of immune cell infiltration. Moreover, the lncRNA signature could predict the effects of immunotherapy in patients with HCC. Furthermore, three lncRNAs (SNHG1, LINC00261, and SNHG7) were identified that were highly correlated with FA metabolism. Additionally, SNHG1 and SNHG7 were found to regulate various FA metabolism-related genes and ferroptosis-related genes in vitro experiments. GSEA analysis revealed that SNHG1 and SNHG7 promote fatty acid beta-oxidation. SNHG1 and SNHG7 silencing dramatically reduced lipid droplets in HCC cells. Many immune-infiltration genes and TFs were overexpressed in HCC tissues with SNHG1 and SNHG7 high expression. Conclusions A novel molecular model of FA metabolism-related lncRNAs was developed, which has significantly prognostic potential in HCC diagnosis and aids in clinical decision making.

Fatty acid metabolism LncRNA Immune infiltrations Hepatocellular carcinoma Ferroptosis

SCI

English

First ; Corresponding

China Postdoctoral Science Foundation["2020M682779","2021T140295"] ; NSFC["81972766","82173336","81972420"] ; Science, Technology and Innovation Commission of.Shenzhen Municipality["JCYJ20190809161811237","JCYJ2021032410424040","JCYJ20190809095801653","JCYJ20190809100217290","JCYJ20170412154619484"]

Oncology

Oncology

WOS:000863843700004

BMC

CLINICAL MEDICINE

Web of Science

1.Southern Univ Sci & Technol, Sch Med, Shenzhen 518055, Guangdong, Peoples R China
2.Peking Univ, Hepatopancreato Biliary Surg, Shenzhen Hosp, Shenzhen 518036, Guangdong, Peoples R China
3.Peking Univ, Dept Pathol, Shenzhen Hosp, Shenzhen 518036, Guangdong, Peoples R China
4.Wenzhou Med Univ, Dept Ophthalmol, Affiliated Eye Hosp, Wenzhou 325027, Zhejiang, Peoples R China
5.Guangdong Med Univ, Sch Publ Hlth, Zhanjiang 524023, Guangdong, Peoples R China
6.Guangdong Prov Key Lab Cell Microenvironm & Dis R, Shenzhen 518055, Guangdong, Peoples R China

Chen, Erbao,Yi, Jing,Jiang, Jing,et al. Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer[J]. BMC CANCER,2022,22(1).

Chen, Erbao.,Yi, Jing.,Jiang, Jing.,Zou, Zhilin.,Mo, Yuqian.,...&Liu, Jikui.(2022).Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer.BMC CANCER,22(1).

Chen, Erbao,et al."Identification and validation of a fatty acid metabolism-related lncRNA signature as a predictor for prognosis and immunotherapy in patients with liver cancer".BMC CANCER 22.1(2022).