Genome‑wide investigation of the clinical implications and molecular mechanism of long noncoding RNA LINC00668 and protein‑coding genes in hepatocellular carcinoma

Abstract

Hepatocellular carcinoma (HCC) is one of the leading causes of tumor‑related mortalities worldwide. Long noncoding RNAs have been reported to be associated with tumor initiation, progression and prognosis. The present study aimed to explore the association between long noncoding RNA LINC00668 and its co‑expression correlated protein‑coding genes (PCGs) in HCC. Data of 370 HCC patients from The Cancer Genome Atlas database were used for analysis. LINC00668 and its top 10 PCGs were selected to determine their diagnostic and prognostic value. Molecular mechanisms were explored to identify metabolic processes that LINC00668 and its PCGs are involved in. Prognosis‑related clinical factors and PCGs were used to construct a nomogram for predicting prognosis in HCC. A Connectivity Map was constructed to identify candidate target drugs for HCC. The top 10 PCGs identified were: Pyrimidineregic receptor P2Y4 (P2RY4), signal peptidase complex subunit 2 (SPCS2), family with sequence similarity 86 member C1 (FAM86C1), tudor domain containing 5 (TDRD5), ferritin light chain (FTL), stratifin (SFN), nucleolar complex associated 2 homolog (NOC2L), peroxiredoxin 1 (PRDX1), cancer/testis antigen 2 CTAG2 and leucine zipper and CTNNBIP1 domain containing (LZIC). FAM86C1, CTAG2 and SFN had significant diagnostic value for HCC (total area under the curve ≥0.7, P≤0.05); LINC00668, FAM86C1, TDRD5, FTL and SFN were of significant prognostic value for HCC (all P≤0.05). Investigation into the molecular mechanism indicated that LINC00668 affects cell division, cell cycle, mitotic nuclear division, and drug metabolism cytochrome P450 (all P≤0.05). The Connectivity Map identified seven candidate target drugs for the treatment of HCC, which were: Indolylheptylamine, mimosine, disopyramide, lidocaine, NU‑1025, bumetanide, and DQNLAOWBTJPFKL‑PKZXCIMASA‑N (all P≤0.05). Our findings indicated that LINC00668 may function as an oncogene and its overexpression indicates poor prognosis of HCC. FAM86C1, CTAG2 and SFN are of diagnostic significance, while FAM86C1, TDRD5, FTL and SFN are of prognostic significance for HCC.

Figure 1

Expressions of LINC00668 and its co-expression correlated protein-coding genes. (A-J) Expressions of, LINC00668, P2RY4, SPC25 (SPCS2), TDRD5, FTL, SFN, NOC2L, PRDX1, CATG2 and LZIC. CTAG2, cancer/testis antigen 2; FTL, ferritin light chain; LZIC, leucine zipper and CTNNBIP1 domain containing; NOC2L, nucleolar complex associated 2 homolog; P2RY4, pyrimidineregic receptor P2Y4; PRDX1, peroxiredoxin 1; SFN, stratifin; SPCS2, signal peptidase complex subunit 2; TDRD5, tudor domain containing 5.

Figure 2

Scatter plots of LINC00668 and its co-expression correlated protein-coding genes in tumor and non-tumor tissues. (A-K) Scatter plots of, LINC00668, P2RY4, SPCS2, FAM86C1, TDRD5, FTL, SFN, NOC2L, PRDX1, CATG2 and LZIC. CTAG2, cancer/testis antigen 2; FTL, ferritin light chain; LZIC, leucine zipper and CTNNBIP1 domain containing; NOC2L, nucleolar complex associated 2 homolog; P2RY4, pyrimidineregic receptor P2Y4; PRDX1, peroxiredoxin 1; SFN, stratifin; SPCS2, signal peptidase complex subunit 2; FAM86C1, family with sequence similarity 86 member C1; TDRD5, tudor domain containing 5.

Figure 3

Diagnostic receiver operator curves of LINC00668 and its co-expression correlated protein-coding genes. (A-K) Diagnostic ROC curves of, in order, LINC00668, P2RY4, SPCS2, FAM86C1, TDRD5, FTL, SFN, NOC2L, PRDX1, CATG2 and LZIC. CTAG2, cancer/testis antigen 2; FTL, ferritin light chain; LZIC, leucine zipper and CTNNBIP1 domain containing; NOC2L, nucleolar complex associated 2 homolog; P2RY4, pyrimidineregic receptor P2Y4; PRDX1, peroxiredoxin 1; SFN, stratifin; SPCS2, signal peptidase complex subunit 2; FAM86C1, family with sequence similarity 86 member C1; TDRD5, tudor domain containing 5; 95% CI, 95% confidence interval; AUC, area under the curve; ROCs, receiver operator characteristic.

Figure 4

Joint-effect analysis of diagnostic receiver operator curves of LINC00668 and diagnosis related genes. (A-F) Diagnostic receiver operator curves of, in order, LINC00668 and FAM86C1; LINC00668 and SFN; LINC00668 and CTAG2; FAM86C1 and SFN; FAM86C1 and CTAG2; SFN and CTAG2. CTAG2, cancer/testis antigen 2; FAM86C1, family with sequence similarity 86 member C1; SFN, stratifin; 95% CI, 95% confidence interval; AUC, area under the curve.

Figure 5

Kaplan-Meier plots of LINC00668 and its co-expression correlated protein-coding genes. (A-K) Kaplan-Meier plots of, LINC00668, P2RY4, SPCS2, FAM86C1, TDRD5, FTL, SFN, NOC2L, PRDX1, CATG2 and LZIC. CTAG2, cancer/testis antigen 2; FTL, ferritin light chain; LZIC, leucine zipper and CTNNBIP1 domain containing; NOC2L, nucleolar complex associated 2 homolog; P2RY4, pyrimidineregic receptor P2Y4; PRDX1, peroxiredoxin 1; SFN, stratifin; SPCS2, signal peptidase complex subunit 2; FAM86C1, family with sequence similarity 86 member C1; TDRD5, tudor domain containing 5.

Figure 6

Joint-effect analysis of Kaplan-Meier plots of LINC00668 and diagnosis-related genes. (A-J) Kaplan-Meier plots of LINC00668 and FAM86C1; LINC00668 and TDRD5; LINC00668 and FTL; LINC00668 and SFN; FAM86C1 and TDRD5; FAM86C1 and FTL; FAM86C1 and SFN; TDRD5 and FTL; TDRD5 and SFN; and FTL and SFN. FTL, ferritin light chain; FAM86C1, family with sequence similarity 86 member C1; SFN, stratifin; TDRD5, tudor domain containing 5.

Figure 7

Gene Set Enrichment Analysis of LINC00668 using GO and KEGG pathways. (A-I) Gene ontology results of LINC00668; (J-L) KEGG pathway results of LINC00668. GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; FDR, false discovery rate; NES, normalized enrichment score.

Figure 8

Gene Set Enrichment Analysis of FAM86C1 using GO and KEGG pathways. (A-I) Gene ontology results of FAM86C1; (J-L) KEGG pathway results of FAM86C1. FAM86C1, family with sequence similarity 86 member C1; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; FDR, false discovery rate; NES, normalized enrichment score.

Figure 9

Gene Set Enrichment Analysis of FTL using GO and KEGG pathways. (A-I) Gene ontology results of FTL; (J-L) KEGG pathway results of FTL. FTL, ferritin light chain; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; FDR, false discovery rate; NES, normalized enrichment score.

Figure 10

Nomogram, co-expression matrix and gene-gene interaction network of LINC00668 and protein-coding genes. (A) Nomogram constructed using LINC00668, FAM86C1, TDRD5, FTL, SFN, tumor stage, radical resection and HBV infection status; (B) Co-expression matrix of LINC00668 and its protein-coding genes; blue and red indicate positive and negative correlation, respectively. ^*, ^**, and ^*** denote P≤0.05, 0.01, and 0.001, respectively. (C) Co-expression network of gene-gene interactions of LINC00668 and its protein-coding genes. HBV, hepatitis B virus; FTL, ferritin light chain; FAM86C1, family with sequence similarity 86 member C1; SFN, stratifin; TDRD5, tudor domain containing 5.

Figure 10

Nomogram, co-expression matrix and gene-gene interaction network of LINC00668 and protein-coding genes. (A) Nomogram constructed using LINC00668, FAM86C1, TDRD5, FTL, SFN, tumor stage, radical resection and HBV infection status; (B) Co-expression matrix of LINC00668 and its protein-coding genes; blue and red indicate positive and negative correlation, respectively. ^*, ^**, and ^*** denote P≤0.05, 0.01, and 0.001, respectively. (C) Co-expression network of gene-gene interactions of LINC00668 and its protein-coding genes. HBV, hepatitis B virus; FTL, ferritin light chain; FAM86C1, family with sequence similarity 86 member C1; SFN, stratifin; TDRD5, tudor domain containing 5.