Selecting lncRNAs in gastric cancer cells for directed therapy with bioactive peptides and chemotherapy drugs

Abstract

Selecting lncRNAs for directed therapy with bioactive peptides and chemotherapy drugs may be an effective approach to treating gastric cancer (GC). We show genome-scale identification and characterization of differentially expressed lncRNAs in GC cells treated with a novel anti-cancer bioactive peptide (ACBP) and the chemotherapy drug oxaliplatin (ASLB). A total of 17,897 lncRNAs were identified through pairwise comparison, including 2,074 novel lncRNAs. Of those, 1,386 lncRNAs were differentially expressed (over 1.5-fold change vs. control, q-value < 0.05) in response to ACBP and ASLB treatment. These included 914 upregulated and 472 downregulated lincRNAs. Functional annotation of these lncRNAs through Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed they activate metabolic pathways and protein-binding processes. Moreover, suppression of the DNA replication process and upregulation of AMP-activated protein kinase (AMPK) signaling in MKN45 cells exposed to ACBP alone or in combination with ASLB was predicted by hierarchical clustering analysis. By providing new insight into the transcriptomic effects of ACBP and ASLB in GC cells, these results provide the first evidence of ACBP inhibition of lincRNAs and may provide new mechanisms of action for ACBP and ASLB.

Keywords: anti-cancer bioactive peptide; gastric cancer; lncRNAs; profile.

Figure 1. Schematic diagram of the methodology utilized for discovery and characterization of LncRNAs and mRNAs in this study

Figure 2. Schematic of the process of lncRNA screening

Figure 3. The Venn diagrams of identified lncRNA

(A) The total number of lncRNAs identified compared with the Gencode v22 data set. (B) The number of lncRNAs identified by each tool.

Figure 4. Correlation of expression patterns in each sample

The box plots (A) and density distribution (B) show the expression feature of transcripts in each sample. (C) Calculated Pearson correlation coefficients distribution between each two samples.

Figure 5

A hierarchical heat map of differentially expressed lncRNAs with transformed expression fold values by GO (A) and KEGG (B) analyses.

Figure 6. The qPCR confirmation results show consistency with the RNA-seq data

Note: * indicates P < 0.05; ** indicates significant difference (P < 0.01); # indicates P > 0.05.

Figure 7. Genomic features of predicted lncRNAs and mRNAs

(A) Exon number distribution. (B) Length distribution. (C) Orf length distribution.

Figure 8. Conservation of predicted protein-coding transcripts and lncRNAs

Figure 9

Differentially expressed lncRNA transcripts identified in ACBP (B), ASLB (C) alone, and combined ACBP and ASLB (A) treated MKN45 GC cells (over 1.5-fold changes, q-value <0.05).

Figure 10

GO (A) and KEGG (B) analyses of lncRNA functions in ACBP-treated MKN45 cells.

Figure 11

GO (A) and KEGG (B) analyses of lncRNA functions in ASLB-treated MKN45 cells.

Figure 12

GO (A) and KEGG (B) analyses of lncRNA functions in combined ACBP and ASLB treated MKN45 cells.