| Literature DB >> 31748426 |
Lihong Wu1, Yingtong Jiang1, Zhichao Zheng1, Hongtao Li2, Meijuan Cai1, Janak L Pathak1, Zhicong Li1, Lihuan Huang1, Mingtao Zeng1,3, Huade Zheng4,5,6, Kexiong Ouyang1, Jie Gao1.
Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs), a novel class of noncoding RNAs, are involved in the carcinogenesis. However, the functional significance of piRNAs in oral squamous cell carcinoma (OSCC) remains unknown. In the present study, we used chemical carcinogen 4-nitroquinoline-1-oxide (4NQO) induced OSCC mouse model. piRNAs and mRNAs were profiled using next-generation sequencing in the tongue tumor tissues from 4NQO induction and healthy tongue tissues from control mice. Furthermore, we analyzed the differential gene expression of human OSCC in Gene Expression Omnibus (GEO) database. According to the common differentially expressed genes in the 4NQO model and human OSCC tissues, piRNAs and mRNAs network were established based on informatics method. A total of 14 known piRNAs and 435 novel predicted piRNAs were differently expressed in tumor tissue compared to healthy tissue. Among differently expressed piRNAs 260 were downregulated, and 189 were upregulated. The mRNA targets for the differentially expressed piRNAs were identified using RNAhybrid software. Primary immunodeficiency and herpes simplex infection were the most enriched pathways. A total of 22 mRNAs overlapped in human and mice OSCC. Moreover, we established the regulatory network of 11 mRNAs, including Tmc5, Galnt6, Spedf, Mybl2, Muc5b, Six31, Pigr, Lamc2, Mmp13, Mal, and Mamdc2, and 11 novel piRNAs. Our data showed the interaction between piRNAs and mRNAs in OSCC, which might provide new insights in the development of diagnostic biomarkers and therapeutic targets of OSCC.Entities:
Keywords: 4-nitroquinoline-1-oxide; P-element-induced wimpy testis-interacting RNAs; mRNAs; oral squamous cell carcinoma; regulatory network
Year: 2019 PMID: 31748426 PMCID: PMC7220707 DOI: 10.1538/expanim.19-0042
Source DB: PubMed Journal: Exp Anim ISSN: 0007-5124
Fig. 1.Schematic illustration showing the experimental set up. b: the time for oral and tongue examination. Black arrow: the beginning to 4-nitroquinoline-1-oxide (4NQO) treatment; red arrow: mice sacrificed for tissue collection; green arrow: the endpoint examination of survival rate in mice.
Fig. 2.Pathophysiological examination of oral squamous cell carcinoma (OSCC) mice model. (A) Mean body weight curve after treatment, (B) Survival analysis., (C) Gross examination of OSCC developed in tounge (left panel), and histopathological examination of tongue tissue (hematoxylin and eosin staining, right panel). Yellow arrows: OSCC (white spots) on tongue dorsum and papillary, and cauliflower-like lesions on tongue ventrum.
Fig. 3.Bioinformatic analysis of 4-nitroquinoline-1-oxide (4NQO) induced P-element-induced wimpy testis-interacting RNAs (piRNAs). (A) Heatmap of piRNA-seq. (B) Altered piRNA expression in healthy and oral squamous cell carcinoma (OSCC) mice tongue tissue. (C) gene ontology (GO) analysis. (D) Kyoto encyclopedia of genes and genomes (KEGG) analysis.
Fig. 4.Bioinformatic analysis of 4-nitroquinoline-1-oxide (4NQO) induced genes in mice. (A) Heatmap of RNA-seq. (B) gene ontology (GO) analysis. (C) Kyoto encyclopedia of genes and genomes (KEGG) analysis.
Fig. 5.Joint analysis of differentially expressed genes in mice and human oral squamous cell carcinoma (OSCC) tissues. (A) Volcanic plot of the degree of differences in the mRNA expression profile of OSCC in (a) mice model and (b) human. X-axis: log2 (fold change); Y-axis: -log10(P value); red plots: significantly upregulated genes; blue plots: significantly downregulated genes; gray plots: no significant difference in gene expression. Each dot represents one gene. (B) Venn diagram of mRNAs in mice and human OSCC tissues.
Differentially expressed genes shared between human and mouse.
| Gene symbol | Mouse | Human | ||
|---|---|---|---|---|
| log2FC1 | FDR | log2FC2 | Pvalue | |
| 6.82981 | 6.73E-07 | 1.93714 | 0.04887 | |
| 6.69051 | 6.64E-06 | 2.23298 | 0.049096 | |
| 5.36666 | 0.000446 | 1.99152 | 0.010736 | |
| 5.06897 | 0.019397 | 1.56553 | 0.004034 | |
| 4.48639 | 0.00626 | 2.79622 | 0.006182 | |
| 4.46587 | 0.002871 | 1.26227 | 0.027927 | |
| 4.17139 | 0.009688 | 2.05019 | 0.002819 | |
| 4.11138 | 0.036795 | 1.21168 | 0.003502 | |
| 4.09333 | 0.024075 | 1.75301 | 0.010392 | |
| 3.91967 | 0.022035 | 1.12481 | 0.020356 | |
| 3.84423 | 0.001197 | 1.23063 | 0.034295 | |
| 3.66396 | 0.027066 | 2.43418 | 0.001052 | |
| 3.5792 | 0.017623 | 2.48925 | 7.13E-05 | |
| 3.46095 | 0.000182 | 1.84839 | 0.002336 | |
| 1.59186 | 0.001786 | 1.08741 | 0.000762 | |
| 1.45573 | 2.06E-05 | 1.12566 | 0.010822 | |
| 1.2333 | 0.00058 | 1.67722 | 0.022154 | |
| 1.09247 | 0.011109 | 1.87739 | 0.001406 | |
| 1.04804 | 2.85E-08 | 1.5097 | 0.008976 | |
| –3.6658 | 4.02E-10 | –1.7355 | 0.002078 | |
| –1.5406 | 0.045645 | –4.0425 | 3.40E-05 | |
| –1.0031 | 2.84E-06 | –1.3796 | 0.009422 | |
Fig. 6.Correlation analysis of common differentially expressed 11 novel P-element-induced wimpy testis-interacting RNAs (piRNAs) and 11 mRNAs.
Differentially expressed P-element-induced wimpy testis-interacting RNAs (piRNAs) in mouse
| piRNA Name | piRNA-seq | qRT-PCR | ||
|---|---|---|---|---|
| log2FC | FDR | log2FC | ||
| novel_pir494 | 3.14824 | 0.02252 | 4.19470 | 0.00839 |
| novel_pir1185 | 2.67348 | 0.02909 | 2.36051 | 0.07796 |
| novel_pir354 | –3.57708 | 0.00602 | –4.31661 | 0.00013 |
| novel_pir1584 | –3.21002 | 3.99E-07 | –1.86931 | 0.08440 |
| novel_pir446 | –2.70392 | 0.01790 | –4.46402 | 0.00625 |
| novel_pir984 | –2.13506 | 8.84E-11 | –1.66983 | 0.00063 |
| novel_pir415 | –3.07616 | 0.00030 | –2.76652 | 0.01861 |
| novel_pir443 | –0.90079 | 0.05417 | – | – |
| novel_pir832 | –1.24083 | 5.57E-07 | – | – |
| novel_pir444 | –1.55797 | 8.77E-05 | – | – |
| novel_pir162 | –1.77282 | 3.41E-07 | – | – |
-,not detected.