Bioinformatics analysis about point mutation of exon 7 in LMNA in prostate tissues and cell lines

doi:10.3969/j.issn.1006-7795.2017.06.021

Abstract

Abstract: Objective Our research focuses on investigating the associations between point mutation of exon 7 in LMNA and its expression in prostate cancer.Methods A lamin A/C (LMNA) genomic missense variation C.1159C>CA (p.L387LI, located chr1:156106006), identified by DNA sequencing for all 12 exons of LMNA, in HPV-immobilized normal epithelium(RWPE-1)and high-invasive prostate cancer cell line(PC-3M-1E8)models was recognized. To verify these point mutations in prostate cancer patients, we downloaded three group data from PubMed GEO datasets, respectively from global RNA sequencing data, paraffin-embedded (FFPE) prostatectomy samples from 100 patients, from the transcriptome (polyA+) data of 20 prostate cancer tumors and 10 matched normal tissues and from sequencing data from 21 prostate cell lines. All reads were selected on the range from 156105950 to 156106055 on chr1 and these reads were aligned with CTACGCCTG or NTACGCCTGTCCCCCAGCCC. The length of reads analyzed is 50 nt for one time. Further, we analyzed the function of the sequence around the mutation point using GEO database. At last, we analyzed the effects of LMNA mutation by Western blotting in transfected mutation plasmid cells. Results We found that missense mutation has two forms of C/CA (p.L387LI) and C/CG (p.L387LV), however same-sense mutation has four forms of C/CT (p.L387L), C/CA (p.R388R), C/CT (p.R388R) and C/CG (p.R388R) in the range from 156106006 to 156106011 of exon 7 of chr1 in LMNA from samples or cell lines. However, the incidence of missense mutation accounted for respectively 40%, 11%, 2% and 6% in normal, Gleason score 5-6, 7 and 8-10 of patient samples. In 16 prostate cancer cell lines and 5 prostate benign cell lines, the incidence of missense mutation accounted for respectively 31% and 60% in cancer and benign cell lines. In addition, this sequence from 156106008 to 156106066 on chr1 was transcription factors (TFs) binding site; The common TFs in this region were PAX5, HEN1 (NHLH1), HTF, P53, MIF1, COMP1 and NGFIC (NGF4). By functional cluster analysis, the function of these TFs focuses on chromatin organization, positive regulation of RNA metabolic process, regulation of histone modification, regulation of chromosome organization and negative regulation of programmed cell death. Mutation led to a downregulation of in LMNA and phosphor-LMNA expression levels.Conclusion Missense mutation incidence of 156106006 on chr1 in both prostate cancer tissues and prostate cancer cell lines is lower than that of prostate normal tissue and prostate benign cell lines. It is possible to have relationship between the mutation and expression level or a heterogeneous expression pattern of LMNA.

Key words: prostate cancer, lamin A/C (LMNA), mutation, bioinformatics analysis

CLC Number:

R329.2

Zuo Lingkun, Yang Ronghui, Ma Hui, Zhou Ping, Kong Lu. Bioinformatics analysis about point mutation of exon 7 in LMNA in prostate tissues and cell lines[J]. Journal of Capital Medical University, 2017, 38(6): 884-890.

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URL: https://journal03.magtech.org.cn/Jweb_sdykdxxb/EN/10.3969/j.issn.1006-7795.2017.06.021

https://journal03.magtech.org.cn/Jweb_sdykdxxb/EN/Y2017/V38/I6/884

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