| Literature DB >> 34079751 |
Ji Li1, Wang Jing2, Wenxiao Jia2, Xiaoyang Zhai2, Hui Zhu2, Jinming Yu1.
Abstract
Purpose: The purpose of this study was to identify aberrant long non-coding RNAs (lncRNAs) and explore the predictive value of lncRNA expression patterns on the risk of brain metastases (BMs) in patients with limited-stage small-cell lung cancer (SCLC). Patients andEntities:
Keywords: NET; brain metastasis; lncRNA; risk factors; small cell lung cancer
Year: 2021 PMID: 34079751 PMCID: PMC8166247 DOI: 10.3389/fonc.2021.603271
Source DB: PubMed Journal: Front Oncol ISSN: 2234-943X Impact factor: 6.244
Figure 1A comprehensive overview of aberrantly expressed lncRNAs and mRNAs in the comparison between BM-SCLC and non-BM-SCLC samples. (A) A total of 67 lncRNAs (27 upregulated and 40 downregulated) and 47 mRNAs (20 upregulated and 27 downregulated) were differentially expressed between BM-SCLC (n = 6) and SCLC patients without BM (n = 6). The scatter plot was used to assess lncRNA (B) and mRNA (C) expression patterns between BM-SCLC patients and controls. X-axis: log2 expression value. Y-axis: log2 expression value. Red: upregulated. Green: downregulated. (D) LncRNA expression levels, as determined by microarray and real-time PCR analyses. (E) The comparison between LncRNA XR_429159.1 levels between 11 pairs of patients with and without BM. *p < 0.05.
Sixty-seven lncRNAs expressed in BM-SCLC.
| ENST00000443576.2 | p4009 | 0.024 | TCONS_00022863 | p19374 | 0.029 |
| ENST00000433357.2 | p16736 | 0.002 | XR_109582.2 | p25097 | 0.017 |
| TCONS_00022087 | p19097 | 0.038 | ENST00000530576.1 | p2682 | 0.037 |
| ENST00000502776.1 | p13887 | 0.030 | TCONS_00008533 | p22324 | 0.017 |
| NR_026881.1 | p25115 | 0.035 | XR_429159.1 | p42511_v4 | 0.013 |
| ENST00000442829.1 | p9753 | 0.012 | ENST00000509873.1 | p12911 | 0.031 |
| ENST00000547326.1 | p3297 | 0.019 | TCONS_00014251 | p23618 | 0.020 |
| TCONS_00015196 | p24068 | 0.004 | RNA33685|snoRNA_scaRNA_281_75 | RNA33685|snoRNA_scaRNA_281_75 | 0.016 |
| TCONS_00012509 | p23458 | 0.016 | ENST00000547777.1 | p3643 | 0.013 |
| ENST00000569037.1 | p6036 | 0.045 | ENST00000599524.1 | p8239 | 0.012 |
| XR_428476.1 | p41744_v4 | 0.001 | ENST00000552511.1 | p34336_v4 | 0.021 |
| TCONS_00010550 | p22837 | 0.007 | XR_426705.1 | p39308_v4 | 0.045 |
| TCONS_00019442 | p18518 | 0.011 | ENST00000536112.1 | p34230_v4 | 0.044 |
| ENST00000441205.1 | p9450 | 0.003 | ENST00000596996.1 | p8237 | 0.043 |
| TCONS_00026648 | p20573 | 0.035 | ENST00000596705.1 | p34609_v4 | 0.004 |
| ENST00000432973.1 | p6336 | 0.020 | ENST00000560026.1 | p5053 | 0.003 |
| ENST00000452503.1 | p186 | 0.018 | TCONS_00022023 | p19047 | 0.007 |
| XR_244656.1 | p40400_v4 | 0.000 | ENST00000509641.2 | p12309 | 0.046 |
| XR_244697.1 | p40446_v4 | 0.011 | ENST00000415793.1 | p8562 | 0.027 |
| TCONS_00024667 | p19899 | 0.027 | XR_426704.1 | p39309_v4 | 0.019 |
| uc001ugl.3 | p25845 | 0.039 | ENST00000607996.1 | p38259_v4 | 0.029 |
| LIT3591 | p28883 | 0.003 | ENST00000434996.1 | p11660 | 0.004 |
| NR_109815.1 | p43698_v4 | 0.003 | XR_429229.1 | p42634_v4 | 0.042 |
| TCONS_00013445 | p23782 | 0.005 | ENST00000599993.1 | p8236 | 0.018 |
| uc010nlv.1 | p26558 | 0.006 | ENST00000416061.1 | p17015 | 0.006 |
| TCONS_00020666 | p18986 | 0.041 | ENST00000435749.1 | p15383 | 0.048 |
| ENST00000454882.2 | p14463 | 0.008 | ENST00000509350.1 | p16341 | 0.042 |
| ENST00000598981.1 | p29006 | 0.018 | |||
| ENST00000448195.1 | p15382 | 0.018 | |||
| ENST00000610044.1 | p37042_v4 | 0.048 | |||
| TCONS_00021347 | p18641 | 0.041 | |||
| XR_246000.1 | p42510_v4 | 0.008 | |||
| TCONS_00014250 | p23617 | 0.008 | |||
| TCONS_00022866 | p19378 | 0.026 | |||
| ENST00000593653.1 | p34611_v4 | 0.010 | |||
| ENST00000607857.1 | p38428_v4 | 0.042 | |||
| ENST00000420598.1 | p383 | 0.045 | |||
| NR_046095.1 | p33675 | 0.032 | |||
| ENST00000459433.1 | p38665_v4 | 0.033 | |||
| ENST00000504520.1 | p12349 | 0.009 |
The primers of four lncRNAs.
| lnc196-F2 | GGACACAGCAGATAGCAGACC |
| lnc196-R2 | CCACAAGGAAGCCATTGAGACA |
| lnc159-F1 | GCTTGGAGGCTGACAACAAC |
| lnc159-R1 | ACCTGAAGTGAAAAGGAAGAGAAGA |
| lnc793-F1 | AGGAGTGGGCTTTGCTGGAT |
| lnc793-R1 | CTCTAAGTGAAGGAATGTTGTCGTC |
| lnc112-F2 | GGCTTTTAGACCAGGAGACTGTG |
| lnc112-R2 | TCCAGCGAGTGATAGTGGGT |
Figure 2The comparison between LncRNA XR_429159.1 levels between 20 pairs of patients with and without BM.
The characteristics of 43 patients for clinical validation.
| <60 | 11 | 5 (27.8) | 6 (24.0) | 0.779 |
| ≥60 | 32 | 13 (72.2) | 19 (76.0) | |
| Male | 34 | 14 (77.8) | 20 (80.0) | 0.86 |
| Female | 9 | 4 (22.2) | 5 (20.0) | |
| Yes | 29 | 13 (72.2) | 12 (48.0) | 0.57 |
| No | 14 | 5 (27.8) | 13 (52.0) | |
| I | 12 | 6 (33.3) | 6 (24.0) | 0.763 |
| II | 25 | 10 (55.6) | 15 (60.0) | |
| III | 6 | 2 (11.1) | 4 (16.0) | |
| S+C/R | 17 | 5 (27.8) | 12 (48.0) | 0.181 |
| C+R | 26 | 13 (72.2) | 13 (52.0) | |
Figure 3The development time for BM ranged from 7.0 to 26.3 months from the date of diagnosis. The actuarial risk of developing BM at 1 year was 14.3% in patients with high-level lncRNA XR_429159.1 vs. 31.0% in the low-level group. p = 0.035.
Figure 4Significantly enriched KEGG pathways. KEGG analysis showed that lncRNA might be related to ABC transporters, cell adhesion molecules, glucose metabolism, and signal transduction pathways.
Predictive signaling pathway.
| ENSG00000234773.2 | A_33_P3210085 | NET1 | 0.901010299 | 6.33E−05 |
| ENSG00000232274.1 | A_23_P21785 | NSUN3 | 0.921705135 | 2.03E−05 |
| XR_246000.1 | A_33_P3369716 | lnc-APBA2-1 | 0.904952848 | 5.20E−05 |
| XR_429159.1 | A_21_P0011399 | NET1 | 0.926553947 | 1.49E−05 |
| ENSG00000251301.2 | A_33_P3369716 | LOC100507195 | 0.939780957 | 5.63E−06 |
| XR_246000.1 | A_33_P3369716 | LOC100507195 | 0.991972956 | 2.59E−10 |
| ENSG00000232274.1 | A_33_P3361067 | ABCG2 | 0.951285719 | 1.99E−06 |
| XR_426705.1 | A_21_P0010623 | LINC01359 | 0.989767777 | 8.68E−10 |
| XR_426704.1 | A_21_P0010623 | LINC01359 | 0.97878916 | 3.26E−08 |
| XR_244697.1 | A_19_P00320972 | STMN1 | −0.94305485 | 4.28E−06 |
| XR_426705.1 | A_21_P0010621 | LINC01359 | 0.980554456 | 2.12E−08 |
| XR_426704.1 | A_21_P0010621 | LINC01359 | 0.966813467 | 3.00E−07 |
| ENSG00000257497.1 | A_23_P111662 | ABCB5 | −0.901917901 | 6.05E−05 |
| XLOC_007255 | A_33_P3339625 | IL17C | 0.939131971 | 5.94E−06 |
| ENSG00000233064.2 | A_32_P19539 | TMEM56 | −0.903291397 | 5.65E−05 |