Plasma long noncoding RNA expression profiles in patients with Parkinson's disease and the role of lnc-CTSD-5:1 in a PD cell model: a ceRNA microarray-based study

doi:10.12122/j.issn.1673-4254.2024.11.11

Abstract

Abstract:

Objective To explore the key genes and long non-coding RNAs (lncRNAs) associated with Parkinson's disease (PD). Methods Peripheral blood plasma samples were collected from 6 PD patients and 6 healthy individuals. The mRNA and lncRNA expression profiles were detected using ceRNA microarray technology, and the differentially expressed genes were analyzed using bioinformatics methods. The differentially expressed mRNAs transcribed within 10 kb upstream or downstream of the differentially expressed lncRNAs were defined as potential cis-regulatable (Cis) target genes of the lncRNAs. A PD-specific protein-protein interaction network (PPI) was constructed. Competitive endogenous RNA (ceRNA) networks were also constructed using the differential lncRNAs with mRNAs and known microRNAs. Using MPP⁺-treated SH-SY5Y cells as a PD cell model, the expressions of the key lncRNAs and their functions were examined. Results We identified 316 genes and 986 lncRNAs showing significant differential expressions in PD patients (P<0.05). The differentially expressed mRNAs and the potential cis-regulatable target genes of these lncRNAs were functionally annotated using GO and KEGG enrichment analysis, and the targeting relationship of the differentially expressed mRNAs and lncRNAs with microRNAs were predicted. Analysis of the ceRNA networks constructed based on the differentially expressed lncRNAs suggested that lnc-MTG2-1:1, lnc-CTSD-5:1, lnc-PCCA-3:1, lnc-VTCN1-3:1, lnc-ZNF25-7:1, and lnc-DAZ3-1:1 might be the key lncRNAs in PD. In MPP⁺-treated SH-SY5Y cells, the expression of lnc-CTSD-5:1 showed the most significant changes, and silencing lnc-CTSD-5:1 obviously restored the expression level of tyrosine hydroxylase. Conclusion PD patients have significant changes in plasma lncRNA expression profile, and the differentially expressed genes and lncRNAs found in this study may provide new clues for exploring the pathogenesis and identifying potential biomarkers of PD.

Key words: Parkinson's disease, plasma, long non-coding RNA, bioinformatics analysis, tyrosine hydroxylase

Zijing REN, Peiyang ZHOU, Jing TIAN. Plasma long noncoding RNA expression profiles in patients with Parkinson's disease and the role of lnc-CTSD-5:1 in a PD cell model: a ceRNA microarray-based study[J]. Journal of Southern Medical University, 2024, 44(11): 2146-2155.

Figures/Tables 6

Fig.1 Differentially expressed genes (DEGs) and lncRNA (DElncRNAs) between PD and healthy individuals. A, B: Volcanic maps showing differences in plasma lncRNA and mRNA levels between PD patients and healthy control individuals. The significantly up-regulated DEmRNAs and DElncRNAs are shown in green, the significantly down-regulated DemRNAs are shown in blue, and those without significant differences are shown in orange. C, D: Cluster heat map showing all DEmRNAs and DElncRNAs in each sample.

Fig.2 PPI network (A) and GO (B) and KEGG (C) enrichment analysis of the DEGs in PD patients and healthy control individuals.

Fig. 3 PPI network (A) and GO (B) and KEGG (C) enrichment analysis of DElncRNAs candidate cis-regulatory target genes in PD patients and healthy control subjects.

Fig.4 ceRNA network of the upregulated DElncRNAs.

Fig.5 ceRNA network of the down-regulated DElncRNAs.

Fig.6 Validation of DElncRNAs in ceRNA networks in a PD cell model. A: Viability of SH-SY5Y cells determined by CCK-8 method after treatment with MPP+ at different concentrations for 24, 48 and 72 h. B: qRT-PCR for detecting expression levels of lnc-CTSD-5:1, lnc-VTCN1-3:1, lnc-PCCA-3:1, lnc-MTG2-1:1 and lnc-ZNF25-7:1 in SH-SY5Y cells treated with 500 μmol/L MPP+ treatment for 48 h. C: Western blotting for analyzing the expression of TH protein in SH-SY5Y cells treated with 500 μmol/L MPP+ for 48 h. D: lnc-CTSD-5:1 expression in SH-SY5Y cells after transfection with lnc-CTSD-5:1 siRNA detected by qRT-PCR. E: Western blotting for analyzing the expression of TH protein in SH-SY5Y cells with lnc-CTSD-5:1 knockdown treated with 500 μmol/L MPP+ for 48 h. *P<0.05, **P<0.01, ***P<0.001 vs 0 μmol/L, control group, or siNC group.

References 38

1	陈芝君, 马建, 唐娜, 等. 中国帕金森病疾病负担变化趋势分析及预测[J]. 中国慢性病预防与控制, 2022, 30(9): 649-54.
2	刘永文, 焦敏, 王岩, 等. 1990-2019年中国帕金森病疾病负担分析[J]. 疾病监测, 2024, 39(3): 363-8.
3	Morris HR, Spillantini MG, Sue CM, et al. The pathogenesis of Parkinson's disease[J]. Lancet, 2024, 403(10423): 293-304.
4	Li K, Wang ZQ. lncRNA NEAT1: key player in neurodegenerative diseases[J]. Ageing Res Rev, 2023, 86: 101878.
5	Su LN, Li RQ, Zhang ZQ, et al. Identification of altered exosomal microRNAs and mRNAs in Alzheimer's disease[J]. Ageing Res Rev, 2022, 73: 101497.
6	Wang C, Duan YJ, Duan G, et al. Stress induces dynamic, cytotoxicity-antagonizing TDP-43 nuclear bodies via paraspeckle LncRNA NEAT1-mediated liquid-liquid phase separation[J]. Mol Cell, 2020, 79(3): 443-58. e7.
7	Yan PX, Luo S, Lu JY, et al. Cis- and trans-acting lncRNAs in pluripotency and reprogramming[J]. Curr Opin Genet Dev, 2017, 46: 170-8.
8	Li LL, Li ZW, Meng XQ, et al. Histone lactylation-derived LINC01127 promotes the self-renewal of glioblastoma stem cells via the cis-regulating the MAP4K4 to activate JNK pathway[J]. Cancer Lett, 2023, 579: 216467.
9	Ben-Tov Perry R, Tsoory M, Tolmasov M, et al. Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation[J]. Cell Rep, 2023, 42(10): 113168.
10	Bazrgar M, Mirmotalebisohi SA, Ahmadi M, et al. Comprehensive analysis of lncRNA-associated ceRNA network reveals novel potential prognostic regulatory axes in glioblastoma multiforme[J]. J Cell Mol Med, 2024, 28(11): e18392.
11	Zhao J, Feng ZY, Deng H, et al. Bioinformatics-based analysis reveals IDR-1018-mediated ceRNA regulation network for protective effect on hypoxia-ischemic brain injury in neonatal mice[J]. Exp Neurol, 2022, 357: 114159.
12	Simchovitz A, Hanan M, Niederhoffer N, et al. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress[J]. FASEB J, 2019, 33(10): 11223-34.
13	Boros FA, Maszlag-Török R, Vécsei L, et al. Increased level of NEAT1 long non-coding RNA is detectable in peripheral blood cells of patients with Parkinson's disease[J]. Brain Res, 2020, 1730: 146672.
14	Sun Q, Zhang YL, Wang SL, et al. NEAT1 decreasing suppresses Parkinson's disease progression via acting as miR-1301-3p sponge[J]. J Mol Neurosci, 2021, 71(2): 369-78.
15	Yuan XJ, Wu YN, Lu L, et al. Long noncoding RNA SNHG14 knockdown exerts a neuroprotective role in MPP⁺-induced Parkinson's disease cell model through mediating miR-135b-5p/KPNA4 axis[J]. Metab Brain Dis, 2022, 37(7): 2363-73.
16	Liu S, Cui B, Dai ZX, et al. Long non-coding RNA HOTAIR promotes Parkinson's disease induced by MPTP through up-regulating the expression of LRRK2[J]. Curr Neurovasc Res, 2016, 13(2): 115-20.
17	Bu LL, Xie YY, Lin DY, et al. LncRNA-T199678 mitigates α-synuclein-induced dopaminergic neuron injury via miR-101-3p[J]. Front Aging Neurosci, 2020, 12: 599246.
18	Zhou Q, Zhang MM, Liu M, et al. LncRNA XIST sponges miR-199a-3p to modulate the Sp1/LRRK2 signal pathway to accelerate Parkinson's disease progression[J]. Aging, 2021, 13(3): 4115-37.
19	Zhang QS, Wang ZH, Zhang JL, et al. Beta-asarone protects against MPTP-induced Parkinson's disease via regulating long non-coding RNA MALAT1 and inhibiting α‑synuclein protein expression[J]. Biomed Pharmacother, 2016, 83: 153-9.
20	Xia DJ, Sui RB, Zhang Z. Administration of resveratrol improved Parkinson's disease-like phenotype by suppressing apoptosis of neurons via modulating the MALAT1/miR-129/SNCA signaling pathway[J]. J Cell Biochem, 2019, 120(4): 4942-51.
21	Snead DM, Matyszewski M, Dickey AM, et al. Structural basis for Parkinson's disease-linked LRRK2's binding to microtubules[J]. Nat Struct Mol Biol, 2022, 29(12): 1196-207.
22	Sosero YL, Gan-Or Z. LRRK2 and Parkinson's disease: from genetics to targeted therapy[J]. Ann Clin Transl Neurol, 2023, 10(6): 850-64.
23	Jennings D, Huntwork-Rodriguez S, Vissers MFJM, et al. LRRK2 inhibition by BIIB122 in healthy participants and patients with Parkinson's disease[J]. Mov Disord, 2023, 38(3): 386-98.
24	赵丽丽, 张硕, 张洋, 等. 汉族人群LRRK2基因突变携带者与非携带者患家族性帕金森病的风险预测[J]. 中国老年学杂志, 2024, 44(5): 1099-101.
25	Watanabe R, Buschauer R, Böhning J, et al. The in situ structure of Parkinson's disease-linked LRRK2[J]. Cell, 2020, 182(6): 1508-18.e16.
26	Zhang Q, Xu Y, Lee J, et al. A myosin-7B-dependent endocytosis pathway mediates cellular entry of α‑synuclein fibrils and polycation-bearing cargos[J]. Proc Natl Acad Sci USA, 2020, 117(20): 10865-75.
27	Zhou HY, Simion V, Pierce JB, et al. LncRNA-MAP3K4 regulates vascular inflammation through the p38 MAPK signaling pathway and cis-modulation of MAP3K4[J]. FASEB J, 2021, 35(1): e21133.
28	Winkler L, Jimenez M, Zimmer JT, et al. Functional elements of the cis-regulatory lincRNA-p21[J]. Cell Rep, 2022, 39(3): 110687.
29	Li J, Yang TT, Tang HF, et al. Inhibition of lncRNA MAAT controls multiple types of muscle atrophy by cis- and trans-regulatory actions[J]. Mol Ther, 2021, 29(3): 1102-19.
30	Marchetti B, Tirolo C, L’Episcopo F, et al. Parkinson's disease, aging and adult neurogenesis: Wnt/β-catenin signalling as the key to unlock the mystery of endogenous brain repair[J]. Aging Cell, 2020, 19(3): e13101.
31	Gamit N, Dharmarajan A, Sethi G, et al. Want of Wnt in Parkinson's disease: could sFRP disrupt interplay between Nurr1 and Wnt signaling?[J]. Biochem Pharmacol, 2023, 212: 115566.
32	Liu L, Zhou TT, Li T, et al. LncRNA DLX6-AS1 promotes microglial inflammatory response in Parkinson's disease by regulating the miR-223-3p/NRP1 axis[J]. Behav Brain Res, 2022, 431: 113923.
33	Xu W, Zhang L, Geng Y, et al. Long noncoding RNA GAS5 promotes microglial inflammatory response in Parkinson's disease by regulating NLRP3 pathway through sponging miR-223-3p[J]. Int Immunopharmacol, 2020, 85: 106614.
34	Ma JJ, Sun WH, Chen SY, et al. The long noncoding RNA GAS5 potentiates neuronal injury in Parkinson's disease by binding to microRNA-150 to regulate Fosl1 expression[J]. Exp Neurol, 2022, 347: 113904.
35	Yousefi M, Peymani M, Ghaedi K, et al. Significant modulations of linc001128 and linc0938 with miR-24-3p and miR-30c-5p in Parkinson disease[J]. Sci Rep, 2022, 12(1): 2569.
36	Honarmand Tamizkar K, Gorji P, Gholipour M, et al. Parkinson's disease is associated with dysregulation of circulatory levels of lncRNAs[J]. Front Immunol, 2021, 12: 763323.
37	Ozdilek B, Kaya Alper I, Demircan B, et al. Clinical significance of serum lncRNA H19, GAS5, HAR1B and linc01783 levels in Parkinson's disease[J]. Ideggyogy Sz, 2023, 76(5/6): 189-96.
38	Tolosa E, Garrido A, Scholz SW, et al. Challenges in the diagnosis of Parkinson's disease[J]. Lancet Neurol, 2021, 20(5): 385-97.

[1]	Hongli YANG, Yayun XIANG, Tingting TAN, Yang LEI. ORY-1001 inhibits glioblastoma cell growth by downregulating the Notch/HES1 pathway via suppressing lysine-specific demethylase 1 expression [J]. Journal of Southern Medical University, 2024, 44(8): 1620-1630.
[2]	LIANG Yihao, LAI Yingjun, YUAN Yanwen, YUAN Wei, ZHANG Xibo, ZHANG Bashan, LU Zhifeng. Screening of differentially expressed genes in gastric cancer based on GEO database and function and pathway enrichment analysis [J]. Journal of Southern Medical University, 2024, 44(3): 605-616.
[3]	FENG Wen, LAI Yuexing, WANG Jing, XU Ping. Long non-coding RNA ABHD11-AS1 promotes glycolysis in gastric cancer cells to accelerate tumor progression [J]. Journal of Southern Medical University, 2023, 43(9): 1485-1492.
[4]	XU Mengqi, SHI Yutong, LIU Junping, WU Minmin, ZHANG Fengmei, HE Zhiqiang, TANG Min. JAG1 affects monocytes-macrophages to reshape the pre-metastatic niche of triple-negative breast cancer through LncRNA MALAT1 in exosomes [J]. Journal of Southern Medical University, 2023, 43(9): 1525-1535.
[5]	ZHANG Mengying, LI Zhi, PEI Weiya, LI Xueqin, YANG Hui, ZHU Xiaolong, LÜ Kun. M2 macrophage-derived exosomal lncRNA NR_028113.1 promotes macrophage polarization possibly by activating the JAK2/STAT3 signaling pathway [J]. Journal of Southern Medical University, 2023, 43(3): 393-399.
[6]	ZHAO Qilin, WANG Nan, LI Yaji, WU Qingchen, WU Lanxiang. Lnc-TMEM132D-AS1 overexpression reduces sensitivity of non-small cell lung cancer cells to osimertinib [J]. Journal of Southern Medical University, 2023, 43(2): 242-250.
[7]	ZHANG Ming, YU Hao, SHAO Yang, SONG Guodong, CHEN Mingrui, LIU Shunli. Effect of nanofat combined with platelet-rich plasma for treatment of pressure injury wounds in rats [J]. Journal of Southern Medical University, 2023, 43(12): 2061-2070.
[8]	LIU Zhiyu, FANG Fengzhu, LI Jing, ZHAO Guangyue, ZANG Quanjin, ZHANG Feng, DIE Jun. RHPN2 is highly expressed in osteosarcoma cells to promote cell proliferation and migration and inhibit apoptosis [J]. Journal of Southern Medical University, 2022, 42(9): 1367-1373.
[9]	CHEN Shuran, DONG Rui, LI Yan, WU Huazhang, LIU Mulin. m⁷G-lncRNAs are potential biomarkers for prognosis and tumor microenvironment in patients with colon cancer [J]. Journal of Southern Medical University, 2022, 42(5): 681-689.
[10]	WANG Hui, LI Wenwen, ZHANG Dongyan. Pan-cancer analysis of the expression pattern of long non-coding RNA MIR22HG [J]. Journal of Southern Medical University, 2022, 42(4): 473-485.
[11]	. The low expression of long non-coding RNA Linc00638 contributes to rheumatoid arthritis progression by regulating inflammation and oxidative stress [J]. Journal of Southern Medical University, 2021, 41(7): 965-971.
[12]	. Role of long noncoding RNA SNHG3 in regulating proliferation, migration and invasion of cervical cancer SiHa cells [J]. Journal of Southern Medical University, 2021, 41(6): 931-936.
[13]	. Platelet-rich plasma alleviates myocardial ischemia-reperfusion injury in rats [J]. Journal of Southern Medical University, 2021, 41(5): 775-782.
[14]	. Value of prediction models for prognosis prediction of colorectal cancer: an analysis based on TCPA database [J]. Journal of Southern Medical University, 2021, 41(3): 439-446.
[15]	. Long non-coding RNA UPK1A-AS1 promotes glycolysis in hepatocellular carcinoma cells via stabilization of HIF-1α [J]. Journal of Southern Medical University, 2021, 41(2): 193-199.