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中华细胞与干细胞杂志(电子版)

中华细胞与干细胞杂志(电子版) ›› 2022, Vol. 12 ›› Issue (05) : 274 -281. doi: 10.3877/cma.j.issn.2095-1221.2022.05.003

论著

多发性骨髓瘤患者骨髓间充质干细胞衰老关键基因和通路的生物信息学分析与验证
周艳群1, 陈鹏2, 刘增慧2, 毛晶晶3, 黎耀和2,†()   
  1. 1. 510000　广州中医药大学第一临床医学院
    2. 510000　广州中医药大学第一临床医学院；510000　广州中医药大学第一附属医院血液科
    3. 510000　石阡县人民医院感染科
  • 收稿日期:2022-04-25 出版日期:2022-10-01
  • 通信作者: 黎耀和
  • 基金资助:
    国家自然科学基金(81903973); 广东省中医药管理局中医药科研项目(20202050)

Screening and verifying key genes and signal pathways involved in senescence of bone marrow mesenchymal stem cells in patients with multiple myeloma based on bioinformatics analysis

Yanqun Zhou1, Peng Chen2, Zenghui Liu2, Jingjing Mao3, Yaohe Li2,†()   

  1. 1. The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou 510000, China
    2. The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou 510000, China; Department of Hematology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510000, China
    3. Department of Infection, Shiqian County People's Hospital, Guizhou 555100, China
  • Received:2022-04-25 Published:2022-10-01
  • Corresponding author: Yaohe Li
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引用本文：

周艳群, 陈鹏, 刘增慧, 毛晶晶, 黎耀和. 多发性骨髓瘤患者骨髓间充质干细胞衰老关键基因和通路的生物信息学分析与验证[J]. 中华细胞与干细胞杂志(电子版), 2022, 12(05): 274-281.

Yanqun Zhou, Peng Chen, Zenghui Liu, Jingjing Mao, Yaohe Li. Screening and verifying key genes and signal pathways involved in senescence of bone marrow mesenchymal stem cells in patients with multiple myeloma based on bioinformatics analysis[J]. Chinese Journal of Cell and Stem Cell(Electronic Edition), 2022, 12(05): 274-281.

目的

利用生物信息学分析方法筛选多发性骨髓瘤（MM）患者骨髓间充质干细胞（BMMSCs）衰老相关差异表达基因（DEGs）及相关信号通路。

方法

从GEO公共数据库中下载MM患者与健康人BMMSCs基因表达矩阵GSE113736，再下载长寿群体（平均年龄93.4岁）与衰老群体（平均年龄61.9岁）的基因表达矩阵GSE16717；应用R软件筛选DEGs，获得MM患者BMMSCs中衰老相关的DEGs；运用STRING在线数据库及Cytoscape软件构建基因网络，筛选出显著模块及关键基因，对DEGs进行KEGG通路分析获取功能基因。然后，对功能基因与关键基因取交集获得hub基因。最后，采用GSE80608数据集验证hub基因筛选的准确性。

结果

通过分析获得372例MM患者BMMSCs中与衰老相关的DEGs。通路富集分析显示，DEGs在细胞凋亡、白介素介导的信号通路、蛋白质翻译后磷酸化和FOXO介导的信号通路等方面富集。通过进一步筛选，鉴定出MM患者BMMSCs中与衰老相关的4个hub基因，ANXA1、CKAP4、BTG1及ACTB。这4个hub基因在验证数据集GSE80608中亦有差异表达。

结论

MM患者BMMSCs的衰老现象可能与ANXA1、ACTB、CKAP4和BTG1的异常表达有关，通过影响细胞凋亡、白介素介导的信号通路、蛋白质翻译后的磷酸化及FOXO介导的转录，促进/加速MM患者BMMSCs衰老。

关键词: 骨髓间充质干细胞, 衰老, 多发性骨髓瘤, 生物信息学
Objective

To identify the differentially expressed genes (DEGs) and pathways involved in the senescence of bone marrow mesenchymal stem cells (BMMSCs) in patients with multiple myeloma (MM) based on bioinformatics analysis.

Methods

The BMMSCs-related gene expression matrix GSE113736 dataset of MM patients and healthy individuals and the ageing-related matrix GSE16717 dataset from healthy people, which included the longevity group with an average age of 93.4 years and the aging group with an average age of 61.9 years, were downloaded from the GEO database. Then the R software was applied to screen the DEGs, which are senescence-related in BMMSCs of MM. The STRING online database and Cytoscape software were used to construct the gene network from which the most significant modules and essencial genes were screened. The DEGs were analyzed on KEGG pathway to obtain the functional genes. Finally, hub genes were obtained by intersecting the two sets of functional genes and the key genes, and the accuracy of hub gene screening was verified by the GSE80608 data set.

Results

There 372 senescence-related DEGs were screened out from BMMSCs of MM patients. The protein interaction network of DEGs was constructed by STRING and Cytoscape, and the important node genes in the network were screened out. DEGs were significantly enriched in the apoptotic signal pathway, signaling by interleukins, post-translational protein phosphorylation and FOXO-mediated transcription. Through further screening, four hub genes were identified as ANXA1, CKAP4, BTG1 and ACTB. These four hub genes were expressed significantly and differentially in the validation dataset GSE80608.

Conclusion

The senescence of BMMSCs in MM patients may be related to the abnormal expression of ANXA1, ACTB, CKAP4 and BTG1; these genes accelerate and promote senescence by regulating apoptosis, interleukin-mediated signaling pathway, phosphorylation after protein translation, and FOXO-mediated transcription.

Key words: Bone marrow mesenchymal stem cells, Senescence, Multiple myeloma, Bioinformatics
图1 本研究流程
图2 ClusterONE与MCODE聚类最显著模块及其中X值> X平均值的基因 注：a图为ClusterONE聚类最显著模块（P = 0，nodes = 37）；b图为MCODE聚类最显著模块（nodes = 50，edges = 500）；图中所有圆形代表的基因为ClusterONE、MCODE聚类最显著的模块包括的基因，其中蓝色圆形提示该基因在ClusterONE与MCODE聚类最显著模块中富集的同时，尚满足其X值> X平均值的筛选条件
表1 聚类良好且X值最大的前20个基因
基因名 平均最短路径 介数 X值
FAM49A 1 0.788889 0.759631
ACTB 1 0.822222 0.737666
C10orf10 1 0.733333 0.714939
PXDC1 1 0.588889 0.678007
ABHD5 1 0.471852 0.648083
FBLIM1 1 0.459259 0.644863
PPAP2B 1 0.440741 0.640128
FAXDC2 1 0.380952 0.624842
SMEK2 1 0.164815 0.569579
FAM49A 1 0.788889 0.759631
BTG1 1 0.164815 0.569579
MMS19 1 0.046296 0.539276
ERCC2 1 0.046296 0.539276
CIAO1 1 0.046296 0.539276
GGT1 1.35 0.532895 0.533007
PPP4C 1.1 0.101852 0.501401
ANXA1 1.1 0.027778 0.482461
NUBP1 1.1 0.011111 0.4782
NUBP2 1.1 0.011111 0.4782
NARFL 1.1 0.011111 0.4782
图3 DEGs所富集到的KEGG通路及相关DEGs在GSE113736中的表达量 注：图中右侧不同颜色区域提示DEGs所富集到的不同KEGG通路；红色区域提示DEGs富集的通路为细胞凋亡，浅绿色区域提示DEGs富集的通路为白介素介导的信号通路，浅蓝色区域提示DEGs富集的通路为蛋白质翻译后的磷酸化，紫色区域提示DEGs富集的通路为FOXO介导的转录。其中，同一颜色所占弧形长度越长，提示富集在该通路的DEGs越多
图4 Hub基因在验证数据集GSE80608中的表达情况 注：a图为ACTB基因，其表达在验证数据集中下调；b图为ANXA1基因，其表达在验证数据集中上调；c图为CKAP1基因，其表达在验证数据集中上调；d图为BTG1基因，其表达在验证数据集中上调
1
Gay F, Palumbo A. Management of older patients with multiple myeloma[J]. Blood Rev, 2011, 25(2): 65-73.
2
Hideshima T, Mitsiades C, Tonon G, et al. Understanding multiple myeloma pathogenesis in the bone marrowto identify new therapeutic targets[J]. Nat Rev Cancer, 2007, 7 (8):585-598.
3
Keating A. Mesenchymal stromal cells: new directions[J]. Cell stem cell, 2012, 10(6):709-716.
4
Singer NG, Caplan AI. Mesenchymal stem cells: mechanisms of inflammation[J]. Annu Rev Pathol, 2011, 6:457-478.
5
陈亚芳. 间充质干细胞通过分泌趋化因子CXCL13调节骨髓瘤细胞的侵袭及耐药作用[D]. 天津：天津医科大学, 2017.
6
Xu S, Menu E, De Becker A, et al. Bone marrow-derived mesenchymal stromal cells are attracted by multiplemyeloma cell-produced chemokine CCL25 and favor myeloma cell growth in vitro and in vivo[J]. Stem Cells, 2012, 30(2):266-279.
7
陈燕. IL-17A促进骨髓瘤间充质干细胞成骨分化研究[D]. 福州：福建医科大学, 2018.
8
蔡啸, 扆雪涛, 姚菁青, 等. 人骨髓间充质干细胞分泌的外泌体调控恶性胶质瘤相关巨噬细胞的极化[J].昆明医科大学学报, 2021, 42(1):38-45.
9
邓震. 骨髓间充质干细胞通过mi R-29c抑制前列腺癌细胞的功能及机制研究[D]. 上海：第二军医大学, 2014.
10
Xu X, Yang J, Tang Y, et al. In vitro migratory aberrancies of mesenchymal stem cells derived from multiple myeloma patients only partially modulated by bortezomib[J]. Int J Clin Exp Pathol, 2014, 7(10):6705-6715.
11
Wang X, Zhang Z, Yao C. Angiogenic activity of mesenchymal stem cells in multiple myeloma[J]. Cancer Invest, 2011, 29(1):37-41.
12
Shyh-Chang N, Daley GQ，Cantley LC. Stem cell metabolism in tissue development and aging[J]. Development, 2013, 140(12): 2535-2547.
13
Muraglia A, Cancedda R, Quarto R. Clonal mesenchymal progenitors from human bone marrow differentiate in vitro according to a hierarchical model[J]. J Cell Sci, 2000, 113:1161-1166.
14
Zhang M, Methot D, Poppa V, et al. Cardiomyocyte grafting for cardiac repair: graft cell death and anti-death strategies[J]. J Mol Cell Cardiol, 2001, 33(5):907-921.
15
lyer S, Brooks R, Gumbleton M, et al. SHIP1-expressing mesenchymal stem cells regulate hematopoietic stem cell homeostasis and lineage commitment during aging[J]. Stem Cells Dev, 2015, 24(9): 1073-1081.
16
Alessio N, Stellavato A, Squillaro T, et al. Hybrid complexes of high and low molecular weight hyaluronan delay in vitro replicative senescence of mesenchymal stromal cells: a pilot study for future therapeutic application[J]. Aging (Abany NY), 2018, 10(7):1575-1585.
17
Passtoors WM, Boer JM, Goeman JJ, et al. Transcriptional profiling of human familial longevity indicates a role for ASF1A and IL7R[J]. PLoS One, 2012, 7(1):e27759. doi: 10.1371/journal.pone.0027759.
18
Piao J, Sun J, Yang Y, et al. Target gene screening and evaluation of prognostic values in non-small cell lung cancers by bioinformatics analysis[J]. Gene, 2018, 647: 306-311.
19
Anitha P, Anbarasu A, Ramaiah S. Gene network analysis reveals the association of important functional partners involved in antibiotic resistance: a report on an important pathogenic bacterium Staphylococcus aureus[J]. Gene, 2016, 575:253-263.
20
Gao LM, Xie CY, Zhang TY, et al. Maternal supplementation with calcium varying with feeding time daily during late pregnancy affects lipid metabolism and transport of placenta in pigs[J]. Biochem Biophys Res Commun, 2018, 505(2):624-630.
21
Li J, Zhou Y, Du G, et al. Integration of transcriptomics and network analysis deciphers the mechanisms of baicalein in improving learning and memory impairment in senescence-accelerated mouse prone 8 (SAMP8) [J]. Eur J Pharmacol, 2019, 865:172789. doi: 10.1016/j.ejphar.2019.172789.
22
詹渊博, 刘昕朋, 许文霞, 等. 组蛋白去乙酰化酶9在骨髓间充质干细胞衰老过程中的表达[J]. 中国组织工程研究, 2022, 26(30): 4762-4766.
23
麦丽萍, 何国东, 陈少贤, 等. 乙醛脱氢酶3B1在人骨髓间充质干细胞自然衰老过程中的表达[J]. 中国组织工程研究, 2022, 26(1): 40-44.
24
Xin Z, Ma Z, Hu W, et al. FOXO1/3: potential suppressors of fibrosis[J]. Ageing Res Rev, 2018, 41:42-52.
25
Yadav RK, Chauhan AS, Zhuang L, et al. Foxo transcription factors in cancer metabolism[J]. Semin Cancer Biol, 2018, 50:65-76.
26
吴平平, 胡文龙, 殷嫦嫦, 等. FOXO4通过抑制凋亡维持人脐带间充质干细胞衰老[J]. 生理学报, 2020, 72(4):426-432.
27
Wilson MS, Brosens JJ, Schwenen HD, et al. FOXO and FOXM1 in cancer: the FOXO-FOXM1 axis shapes the outcome of cancer chemotherapy[J]. Curr Drug Targets, 2011, 12(9):1256-1266.
28
张胜. 山奈酚通过调控FoxO通路抑制氧化应激介导的间充质干细胞凋亡机制研究[D]. 南昌：南昌大学, 2016.
29
马林. miR-223-3p调控人骨髓间充质干细胞成骨分化的机制研究[D]. 昆明：昆明医科大学, 2020.
30
Adamopoulos IE, Chao CC, Geissler R, et al. Interleukin-17A upregulates receptor activator of NF-KB on osteoclast precursors[J]. Arthritis Res Ther, 2010, 12(1):R29. doi: 10.1186/ar2936.
31
Miyauchi H, Minamino T, Tateno K, et al. Akt negatively regulates the in vitro lifespan of human endothelial cells via a p53/p21-dependent pathway[J]. EMBO J, 2004, 23(1):212-220.
32
Foo SL, Yap G, Cui J, et al. Annexin-A1- A blessing or a curse in cancer?[J]. Trends Mol Med, 2019, 25(4):315-327.
33
游沁怡, 柯一郎, 洪华山. 膜联蛋白A1与衰老及其相关性疾病的研究进展[J]. 中华老年医学杂志, 2021, 40(3):383-387.
34
Rimokh R, Rouault JP, Wahbi K, et al. A chromosome 12 coding reg1on is juxtaposed to the MYC protooncogene locus in at(8;12)(q24;q22)translocation in a case of B-cell chronic lymphocytic leukemia[J]. Genes Chromosomes Cancer, 1991, 3(1):24-36.
35
Cho JW, Kim JJ, Park SG, et al. Identification of B-cell translocation gene 1 as a biomarker for monitoring the remission of acute myeloid leukemia[J]. Proteomics, 2004, 4 (11):3456-3463.
36
Kimura H, Fumoto K, Shojima K, et al. CKAP4 is a Dickkopf1 receptor and is involved in tumor progression[J]. J Clin Invest, 2016, 126(7):2689-2705.
37
Hobbs GA, Zhou B, Cox AD, et al. Rho GTPases, oxidation, and cell redox control[J]. Small GTPases, 2014, 5:e28579. doi: 10.4161/sgtp.28579.
38
Dominguez R，Holmes KC. Actin structure and function[J]. Annu Rev Biophys, 2011, 40:169-186.
39
Freitas JL, Vale TC, Barsottini OGP, et al. Expanding the phenotype of dystonia-deafness syndrome caused by ACTB gene mutation[J]. Mov Disord Clin Pract, 2019, 7(1):86-87.
40
Mo JS, Park HW, Guan KL. The Hippo signaling pathway in stem cell biology and cancer[J]. EMBO Rep, 2014, 15(6):642-56.
41
Terpos E, Ntanasis-Stathopoulos I, Gavriatopoulou M, et al. Pathogenesis of bone disease in multiple myeloma: from bench to bedside[J]. Blood Cancer J, 2018, 8(1):7. doi: 10.1038/s41408-017-0037-4.
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