国际生殖健康/计划生育 ›› 2022, Vol. 41 ›› Issue (6): 487-493.doi: 10.12280/gjszjk.20220361
收稿日期:
2022-07-28
出版日期:
2022-11-15
发布日期:
2022-11-18
通讯作者:
刘悦,丁之德
E-mail:liuyue@shsmu.edu.cn;zding@shsmu.edu.cn
基金资助:
ZHOU Li-wei, ZHENG Shu-dong, HUANG Shuo, LU Ting, LIU Yue(), DING Zhi-de(
)
Received:
2022-07-28
Published:
2022-11-15
Online:
2022-11-18
Contact:
LIU Yue,DING Zhi-de
E-mail:liuyue@shsmu.edu.cn;zding@shsmu.edu.cn
摘要:
生物信息学(bioinformatics)在生殖系统的研究中被广泛应用于各个技术层面,包括基因组、转录组、蛋白组和代谢组。通过数据的系统化采集和可视化处理,生殖过程中各种关键分子的作用机制正逐步被发现并阐明。生物信息学技术在生殖系统研究中的应用,既在保障严谨性和科学性的基础上有效地推动了生殖系统研究的发展与创新,如从基因组、转录组、蛋白组和代谢组等不同层次水平上分析生殖系统中不同器官的正常功能或其异常病理现象;同时也促进了生殖系统相关疾病临床诊断和治疗的进展,如在对疾病诊治中,新的临床疾病标志物及药物靶点的发现等。综述近年生殖医学前沿研究的最新生物信息学技术并总结现有生殖医学相关生物信息学研究的主要进展,这也为后续的各类研究提供了重要的方向和思路。
周理韡, 郑书栋, 黄硕, 鲁婷, 刘悦, 丁之德. 生物信息学技术在生殖领域中的研究进展[J]. 国际生殖健康/计划生育, 2022, 41(6): 487-493.
ZHOU Li-wei, ZHENG Shu-dong, HUANG Shuo, LU Ting, LIU Yue, DING Zhi-de. Research Progress of Bioinformatics Technology in Reproductive System[J]. Journal of International Reproductive Health/Family Planning, 2022, 41(6): 487-493.
[1] | National Human Genome Research Institute. Bioinformatics[EB/OL]. https://www.genome.gov/genetics-glossary/Bioinformatics. |
[2] |
Wei L, Wang J, Lampert E, et al. Intratumoral and Intertumoral Genomic Heterogeneity of Multifocal Localized Prostate Cancer Impacts Molecular Classifications and Genomic Prognosticators[J]. Eur Urol, 2017, 71(2):183-192. doi: 10.1016/j.eururo.2016.07.008.
doi: S0302-2838(16)30406-7 pmid: 27451135 |
[3] |
Ballabio S, Craparotta I, Paracchini L, et al. Multisite analysis of high-grade serous epithelial ovarian cancers identifies genomic regions of focal and recurrent copy number alteration in 3q26.2 and 8q24.3[J]. Int J Cancer, 2019, 145(10):2670-2681. doi: 10.1002/ijc.32288.
doi: 10.1002/ijc.32288 pmid: 30892690 |
[4] |
Lee YJ, Kim D, Shim JE, et al. Genomic profiling of the residual disease of advanced high-grade serous ovarian cancer after neoadjuvant chemotherapy[J]. Int J Cancer, 2020, 146(7):1851-1861. doi: 10.1002/ijc.32729.
doi: 10.1002/ijc.32729 pmid: 31603993 |
[5] |
Stelloo S, Nevedomskaya E, Kim Y, et al. Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis[J]. Oncogene, 2018, 37(3):313-322. doi: 10.1038/onc.2017.330.
doi: 10.1038/onc.2017.330 pmid: 28925401 |
[6] |
Corona RI, Seo JH, Lin X, et al. Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer[J]. Nat Commun, 2020, 11(1):2020. doi: 10.1038/s41467-020-15951-0.
doi: 10.1038/s41467-020-15951-0 |
[7] |
Yatsenko SA, Wood-Trageser M, Chu T, et al. A high-resolution X chromosome copy-number variation map in fertile females and women with primary ovarian insufficiency[J]. Genet Med, 2019, 21(10):2275-2284. doi: 10.1038/s41436-019-0505-2.
doi: 10.1038/s41436-019-0505-2 pmid: 30948856 |
[8] |
Cariati F, D′Argenio V, Tomaiuolo R. The evolving role of genetic tests in reproductive medicine[J]. J Transl Med, 2019, 17(1):267. doi: 10.1186/s12967-019-2019-8.
doi: 10.1186/s12967-019-2019-8 pmid: 31412890 |
[9] |
Cuppens T, Moisse M, Depreeuw J, et al. Integrated genome analysis of uterine leiomyosarcoma to identify novel driver genes and targetable pathways[J]. Int J Cancer, 2018, 142(6):1230-1243. doi: 10.1002/ijc.31129.
doi: 10.1002/ijc.31129 pmid: 29063609 |
[10] |
Guo J, Grow EJ, Yi C, et al. Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development[J]. Cell Stem Cell, 2017, 21(4):533-546.e6. doi: 10.1016/j.stem.2017.09.003.
doi: S1934-5909(17)30370-3 pmid: 28985528 |
[11] |
Stévant I, Kühne F, Greenfield A, et al. Dissecting Cell Lineage Specification and Sex Fate Determination in Gonadal Somatic Cells Using Single-Cell Transcriptomics[J]. Cell Rep, 2019, 26(12):3272-3283.e3. doi: 10.1016/j.celrep.2019.02.069.
doi: S2211-1247(19)30248-7 pmid: 30893600 |
[12] |
Wang JJ, Ge W, Zhai QY, et al. Single-cell transcriptome landscape of ovarian cells during primordial follicle assembly in mice[J]. PLoS Biol, 2020, 18(12):e3001025. doi: 10.1371/journal.pbio.3001025.
doi: 10.1371/journal.pbio.3001025 URL |
[13] |
Berglund E, Maaskola J, Schultz N, et al. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity[J]. Nat Commun, 2018, 9(1):2419. doi: 10.1038/s41467-018-04724-5.
doi: 10.1038/s41467-018-04724-5 pmid: 29925878 |
[14] |
Garcia-Alonso L, Handfield LF, Roberts K, et al. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro[J]. Nat Genet, 2021, 53(12):1698-1711. doi: 10.1038/s41588-021-00972-2.
doi: 10.1038/s41588-021-00972-2 pmid: 34857954 |
[15] |
Cao J, Spielmann M, Qiu X, et al. The single-cell transcriptional landscape of mammalian organogenesis[J]. Nature, 2019, 566(7745):496-502. doi: 10.1038/s41586-019-0969-x.
doi: 10.1038/s41586-019-0969-x URL |
[16] |
Zeng Z, Lin X, Xia T, et al. Identification of Crucial lncRNAs, miRNAs, mRNAs, and Potential Therapeutic Compounds for Polycystic Ovary Syndrome by Bioinformatics Analysis[J]. Biomed Res Int, 2020, 2020:1817094. doi: 10.1155/2020/1817094.
doi: 10.1155/2020/1817094 |
[17] |
Guo Y, Bai D, Liu W, et al. Altered sperm tsRNAs in aged male contribute to anxiety-like behavior in offspring[J]. Aging Cell, 2021, 20(9):e13466. doi: 10.1111/acel.13466.
doi: 10.1111/acel.13466 |
[18] |
Hashimoto Y, Greco TM, Cristea IM. Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology[J]. Adv Exp Med Biol, 2019, 1140:143-154. doi: 10.1007/978-3-030-15950-4_8.
doi: 10.1007/978-3-030-15950-4_8 pmid: 31347046 |
[19] |
Bernardino RMM, Leão R, Henrique R, et al. Extracellular Vesicle Proteome in Prostate Cancer: A Comparative Analysis of Mass Spectrometry Studies[J]. Int J Mol Sci, 2021, 22(24):13605. doi: 10.3390/ijms222413605.
doi: 10.3390/ijms222413605 URL |
[20] | 张英杰, 路芳, 隋凯悦. 益胃汤对初老雌性大鼠生殖机能影响的蛋白质组学研究[J]. 中药药理与临床, 2018, 34(3):11-13,192. |
[21] |
Bittremieux W, Tabb DL, Impens F, et al. Quality control in mass spectrometry-based proteomics[J]. Mass Spectrom Rev, 2018, 37(5):697-711. doi: 10.1002/mas.21544.
doi: 10.1002/mas.21544 pmid: 28802010 |
[22] |
Lahiri S, Aftab W, Walenta L, et al. MALDI-IMS combined with shotgun proteomics identify and localize new factors in male infertility[J]. Life Sci Alliance, 2021, 4(3):e202000672. doi: 10.26508/lsa.202000672.
doi: 10.26508/lsa.202000672 URL |
[23] |
邱晓菲, 李昌, 徐娟. 应用基质辅助激光解吸电离飞行时间质谱分析宫颈鳞癌早期浸润蛋白质[J]. 中华妇幼临床医学杂志(电子版), 2011, 7(4):324-328. doi: 10.3877/cma.j.issn.1673-5250.2011.04.010.
doi: 10.3877/cma.j.issn.1673-5250.2011.04.010 |
[24] | 朱宇. 质谱技术在多囊卵巢综合征子宫内膜生物标记物研究中的应用[D]. 北京: 中国医学科学院北京协和医学院, 2020. |
[25] |
Kumar B, Dey AK, Saha S, et al. Dynamic Alteration in the Vaginal Secretory Proteome across the Early and Mid-Trimesters of Pregnancy[J]. J Proteome Res, 2021, 20(2):1190-1205. doi: 10.1021/acs.jproteome.0c00433.
doi: 10.1021/acs.jproteome.0c00433 pmid: 33497241 |
[26] |
Berard AR, Perner M, Mutch S, et al. Understanding mucosal and microbial functionality of the female reproductive tract by metaproteomics: Implications for HIV transmission[J]. Am J Reprod Immunol, 2018, 80(2):e12977. doi: 10.1111/aji.12977.
doi: 10.1111/aji.12977 URL |
[27] |
Chen D, Fan F, Zhao X, et al. Single Cell Chemical Proteomics with Membrane-Permeable Activity-Based Probe for Identification of Functional Proteins in Lysosome of Tumors[J]. Anal Chem, 2016, 88(4):2466-2471. doi: 10.1021/acs.analchem.5b04645.
doi: 10.1021/acs.analchem.5b04645 pmid: 26810843 |
[28] |
Hitit M, Özbek M, Ayaz-Guner S, et al. Proteomic fertility markers in ram sperm[J]. Anim Reprod Sci, 2021, 235:106882. doi: 10.1016/j.anireprosci.2021.106882.
doi: 10.1016/j.anireprosci.2021.106882 URL |
[29] |
Zhao J, Zhai X, Ma Y, et al. Anatomic characteristics of epididymis based on histology, proteomic, and 3D reconstruction[J]. Andrology, 2020, 8(6):1787-1794. doi: 10.1111/andr.12842.
doi: 10.1111/andr.12842 URL |
[30] |
Jarvis S, Gethings LA, Samanta L, et al. High fat diet causes distinct aberrations in the testicular proteome[J]. Int J Obes(Lond), 2020, 44(9):1958-1969. doi: 10.1038/s41366-020-0595-6.
doi: 10.1038/s41366-020-0595-6 URL |
[31] |
McClements L, Richards C, Patel N, et al. Impact of reduced uterine perfusion pressure model of preeclampsia on metabolism of placenta, maternal and fetal hearts[J]. Sci Rep, 2022, 12(1):1111. doi: 10.1038/s41598-022-05120-2.
doi: 10.1038/s41598-022-05120-2 pmid: 35064159 |
[32] |
Reynolds S, Calvert SJ, Paley MN, et al. 1H Magnetic Resonance Spectroscopy of live human sperm[J]. Mol Hum Reprod, 2017, 23(7):441-451. doi: 10.1093/molehr/gax025.
doi: 10.1093/molehr/gax025 pmid: 28431025 |
[33] |
Engel KM, Baumann S, Rolle-Kampczyk U, et al. Metabolomic profiling reveals correlations between spermiogram parameters and the metabolites present in human spermatozoa and seminal plasma[J]. PLoS One, 2019, 14(2):e0211679. doi: 10.1371/journal.pone.0211679.
doi: 10.1371/journal.pone.0211679 URL |
[34] |
Walters KA, Eid S, Edwards MC, et al. Steroid profiles by liquid chromatography-mass spectrometry of matched serum and single dominant ovarian follicular fluid from women undergoing IVF[J]. Reprod Biomed Online, 2019, 38(1):30-37. doi: 10.1016/j.rbmo.2018.10.006.
doi: S1472-6483(18)30570-4 pmid: 30527851 |
[35] |
Yuan X, Hu S, Li L, et al. Metabolomic Analysis of SCD during Goose Follicular Development: Implications for Lipid Metabolism[J]. Genes (Basel), 2020, 11(9):1001. doi: 10.3390/genes11091001.
doi: 10.3390/genes11091001 URL |
[36] |
Yu L, Yang X, Ma B, et al. Abnormal arachidonic acid metabolic network may reduce sperm motility via P38 MAPK[J]. Open Biol, 2019, 9(4):180091. doi: 10.1098/rsob.180091.
doi: 10.1098/rsob.180091 URL |
[37] |
Zhao K, Zhang J, Xu Z, et al. Metabolomic Profiling of Human Spermatozoa in Idiopathic Asthenozoospermia Patients Using Gas Chromatography-Mass Spectrometry[J]. Biomed Res Int, 2018, 2018:8327506. doi: 10.1155/2018/8327506.
doi: 10.1155/2018/8327506 |
[38] |
Ilhan ZE, Łaniewski P, Thomas N, et al. Deciphering the complex interplay between microbiota, HPV, inflammation and cancer through cervicovaginal metabolic profiling[J]. EBioMedicine, 2019, 44:675-690. doi: 10.1016/j.ebiom.2019.04.028.
doi: S2352-3964(19)30267-1 pmid: 31027917 |
[39] |
Shi F, Zhang Z, Wang J, et al. Analysis by Metabolomics and Transcriptomics for the Energy Metabolism Disorder and the Aryl Hydrocarbon Receptor Activation in Male Reproduction of Mice and GC-2spd Cells Exposed to PM2.5[J]. Front Endocrinol(Lausanne), 2022, 12:807374. doi: 10.3389/fendo.2021.807374.
doi: 10.3389/fendo.2021.807374 |
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