单细胞RNA测序应用于继发性肾病的研究进展

doi:10.3760/cma.j.issn.1007-1245.2024.06.011

摘要/Abstract

摘要：

糖尿病肾病、狼疮性肾炎是主要的继发性肾病，是导致终末期肾病的重要原因。探究继发性肾病发生发展过程有利于减少肾功能损害。肾脏细胞具有高度分化且结构复杂的特点，传统测序方法只能探究一类细胞的平均转录水平及关系。近年来，单细胞RNA测序（single-cell RNA-sequencing，scRNA-seq）技术迅猛发展，以高通量及高分辨率对肾组织、血液、尿液细胞样本进行分析，识别新的细胞类型和状态，绘制细胞图谱，从细胞水平维度揭示肾脏疾病的复杂机制，发现生物标志物和细胞特异性。该文就scRNA-seq技术在常见继发性肾病的应用进展进行综述。

关键词:

单细胞测序, 单细胞RNA测序, 糖尿病肾病, 狼疮性肾炎, 终末期肾病, 进展

Abstract:

Diabetic nephropathy (DN) and lupus nephritis (LN) are the major secondary nephropathy and are important causes of end-stage renal disease (ESRD). Exploring the developmental process of secondary nephrosis is conducive to reducing the renal function damage. Kidney cells have the characteristics of high degree of differentiation and complex structure. Bulk RNA sequencing can only explore the average transcription level and relationship of one type of cells. In recent years, single-cell RNA sequencing (scRNA-seq) technology has developed rapidly. Its high throughput and unprecedented resolution make it possible to analyze the renal tissue, blood, and urine cell samples, to identify the new cell types and states, to draw the cell atlas, to unravel the complex mechanisms of kidney disease from the cellular level dimension, and to discover the biomarkers and cell specificity. This reviews focuses on the latest research advances in scRNA-seq in common secondary nephrosis.

Key words:

Single-cell sequencing, Single-cell RNA-sequencing, Diabetic nephropathy, Lupus nephritis, End-stage renal disease, Progress

邹皓珍杨佳席哲帆纪瑞董华.

单细胞RNA测序应用于继发性肾病的研究进展 [J]. 国际医药卫生导报, 2024, 30(6): 936-940.

Zou Haozhen, Yang Jia, Xi Zhefan, Ji Rui, Dong Hua.

Advances in single-cell RNA sequencing in secondary nephrosis [J]. International Medicine and Health Guidance News, 2024, 30(6): 936-940.

参考文献

[1] 王梦洁,董伟,梁馨苓. 单细胞RNA测序在肾脏疾病研究中的应用与前景[J]. 临床肾脏病杂志,2021,21(8):681-684. DOI:10.3969/j.issn.1671-2390.y20-118.
[2] 周莹,黄华艺. 单细胞测序技术及其在肿瘤研究和临床诊断中的应用[J]. 分子诊断与治疗杂志,2017,9(3):147-153,172. DOI:10.3969/j.issn.1674-6929.2017.03.001.
[3] 陈麒麟. 单细胞RNA测序在肾脏疾病研究中的应用[J]. 肾脏病与透析肾移植杂志,2019,28(4):355-359. DOI:10.3969/j.issn.1006-298X.2019.04.012.
[4] Tang F, Barbacioru C, Wang Y, et al. mRNA-Seq whole-transcriptome analysis of a single cell[J]. Nat Methods, 2009, 6(5):377-382. DOI: 10.1038/nmeth.1315.
[5] Zhang X, Marjani SL, Hu Z, et al. Single-cell sequencing for precise cancer research: progress and prospects[J]. Cancer Res, 2016,76(6):1305-1312. DOI: 10.1158/0008-5472.CAN-15-1907.
[6] Guo H, Zhu P, Guo F, et al. Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing[J]. Nat Protoc, 2015,10(5):645-659. DOI: 10.138/nprot.2015.039.
[7] Buenrostro JD, Wu B, Litzenburger UM, et al. Single-cell chromatin accessibility reveals principles of regulatory variation[J]. Nature, 2015,523(7561): 486-490. DOI: 10.1038/nature14590.
[8] Wang YJ, Zhao MM, Zhang Y. Integrated analysis of single-cell RNA-seq and bulk RNA-seq in the identification of a novel ceRNA network and key biomarkers in diabetic kidney disease[J]. INT J GEN MED, 2022,15:1985-2001. DOI:10.214 7/IJGM.S351971.
[9] Mohan A, Singh RS, Kumari M, et al. Urinary exosomal microRNA-451-5p is a potential early biomarker of diabetic nephropathy in rats[J]. PLoS One, 2016,11(4): e154055. DOI: 10.1371/journal.pone.0154055.
[10] Zhang X, Chao P, Zhang L, et al. Single-cell RNA and transcriptome sequencing profiles identify immune-associated key genes in the development of diabetic kidney disease[J]. Front Immunol, 2023, 14: 1030198. DOI: 10.3389/fimmu.2023.1030198.
[11] Liu S, Zhao Y, Lu S, et al. Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy[J]. Genome Med, 2023,15(1):2. DOI: 10.1186/s13073-022-01145-4.
[12] Lu X, Li L, Suo L, et al. Single-cell RNA sequencing profiles identify important pathophysiologic factors in the progression of diabetic nephropathy[J]. Front Cell Dev Biol, 2022,10:798316. DOI: 10.3389/fcell.2022.798316.
[13] Zhang Y, Li W, Zhou Y. Identification of hub genes in diabetic kidney disease via multiple-microarray analysis[J]. Ann Transl Med, 2020,8(16):997. DOI: 10.21037/atm-20-5171.
[14] Fu J, Sun Z, Wang X, et al. The single-cell landscape of kidney immune cells reveals transcriptional heterogeneity in early diabetic kidney disease[J]. Kidney Int, 2022,102(6): 1291-1304. DOI: 10.1016/j.kint.2022. 08.026.
[15] Fu J, Akat KM, Sun Z, et al. Single-cell RNA profiling of glomerular cells shows dynamic changes in experimental diabetic kidney disease[J]. J Am Soc Nephrol, 2019,30(4):533-545. DOI: 10.1681/ASN.2018090896.
[16] Roumeliotis A, Roumeliotis S, Tsetsos F, et al. Oxidative stress genes in diabetes mellitus type 2: association with diabetic kidney disease[J]. Oxid Med Cell Longev, 2021,2021:2531062. DOI: 10.1155/2021/2531062.
[17] McKnight AJ, Patterson CC, Pettigrew KA, et al. A GREM1 gene variant associates with diabetic nephropathy[J]. J Am Soc Nephrol, 2010, 21(5):773-781. DOI: 10.1681/ASN.2009070773.
[18] Kamiyama M, Kobayashi M, Araki S, et al. Polymorphisms in the 3' UTR in the neurocalcin delta gene affect mRNA stability, and confer susceptibility to diabetic nephropathy[J]. Hum Genet, 2007, 122(3-4): 397-407. DOI: 10.1007/s00439-007-0414-3.
[19] Pei D, Huang YJ, Hsieh CH, et al. The genetic background difference between diabetic patients with and without nephropathy in a Taiwanese population by linkage disequilibrium mapping using 382 autosomal STR markers[J]. Genet Test Mol Biomarkers, 2010,14(3):433-438. DOI: 10.1089/gtmb.2009.0179.
[20] Gu HF, Alvarsson A, Efendic S, et al. SOX2 has gender-specific genetic effects on diabetic nephropathy in samples from patients with type 1 diabetes mellitus in the GoKinD study[J]. Gend Med, 2009,6(4):555-564. DOI: 10.1016/j.genm.2009.11.001.
[21] Zhang Y, Zhao X, Li C, et al. Aberrant NAD synthetic flux in podocytes under diabetic conditions and effects of indoleamine 2,3-dioxygenase on promoting de novo NAD synthesis[J]. Biochem Biophys Res Commun, 2023,643:61-68. DOI: 10.1016/j.bbrc.2022.12.059.
[22] Wang Y, Niu A, Pan Y, et al. Profile of podocyte translatome during development of type 2 and type 1 diabetic nephropathy using podocyte-specific TRAP mRNA RNA-seq[J]. Diabetes, 2021,70(10): 2377-2390. DOI: 10.2337/db21-0110.
[23] 翁维维,于生友,于力,等. 自噬相关基因LC3在阿霉素肾病中mRNA表达的意义[J]. 国际医药卫生导报,2020,26(11):1538-1541. DOI:10.3760/cma.j.issn.1007-1245. 2020. 11.015.
[24] Abedini A, Zhu YO, Chatterjee S, et al. Urinary single-cell profiling captures the cellular diversity of the kidney[J]. J Am Soc Nephrol, 2021,32(3): 614-627. DOI:10.1681/ASN.20200 50757.
[25] Stewart BJ, Ferdinand JR, Clatworthy MR. Using single-cell technologies to map the human immune system - implications for nephrology[J]. Nat Rev Nephrol, 2020,16(2):112-128. DOI: 10.1038/s41581-019-0227-3.
[26] Wu J, Sun Z, Yang S, et al. Kidney single-cell transcriptome profile reveals distinct response of proximal tubule cells to SGLT2i and ARB treatment in diabetic mice[J]. Mol Ther, 2022, 30(4): 1741-1753. DOI: 10.1016/j.ymthe. 2021.10.013.
[27] Wu H, Gonzalez Villalobos R, Yao X, et al. Mapping the single-cell transcriptomic response of murine diabetic kidney disease to therapies[J]. Cell Metab,2022,34(7):1064-1078. DOI: 10.1016/j.cmet.2022.05.010.
[28] Dalbøge LS, Christensen M, Madsen MR, et al. Nephroprotective effects of semaglutide as mono-and combination treatment with lisinopril in a mouse model of hypertension-accelerated diabetic kidney disease[J]. Biomedicines, 2022,10(7):1661. DOI: 10.3390/biomedicines10071661.
[29] Wang X, Xiang J, Huang G, et al. Inhibition of podocytes DPP4 activity is a potential mechanism of lobeliae Chinensis herba in treating diabetic kidney disease[J]. Front Pharmacol, 2021, 12:779652. DOI: 10.3389/fphar.2021.779652.
[30] Maria NI, Davidson A. Protecting the kidney in systemic lupus erythematosus: from diagnosis to therapy[J]. Nat Rev Rheumatol, 2020,16(5): 255-267. DOI: 10.1038/s41584-020-0401-9.
[31] Nakano M, Iwasaki Y, Fujio K. Transcriptomic studies of systemic lupus erythematosus[J]. Inflamm Regen, 2021,41(1):11. DOI: 10.1186/s41232-021-00161-y.
[32] Nehar-Belaid D, Hong S, Marches R, et al. Mapping systemic lupus erythematosus heterogeneity at the single-cell level[J]. Nat Immunol, 2020, 21(9): 1094-1106. DOI: 10.1038/s41590-020-0743-0.
[33] Vanarsa K, Soomro S, Zhang T, et al. Quantitative planar array screen of 1000 proteins uncovers novel urinary protein biomarkers of lupus nephritis[J]. Ann Rheum Dis, 2020, 79(10):1349-1361. DOI: 10.1136/annrheumdis- 2019-216312.
[34] Arazi A, Rao DA, Berthier CC, et al. The immune cell landscape in kidneys of patients with lupus nephritis[J]. Nat Immunol, 2019,20(7):902-914. DOI: 10.1038/s41590-019-0398-x.
[35] Fava A, Buyon J, Mohan C, et al. Integrated urine proteomics and renal single-cell genomics identify an IFN-gamma response gradient in lupus nephritis[J]. JCI Insight, 2020, 5(12): e138345. DOI: 10.1172/jci.insight.138345.
[36] Peterson KS, Huang JF, Zhu J, et al. Characterization of heterogeneity in the molecular pathogenesis of lupus nephritis from transcriptional profiles of laser-captured glomeruli[J]. J Clin Invest, 2004,113(12):1722-1733. DOI: 10.1172/JCI19139.
[37] Der E, Suryawanshi H, Morozov P, et al. Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways[J]. Nat Immunol, 2019, 20(7): 915-927. DOI: 10.1038/s41590-019-0386-1.
[38] Der E, Ranabothu S, Suryawanshi H, et al. Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis[J]. JCI Insight, 2017, 2(9): e93009. DOI: 10.1172/jci.insight.93009.
[39] Chen Z, Zhang T, Mao K, et al. A single-cell survey of the human glomerulonephritis[J]. J Cell Mol Med, 2021, 25(10):4684-4695. DOI: 10.1111/jcmm.16407.
[40] Fava A, Rao DA, Mohan C, et al. Urine proteomics and renal single-cell transcriptomics implicate interleukin-16 in lupus nephritis[J]. Arthritis Rheumatol, 2022, 74(5): 829-839. DOI: 10.1002/art.42023.
[41] Zhang T, Li H, Vanarsa K, et al. Association of urine sCD163 with proliferative lupus nephritis, fibrinoid necrosis, cellular crescents and intrarenal M2 macrophages[J]. Front Immunol, 2020, 11: 671. DOI: 10.3389/fimmu.2020.00671.
[42] Tang C, Fang M, Tan G, et al. Discovery of novel circulating immune complexes in lupus nephritis using immunoproteomics[J]. Front Immunol, 2022,13:850015. DOI: 103389/fimmu. 2022.850015.
[43] Song K, Zheng X, Liu X, et al. Genome-wide association study of SNP- and gene-based approaches to identify susceptibility candidates for lupus nephritis in the Han Chinese population[J]. Front Immunol, 2022,13:908851. DOI: 10.3389/fimmu.2022.908851.
[44] Ye H, Su B, Ni H, et al. microRNA-199a may be involved in the pathogenesis of lupus nephritis via modulating the activation of NF-kappaB by targeting Klotho[J]. Mol Immunol, 2018,103:235-242. DOI: 10.1016/j.molimm. 2018.10.003.
[45] Chuang HC, Chen MH, Chen YM, et al. BPI overexpression suppresses Treg differentiation and induces exosome-mediated inflammation in systemic lupus erythematosus[J]. Theranostics, 2021,11(20):9953-9966. DOI: 10.7150/thno.63743.
[46] Qi YY, Zhao XY, Liu XR, et al. Lupus susceptibility region containing CTLA4 rs17268364 functionally reduces CTLA4 expression by binding EWSR1 and correlates IFN-alpha signature[J]. Arthritis Res Ther, 2021,23(1):279. DOI: 10.1186/s13075-021-02664-y.
[47] Zhou C, Bai X, Yang Y, et al. Single-cell sequencing informs that mesenchymal stem cell alleviates renal injury through regulating kidney regional immunity in lupus nephritis[J]. Stem Cells Dev, 2023, 32(15-16):465-483. DOI: 10.1089/scd.2023.0047.
[48] Peng J, Wang Y, Han X, et al. Clinical implications of a new DDX58 pathogenic variant that causes lupus nephritis due to rig-i hyperactivation[J]. J Am Soc Nephrol, 2023,34(2): 258-272. DOI: 10.1681/ASN.2022040477.
[49] Ma Q, Xu M, Jing X, et al. Honokiol suppresses the aberrant interactions between renal resident macrophages and tubular epithelial cells in lupus nephritis through the NLRP3/IL-33/ST2 axis[J]. Cell Death Dis, 2023,14(3):174. DOI: 10.1038/s41419-023- 05680-9.
[50] 邢海帆,范瑛. 单细胞RNA测序应用于肾小球疾病研究的进展[J]. 上海交通大学学报(医学版),2022,42(10):1458-1465. DOI:10.3969/j.issn.1674-8115.2022.10.012.
[51] 高山凤,肖轩,张玲羽,等. 单细胞测序技术在生殖研究中的应用[J]. 中国细胞生物学学报,2020,42(12):2234-2243. DOI:10.11844/cjcb.2020.12.0015.
[52] Kaur H, Advani A. The study of single cells in diabetic kidney disease[J]. J Nephrol, 2021,34(6):1925-1939. DOI: 10.1007/s40620-020-00964-1.