CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES >
Heterogeneity analysis of T cells in liver of mice infected with Echinococcus granulosus based on single-cell RNA sequencing
Received date: 2024-05-18
Revised date: 2024-05-22
Online published: 2024-07-16
Supported by
National Natural Science Foundation of China(82072307);National Natural Science Foundation of China(82272369)
Objective To explore the composition and transcriptional profile characteristics of T cell subtypes in liver tissue microenvironment cells of mice infected with Echinococcus granulosus at different time points at the single-cell level. Methods Data were extracted from the single-cell RNA sequencing dataset (genome sequence archive: CRA008416) of BALB/c mouse liver tissue at 1 month (1 mouse), 3 months (1 mouse) and 6 months (2 mice) after E. granulosus infection and healthy mouse (1 mouse, control group) in the previous study of the research group and quality control was conducted. The uniform manifold approximation and projection (UMAP) method was used to visualize the single cell clusters, and the clustering algorithm adopted shared nearest neighbour (SNN) to obtain the optimal cell clusters. SingleR software package was used for cell type annotation of cell subsets based on the immgen reference dataset. FindMarkers function from Seurat software package was used to analyze differentially expressed genes (DEGs) of regulatory T cells (Tregs) and CD8+ T cells in mice infected at different time points and control group mice. Functional enrichment and pathway enrichment of DEGs were analyzed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), respectively. Results After quality control, 37 760 cells were obtained, which were divided into 8 types after manual optimization. After re-clustering the T cells, 12 cell groups were obtained. Seven T cell subtypes were annotated and identified, including CD4+ naive T cells, CD4+ effector T cells, Tregs, CD8+ naive T cells, CD8+ T cells, proliferative T cells, γδ T cells. The proportion of each T cell subtype did not change significantly at 1 month after E. granulosus infection. The proportion of proliferative T cells (11.91%, 56/470) and Tregs (13.40%, 63/470) were significantly higher than those in control group (3.51%, 38/1 082; 4.34%, 47/1 082) at 3 months after infection. The proportion of CD8+ T cells (30.20%, 1 145/3 791) was significantly higher than that of the control group (15.43%, 167/1 082) at 6 months after infection. Tregs showed high expression of tumor necrosis factor-α-induced protein 8 (Tnfaip8), Maf, IKAROS family zinc finger 3 (Ikzf3) and other Treg-maintaining genes at 3 months after infection, while CD8+ T cells showed high expression of depletion genes such as CD40 ligand (Cd40lg), chitinase-like 3 (Chil3), secreted phosphoprotein 1 (Spp1) at 6 months after infection. GO analysis showed that DEGs of Tregs were mainly concentrated in transforming growth factor beta receptor complex assembly, positive regulation of T cell activation, cyclic adenosine monophosphate (cAMP) mediated signalling pathway at 3 months after infection; while the DEGs of CD8+ T cells were mainly concentrated in the regulation of vascular endothelial growth factor receptor, tryptophan catabolic process, extracellular matrix-cell signalling pathways at 6 months after infection. KEGG analysis showed that DEGs of Tregs were mainly involved in primary immune deficiency and Ras signalling pathway at 3 months after infection; while the DEGs of CD8+ T cells were mainly involved in fatty acid metabolism, glutathione metabolism, folate metabolism and other pathways at 6 months after infection. Conclusion There are differences in T cell subtypes in liver of mice at 3 months and 6 months after E. granulosus infection; the proportion of Tregs increased at 3 months, and CD8+ T cells increased at 6 months after infection. There were differences in DEGs and their main enrichment pathways of Tregs and CD8+ T cells.
JIANG Nan , SU Yaxin , JIANG Xiaofeng , SHEN Yujuan , CAO Jianping . Heterogeneity analysis of T cells in liver of mice infected with Echinococcus granulosus based on single-cell RNA sequencing[J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2024 , 42(3) : 286 -294 . DOI: 10.12140/j.issn.1000-7423.2024.03.002
| [1] | McManus DP, Gray DJ, Zhang WB, et al. Diagnosis, treatment, and management of echinococcosis[J]. BMJ, 2012, 344: e3866. |
| [2] | Kui Y, Xue CZ, Wang X, et al. Progress of echinococcosis control in China, 2022[J]. Chin J Parasitol Parasit Dis, 2024, 42(1): 8-16. (in Chinese) |
| (蒉嫣, 薛垂召, 王旭, 等. 2022年全国棘球蚴病防治工作进展[J]. 中国寄生虫学与寄生虫病杂志, 2024, 42(1): 8-16.) | |
| [3] | Gottstein B, Soboslay P, Ortona E, et al. Chapter one immunology of alveolar and cystic echinococcosis (AE and CE)[J]. Adv Parasitol, 2017, 96: 1-54. |
| [4] | Ammann RW, Eckert J. Cestodes. Echinococcus[J]. Gastroenterol Clin North Am, 1996, 25(3): 655-689. |
| [5] | Govindasamy A, Bhattarai PR, John J. Liver cystic echinococcosis: a parasitic review[J]. Ther Adv Infect Dis, 2023, 10: 20499361231171478. |
| [6] | Zhao JJ, Zhang SY, Liu Y, et al. Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human[J]. Cell Discov, 2020, 6: 22. |
| [7] | Massalha H, Bahar Halpern K, Abu-Gazala S, et al. A single cell atlas of the human liver tumor microenvironment[J]. Mol Syst Biol, 2020, 16(12): e9682. |
| [8] | Hedlund E, Deng QL. Single-cell RNA sequencing: technical advancements and biological applications[J]. Mol Aspects Med, 2018, 59: 36-46. |
| [9] | Chu MJ, Song YF, Lu HH, et al. Advances in the application of single cell sequencing technology in the study of zoonotic parasitic diseases[J]. Chin Vet Sci, 2023, 53(2): 231-238. (in Chinese) |
| (褚梦洁, 宋雅菲, 卢惠红, 等. 单细胞测序技术在人兽共患寄生虫病研究中的应用进展[J]. 中国兽医科学, 2023, 53(2): 231-238.) | |
| [10] | Wendt G, Zhao L, Chen R, et al. A single-cell RNA-seq atlas of Schistosoma mansoni identifies a key regulator of blood feeding[J]. Science, 2020, 369(6511): 1644-1649. |
| [11] | Waldman BS, Schwarz D, Wadsworth MH 2nd, et al. Identification of a master regulator of differentiation in Toxoplasma[J]. Cell, 2020, 180(2): 359-372.e16. |
| [12] | Rawat M, Srivastava A, Johri S, et al. Single-cell RNA sequencing reveals cellular heterogeneity and stage transition under temperature stress in synchronized Plasmodium falciparum cells[J]. Microbiol Spectr, 2021, 9(1): e0000821. |
| [13] | Yang QQ, Jia WZ, Wang XQ, et al. Single-cell RNA sequencing deciphers transcriptional profiles of hepatocytes in mouse with hepatic alveolar echinococcosis[J]. Chin J Schisto Control, 2023, 35(3): 236-243. (in Chinese) |
| (杨清清, 贾万忠, 王向前, 等. 基于单细胞转录组测序解析小鼠肝泡型棘球蚴病肝脏细胞转录谱特征[J]. 中国血吸虫病防治杂志, 2023, 35(3): 236-243.) | |
| [14] | Jiang XF, Zhang XF, Jiang N, et al. The single-cell landscape of cystic echinococcosis in different stages provided insights into endothelial and immune cell heterogeneity[J]. Front Immunol, 2022, 13: 1067338. |
| [15] | Ayers J, Milner RJ, Cortés-Hinojosa G, et al. Novel application of single-cell next-generation sequencing for determination of intratumoral heterogeneity of canine osteosarcoma cell lines[J]. J Vet Diagn Invest, 2021, 33(2): 261-278. |
| [16] | Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner[J]. Bioinformatics, 2013, 29(1): 15-21. |
| [17] | McGinnis CS, Murrow LM, Gartner ZJ. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors[J]. Cell Syst, 2019, 8(4): 329-337.e4. |
| [18] | Aran D, Looney AP, Liu LQ, et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage[J]. Nat Immunol, 2019, 20(2): 163-172. |
| [19] | Heng TS, Painter MW, Immunological Genome Project Consortium. The Immunological Genome Project: networks of gene expression in immune cells[J]. Nat Immunol, 2008, 9(10): 1091-1094. |
| [20] | Pan W, Zhou HJ, Shen YJ, et al. Surveillance on the status of immune cells after Echinnococcus granulosus protoscoleces infection in Balb/c mice[J]. PLoS One, 2013, 8(3): e59746. |
| [21] | Zhang XF, Gong WC, Cao SK, et al. Dynamic changes of myeloid-derived suppressor cells and regulatory T cells in livers of mice infected with Echinococcus granulosus[J]. Chin J Schisto Control, 2019, 31(6): 622-627. (in Chinese) |
| (张小凡, 巩文词, 曹胜魁, 等. 细粒棘球绦虫感染小鼠肝脏髓源抑制性细胞与调节性T细胞比例动态变化[J]. 中国血吸虫病防治杂志, 2019, 31(6): 622-627.) | |
| [22] | Zhang Q, Zhu YR, Lv CJ, et al. AhR activation promotes Treg cell generation by enhancing Lkb1-mediated fatty acid oxidation via the Skp2/K63-ubiquitination pathway[J]. Immunology, 2023, 169(4): 412-430. |
| [23] | Klann JE, Remedios KA, Kim SH, et al. Talin plays a critical role in the maintenance of the regulatory T cell pool[J]. J Immunol, 2017, 198(12): 4639-4651. |
| [24] | Han YH, Kim HJ, Na H, et al. RORα induces KLF4-mediated M2 polarization in the liver macrophages that protect against nonalcoholic steatohepatitis[J]. Cell Rep, 2017, 20(1): 124-135. |
| [25] | Haim-Vilmovsky L, Henriksson J, Walker JA, et al. Mapping Rora expression in resting and activated CD4+ T cells[J]. PLoS One, 2021, 16(5): e0251233. |
| [26] | Overacre-Delgoffe AE, Chikina M, Dadey RE, et al. Interferon-γ drives treg fragility to promote anti-tumor immunity[J]. Cell, 2017, 169(6): 1130-1141.e11. |
| [27] | Andrabi SBA, Batkulwar K, Bhosale SD, et al. HIC1 interacts with FOXP3 multi protein complex: novel pleiotropic mechanisms to regulate human regulatory T cell differentiation and function[J]. Immunol Lett, 2023, 263: 123-132. |
| [28] | Bonazzi S, d’Hennezel E, Beckwith REJ, et al. Discovery and characterization of a selective IKZF2 glue degrader for cancer immunotherapy[J]. Cell Chem Biol, 2023, 30(3): 235-247.e12. |
| [29] | Lou YW, Liu SX. The TIPE (TNFAIP8) family in inflammation, immunity, and cancer[J]. Mol Immunol, 2011, 49(1/2): 4-7. |
| [30] | Xu M, Pokrovskii M, Ding Y, et al. C-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont[J]. Nature, 2018, 554(7692): 373-377. |
| [31] | Wu H, Zhao XF, Hochrein SM, et al. Mitochondrial dysfunction promotes the transition of precursor to terminally exhausted T cells through HIF-1α-mediated glycolytic reprogramming[J]. Nat Commun, 2023, 14(1): 6858. |
| [32] | Klement JD, Paschall AV, Redd PS, et al. An osteopontin/CD44 immune checkpoint controls CD8+ T cell activation and tumor immune evasion[J]. J Clin Invest, 2018, 128(12): 5549-5560. |
| [33] | Soysouvanh F, Rousseau D, Bonnafous S, et al. Osteopontin-driven T-cell accumulation and function in adipose tissue and liver promoted insulin resistance and MAFLD[J]. Obesity, 2023, 31(10): 2568-2582. |
| [34] | Wang KY, Hou HY, Zhang YN, et al. Ovarian cancer-associated immune exhaustion involves SPP1+ T cell and NKT cell, symbolizing more malignant progression[J]. Front Endocrinol, 2023, 14: 1168245. |
| [35] | Sharma P, Sharma A, Vishwakarma AL, et al. Host lung immunity is severely compromised during tropical pulmonary eosinophilia: role of lung eosinophils and macrophages[J]. J Leukoc Biol, 2016, 99(4): 619-628. |
| [36] | Jung IY, Narayan V, McDonald S, et al. BLIMP1 and NR4A3 transcription factors reciprocally regulate antitumor CAR T cell stemness and exhaustion[J]. Sci Transl Med, 2022, 14(670): eabn7336. |
| [37] | Symonds ALJ, Miao TZ, Busharat Z, et al. Egr2 and 3 maintain anti-tumour responses of exhausted tumour infiltrating CD8+ T cells[J]. Cancer Immunol Immunother, 2023, 72(5): 1139-1151. |
| [38] | Bai YM, Hu ML, Chen ZX, et al. Single-cell transcriptome analysis reveals RGS1 as a new marker and promoting factor for T-cell exhaustion in multiple cancers[J]. Front Immunol, 2021, 12: 767070. |
| [39] | Zhuang J, Qu ZB, Chu J, et al. Single-cell transcriptome analysis reveals T population heterogeneity and functions in tumor microenvironment of colorectal cancer metastases[J]. Heliyon, 2023, 9(7): e17119. |
| [40] | Srivastava R, Dervillez X, Khan AA, et al. The herpes simplex virus latency-associated transcript gene is associated with a broader repertoire of virus-specific exhausted CD8+ T cells retained within the trigeminal ganglia of latently infected HLA transgenic rabbits[J]. J Virol, 2016, 90(8): 3913-3928. |
| [41] | Srirat T, Hayakawa T, Mise-Omata S, et al. NR4a1/2 deletion promotes accumulation of TCF1+ stem-like precursors of exhausted CD8+ T cells in the tumor microenvironment[J]. Cell Rep, 2024, 43(3): 113898. |
/
| 〈 |
|
〉 |