Epigenetic regulation of HDAC2 on TBC protein family members of neutrophils in patients with ischemic stroke

doi:10.3969/j.issn.1006-7795.2023.01.010

Abstract

Abstract: Objective To study the molecular mechanism that mediating neutrophil degranulation and phagocytosis after acute ischemic stroke(AIS) and the epigenetic regulatory mechanism of histone deacetylase 2 (HDAC2). Methods Three 60－80 years old male patients from the Department of Emergency, Xuanwu Hospital, Capital Medical University who did not receive thrombolysis or endovascular treatment within 6 h after anterior circulation ischemia onset and three healthy gender and age-matched controls were included in this study. The peripheral blood neutrophils was isolated with density gradient centrifugation method, and the transcriptome difference between AIS patients and healthy controls was analyzed with RNA sequencing (RNA-seq). In addition, HDAC2 binding genes in neutrophils were analyzed with chromatin immunoprecipitation high-throughput sequencing (ChIP-seq). Results (1) RNA-seq results indicated that compared with the healthy control group, the transcription level of 13 TBC1D family molecules changed significantly after AIS, among which TBC protein family members TBC1D10A, TBC1D31, and TBC1D5 were significantly down-regulated, and TBC1D10B, TBC1D10C, TBC1D17, TBC1D2, TBC1D22A, TBC1D26, TBC1D29, TBC1D3H, TBC1D8, and TBC1D9B were significantly up-regulated. (2) ChIP-seq analysis indicated that HDAC2 binding genes of TBC1D family in AIS patients were differentially expressed. Methylation analysis of HDAC2 binding promoters showed that these TBC1D family molecules were modified by hypermethylation and moderate methylation, which were regulated by acetylation and methylation modification. Conclusion This study showed that TBC1D family molecules may be potential targets for regulating neutrophil degranulation and phagocytosis after ischemic stroke, and HDAC2 may have extensive binding sites in the genome of this family.

Key words: ischemic stroke, neutrophil, histone deacetylase 2(HDAC2), TBC1D, degranulation, phagocytosis

CLC Number:

R743.3

Li Xue, Fan Junfen, Wang Rongliang, Ma Qingfeng, Luo Yumin, Zhao Haiping. Epigenetic regulation of HDAC2 on TBC protein family members of neutrophils in patients with ischemic stroke[J]. Journal of Capital Medical University, 2023, 44(1): 62-71.

References

[1] Orellana-Urzúa S, Rojas I, Líbano L, et al. Pathophysiology of ischemic stroke: role of oxidative stress[J]. Curr Pharm Des, 2020, 26(34): 4246-4260.
[2] Paul S, Candelario-Jalil E. Emerging neuroprotective strategies for the treatment of ischemic stroke: an overview of clinical and preclinical studies[J]. Exp Neurol, 2021, 335: 113518.
[3] Xu S B, Lu J A, Shao A W, et al. Glial cells: role of the immune response in ischemic stroke[J]. Front Immunol, 2020, 11: 294.
[4] Maida C D, Norrito R L, Daidone M, et al. Neuroinflammatory mechanisms in ischemic stroke: focus on cardioembolic stroke, background, and therapeutic approaches[J]. Int J Mol Sci, 2020, 21(18): 6454.
[5] Mendelson S J, Prabhakaran S. Diagnosis and management of transient ischemic attack and acute ischemic stroke: a review[J]. JAMA, 2021, 325(11): 1088-1098.
[6] Jia T X, Wang M J, Yan W J, et al. Upregulation of miR-489-3p attenuates cerebral ischemia/reperfusion injury by targeting histone deacetylase 2 (HDAC2)[J]. Neuroscience, 2022, 484: 16-25.
[7] Jian Z H, Liu R, Zhu X Q, et al. The involvement and therapy target of immune cells after ischemic stroke[J]. Front Immunol, 2019, 10: 2167.
[8] Cai W, Liu S X, Hu M Y, et al. Functional dynamics of neutrophils after ischemic stroke[J]. Transl Stroke Res, 2020, 11(1): 108-121.
[9] Otxoa-de-Amezaga A, Gallizioli M, Pedragosa J, et al. Location of neutrophils in different compartments of the damaged mouse brain after severe ischemia/reperfusion[J]. Stroke, 2019, 50(6): 1548-1557.
[10] Kang L J, Yu H L, Yang X, et al. Neutrophil extracellular traps released by neutrophils impair revascularization and vascular remodeling after stroke[J]. Nat Commun, 2020, 11(1): 2488.
[11] Herz J, Sabellek P, Lane T E, et al. Role of neutrophils in exacerbation of brain injury after focal cerebral ischemia in hyperlipidemic mice[J]. Stroke, 2015, 46(10): 2916-2925.
[12] Neumann J, Riek-Burchardt M, Herz J, et al. Very-late-antigen-4 (VLA-4)-mediated brain invasion by neutrophils leads to interactions with microglia, increased ischemic injury and impaired behavior in experimental stroke[J]. Acta Neuropathol, 2015, 129(2): 259-277.
[13] Lehman H K, Segal B H. The role of neutrophils in host defense and disease[J]. J Allergy Clin Immunol, 2020, 145(6): 1535-1544.
[14] Kolaczkowska E, Kubes P. Neutrophil recruitment and function in health and inflammation[J]. Nat Rev Immunol, 2013, 13(3): 159-175.
[15] Anderson M C, Chaze T, Coïc Y M, et al. MUB₄₀ binds to lactoferrin and stands as a specific neutrophil marker[J]. Cell Chem Biol, 2018, 25(4): 483-493.e9.
[16] Anderson M C, Injarabian L, Andre A, et al. The MUB40 peptide for use in detecting neutrophil-mediated inflammation events[J/OL]. J Vis Exp. (2019-01-07)[2021-01-03]. https://pubmed.ncbi.nlm.nih.gov/30663636/.
[17] Palm F, Pussinen P J, Safer A, et al. Serum matrix metalloproteinase-8, tissue inhibitor of metalloproteinase and myeloperoxidase in ischemic stroke[J]. Atherosclerosis, 2018, 271: 9-14.
[18] Kaesmacher J, Boeckh-Behrens T, Simon S, et al. Risk of thrombus fragmentation during endovascular stroke treatment[J]. AJNR Am J Neuroradiol, 2017, 38(5): 991-998.
[19] Abdelnaseer M M, Elfauomy N M, Esmail E H, et al. Matrix metalloproteinase-9 and recovery of acute ischemic stroke[J]. J Stroke Cerebrovasc Dis, 2017, 26(4): 733-740.
[20] Zhong C K, Yang J Y, Xu T, et al. Serum matrix metalloproteinase-9 levels and prognosis of acute ischemic stroke[J]. Neurology, 2017, 89(8): 805-812.
[21] Denorme F, Portier I, Rustad J L, et al. Neutrophil extracellular traps regulate ischemic stroke brain injury[J]. J Clin Invest, 2022, 132(10): e154225.
[22] Nakahashi-Oda C, Fujiyama S, Nakazawa Y, et al. CD300a blockade enhances efferocytosis by infiltrating myeloid cells and ameliorates neuronal deficit after ischemic stroke[J]. Sci Immunol, 2021, 6(64): eabe7915.
[23] Doran A C, Yurdagul A, Jr, Tabas I. Efferocytosis in health and disease[J]. Nat Rev Immunol, 2020, 20(4): 254-267.
[24] Kolb J P, Oguin T H 3rd, Oberst A, et al. Programmed cell death and inflammation: winter is coming[J]. Trends Immunol, 2017, 38(10): 705-718.
[25] Li F F, Zhao H P, Li G W, et al. Intravenous antagomiR-494 lessens brain-infiltrating neutrophils by increasing HDAC2-mediated repression of multiple MMPs in experimental stroke[J]. FASEB J, 2020, 34(5): 6934-6949.
[26] Ramadass M, Catz S D. Molecular mechanisms regulating secretory organelles and endosomes in neutrophils and their implications for inflammation[J]. Immunol Rev, 2016, 273(1): 249-265.
[27] Perskvist N, Roberg K, Kulyté A, et al. Rab5a GTPase regulates fusion between pathogen-containing phagosomes and cytoplasmic organelles in human neutrophils[J]. J Cell Sci, 2002, 115(Pt 6): 1321-1330.
[28] Johnson J L, He J, Ramadass M, et al. Munc13-4 is a Rab11-binding protein that regulates Rab11-positive vesicle trafficking and docking at the plasma membrane[J]. J Biol Chem, 2016, 291(7): 3423-3438.
[29] Vieira O V, Botelho R J, Grinstein S. Phagosome maturation: aging gracefully[J]. Biochem J, 2002, 366(Pt 3): 689-704.
[30] Zerial M, McBride H. Rab proteins as membrane organizers[J]. Nat Rev Mol Cell Biol, 2001, 2(2): 107-117.
[31] Rao X S, Cong X X, Gao X K, et al. AMPK-mediated phosphorylation enhances the auto-inhibition of TBC1D17 to promote Rab5-dependent glucose uptake[J]. Cell Death Differ, 2021, 28(12): 3214-3234.
[32] Toyofuku T, Morimoto K, Sasawatari S, et al. Leucine-rich repeat kinase 1 regulates autophagy through turning on TBC1D2-dependent Rab7 inactivation[J]. Mol Cell Biol, 2015, 35(17): 3044-3058.
[33] Nishino H, Saito T, Wei R, et al. The LMTK1-TBC1D9B-Rab11A cascade regulates dendritic spine formation via endosome trafficking[J]. J Neurosci, 2019, 39(48): 9491-9502.
[34] Xie Y, Mansouri M, Rizk A, et al. Regulation of VEGFR2 trafficking and signaling by Rab GTPase-activating proteins[J]. Sci Rep, 2019, 9(1): 13342.
[35] Biesemann A, Gorontzi A, Barr F, et al. Rab35 protein regulates evoked exocytosis of endothelial Weibel-Palade bodies[J]. J Biol Chem, 2017, 292(28): 11631-11640.
[36] Villagomez F R, Diaz-Valencia J D, Ovalle-García E, et al. TBC1D10C is a cytoskeletal functional linker that modulates cell spreading and phagocytosis in macrophages[J]. Sci Rep, 2021, 11(1): 20946.
[37] Hisanaga S I, Wei R, Huo A N, et al. LMTK1, a novel modulator of endosomal trafficking in neurons[J]. Front Mol Neurosci, 2020, 13: 112.
[38] Liao Y, Li M, Chen X Y, et al. Interaction of TBC1D9B with mammalian ATG8 homologues regulates autophagic flux[J]. Sci Rep, 2018, 8(1): 13496.
[39] Krämer O H. HDAC2: a critical factor in health and disease[J]. Trends Pharmacol Sci, 2009, 30(12): 647-655.
[40] Gediya P, Parikh P K, Vyas V K, et al. Histone deacetylase 2: a potential therapeutic target for cancer and neurodegenerative disorders[J]. Eur J Med Chem, 2021, 216: 113332.
[41] Ito K, Herbert C, Siegle J S, et al. Steroid-resistant neutrophilic inflammation in a mouse model of an acute exacerbation of asthma[J]. Am J Respir Cell Mol Biol, 2008, 39(5): 543-550.
[42] Rodríguez-López G M, Soria-Castro R, Campillo-Navarro M, et al. The histone deacetylase inhibitor valproic acid attenuates phospholipase Cγ2 and IgE-mediated mast cell activation[J]. J Leukoc Biol, 2020, 108(3): 859-866.
[43] Shi X M, Li M, Cui M Z, et al. Epigenetic suppression of the antitumor cytotoxicity of NK cells by histone deacetylase inhibitor valproic acid[J]. Am J Cancer Res, 2016, 6(3): 600-614.
[44] Pace M, Williams J, Kurioka A, et al. Histone deacetylase inhibitors enhance CD4 T cell susceptibility to NK cell killing but reduce NK cell function[J]. PLoS Pathog, 2016, 12(8): e1005782.
[45] Folkerts J, Redegeld F, Folkerts G, et al. Butyrate inhibits human mast cell activation via epigenetic regulation of FcεRI-mediated signaling[J]. Allergy, 2020, 75(8): 1966-1978.