Single-nucleus transcriptomic landscape of primate hippocampal aging

Abstract

The hippocampus plays a crucial role in learning and memory, and its progressive deteriorationwith age is functionally linked to a variety ofhuman neurodegenerative diseases.Yet a systematic profiling of the aging effects on various hippocampal cell types in primates is still missing. Here, we reported a variety of new aging-associated phenotypic changes of the primate hippocampus. These include, in particular, increased DNA damage and heterochromatin erosion with time, alongside loss of proteostasis and elevated inflammation. To understand their cellular and molecular causes, we established the first single-nucleus transcriptomic atlas of primate hippocampal aging. Among the 12 identified cell types, neural transiently amplifying progenitor cell (TAPC) and microglia were most affected by aging. In-depth dissection of gene-expression dynamics revealed impaired TAPC division and compromised neuronal unction along the neurogenesis trajectory; additionally elevated pro-inflammatory responses in the agedmicroglia and oligodendrocyte, as well as dysregulated coagulation pathways in the aged endothelial cells may contribute to a hostile microenvironment for neurogenesis. This rich resource for understanding primate hippocampal aging may provide potential diagnostic biomarkers and therapeutic interventions against age-related neurodegenerative diseases.

Keywords

aging / hippocampus / primate / single-cell RNA sequencing

References

[1] Aging Atlas C (2021) Aging Atlas: a multi-omics database for aging biology. Nucleic Acids Res 49:D825–D830

[2] Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine J-C, Geurts P, Aerts J (2017) SCENIC: single-cell regulatory network inference and clustering. Nat Methods 14:1083–1086

[3] Aimone JB, Li Y, Lee SW, Clemenson GD, Deng W, Gage FH (2014) Regulation and function of adult neurogenesis: from genes to cognition. Physiol Rev 94:991–1026

[4] Angelidis I, Simon LM, Fernandez IE, Strunz M, Mayr CH, Greiffo FR, Tsitsiridis G, Ansari M, Graf E, Strom TM (2019) An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics. Nat Commun 10:963

[5] Artegiani B, Lyubimova A, Muraro M, van Es JH, van Oudenaarden A, Clevers H (2017) A single-cell RNA sequencing study reveals cellular and molecular dynamics of the hippocampal neurogenic niche. Cell Rep 21:3271–3284

[6] Baird GS, Nelson SK, Keeney TR, Stewart A, Williams S, Kraemer S, Peskind ER, Montine TJ (2012) Age-dependent changes in the cerebrospinal fluid proteome by slow off-rate modified aptamer array. Am J Pathol 180:446–456

[7] Baker DJ, Petersen RC (2018) Cellular senescence in brain aging and neurodegenerative diseases: evidence and perspectives. J Clin Investig 128:1208–1216

[8] Bedrosian TA, Houtman J, Eguiguren JS, Ghassemzadeh S, Rund N, Novaresi NM, Hu L, Parylak SL, Denli AM, Randolph-Moore L(2021) Lamin B1 decline underlies age-related loss of adult hippocampal neurogenesis. EMBO J 40:e105819

[9] Bengoa-Vergniory N, Kypta RM (2015) Canonical and noncanonical Wnt signaling in neural stem/progenitor cells. Cell Mol Life Sci 72:4157–4172

[10] Bi S, Liu Z, Wu Z, Wang Z, Liu X, Wang S, Ren J, Yao Y, Zhang W, Song M (2020) SIRT7 antagonizes human stem cell aging as a heterochromatin stabilizer. Protein Cell 11:483–504

[11] Bin Imtiaz MK, Jaeger BN, Bottes S, Machado RAC, Vidmar M, Moore DL, Jessberger S (2021) Declining lamin B1 expression mediates age-dependent decreases of hippocampal stem cell activity. Cell Stem Cell.https://doi.org/10.1016/j.stem.2021.01. 015

[12] Boldrini M, Fulmore CA, Tartt AN, Simeon LR, Pavlova I, Poposka V, Rosoklija GB, Stankov A, Arango V, Dwork AJ (2018) Human hippocampal neurogenesis persists throughout aging. Cell Stem Cell 22(589–599):e585

[13] Brunk UT, Terman A (2002) The mitochondrial-lysosomal axis theory of aging. Eur J Biochem 269:1996–2002

[14] Bryan KJ, Zhu X, Harris PL, Perry G, Castellani RJ, Smith MA, Casadesus G (2008) Expression of CD74 is increased in neurofibrillary tangles in Alzheimer’s disease. Mol Neurodegener 3:13

[15] Buchwalter A, Kaneshiro JM, Hetzer MW (2019) Coaching from the sidelines: the nuclear periphery in genome regulation. Nat Rev Genet 20:39–50

[16] Buckig A, Tikkanen R, Herzog V, Schmitz A (2002) Cytosolic and nuclear aggregation of the amyloid beta-peptide following its expression in the endoplasmic reticulum. Histochem Cell Biol 118:353–360

[17] Butler A, Hoffman P, Smibert P, Papalexi E, Satija R (2018) Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 36:411–420

[18] Chen Y, Niu Y, Ji W(2012) Transgenic nonhuman primate models for human diseases: approaches and contributing factors. J Genet Genom 39:247–251

[19] Chen Y, Niu Y, Ji W (2016) Genome editing in nonhuman primates: approach to generating human disease models. J Intern Med 280:246–251

[20] Chen Y, Yu J, Niu Y, Qin D, Liu H, Li G, Hu Y, Wang J, Lu Y, Kang Y (2017) Modeling Rett syndrome using TALEN-edited MECP2 mutant cynomolgus monkeys. Cell 169(945–955):

[21] Chen WT, Lu A, Craessaerts K, Pavie B, Sala Frigerio C, Corthout N, Qian X, Lalakova J, Kuhnemund M, Voytyuk I (2020) Spatial transcriptomics and in situ sequencing to study Alzheimer’s disease. Cell 182(976–991):e919

[22] Chow HM, Shi M, Cheng A, Gao Y, Chen G, Song X, So RWL, Zhang J, Herrup K (2019) Age-related hyperinsulinemia leads to insulin resistance in neurons and cell-cycle-induced senescence. Nat Neurosci 22:1806–1819

[23] Colman RJ (2018) Non-human primates as a model for aging. Biochim Biophys Acta Mol Basis Dis 1864:2733–2741

[24] Costa-Mattioli M, Walter P (2020) The integrated stress response: from mechanism to disease. Science 368:eaat5314

[25] De Cecco M, Ito T, Petrashen AP, Elias AE, Skvir NJ, Criscione SW, Caligiana A, Brocculi G, Adney EM, Boeke JD(2019) L1 drives IFN in senescent cells and promotes age-associated inflammation. Nature 566:73–78

[26] Debacq-Chainiaux F, Erusalimsky JD, Campisi J, Toussaint O (2009) Protocols to detect senescence-associated beta-galactosidase (SA-βgal) activity, a biomarker of senescent cells in culture and in vivo. Nat Protoc 4:1798–1806

[27] Deng L, Ren R, Liu Z, Song M, Li J, Wu Z, Ren X, Fu L, Li W, Zhang W(2019) Stabilizing heterochromatin by DGCR8 alleviates senescence and osteoarthritis. Nat Commun 10:3329

[28] Diao Z, Ji Q, Wu Z, Zhang W, Cai Y, Wang Z, Hu J, Liu Z, Wang Q, Bi S (2021) SIRT3 consolidates heterochromatin and counteracts senescence. Nucleic Acids Res 49:4203–4219

[29] Dou Z, Xu C, Donahue G, Shimi T, Pan JA, Zhu J, Ivanov A, Capell BC, Drake AM, Shah PP (2015) Autophagy mediates degradation of nuclear lamina. Nature 527:105–109

[30] Dulken BW, Buckley MT, Navarro Negredo P, Saligrama N, Cayrol R, Leeman DS, George BM, Boutet SC, Hebestreit K, Pluvinage JV (2019) Single-cell analysis reveals T cell infiltration in old neurogenic niches. Nature 571:205–210

[31] Efremova M, Vento-Tormo M, Teichmann SA, Vento-Tormo R (2020) Cell PhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes. Nat Protoc 15:1484–1506

[32] Encinas JM, Michurina TV, Peunova N, Park JH, Tordo J, Peterson DA, Fishell G, Koulakov A, Enikolopov G (2011) Division-coupled astrocytic differentiation and age-related depletion of neural stem cells in the adult hippocampus. Cell Stem Cell 8:566–579

[33] Fan X, Wheatley EG, Villeda SA (2017) Mechanisms of hippocampal aging and the potential for rejuvenation. Annu Rev Neurosci 40:251–272

[34] Frost B (2016) Alzheimer’s disease: an acquired neurodegenerative laminopathy. Nucleus 7:275–283

[35] Geng L, Liu Z, Wang S, Sun S, Ma S, Liu X, Chan P, Sun L, Song M, Zhang W (2019) Low-dose quercetin positively regulates mouse healthspan. Protein Cell 10:770–775

[36] Geutskens SB, Hordijk PL, van Hennik PB (2010) The chemorepellent Slit3 promotes monocyte migration. J Immunol 185:7691–7698

[37] Giacobini E, Gold G (2013) Alzheimer disease therapy–moving from amyloid-beta to tau. Nat Rev Neurol 9:677–686

[38] Gu SX, Tyagi T, Jain K, Gu VW, Lee SH, Hwa JM, Kwan JM, Krause DS, Lee AI, Halene S(2021) Thrombocytopathy and endotheliopathy: crucial contributors to COVID-19 thromboinflammation. Nat Rev Cardiol 18:194–209

[39] Gust J, Hay KA, Hanafi LA, Li D, Myerson D, Gonzalez-Cuyar LF, Yeung C, Liles WC, Wurfel M, Lopez JA (2017) Endothelial activation and blood-brain barrier disruption in neurotoxicity after adoptive immunotherapy with CD19 CAR-T cells. Cancer Discov 7:1404–1419

[40] Habib N, Li Y, Heidenreich M, Swiech L, Avraham-Davidi I, Trombetta JJ, Hession C, Zhang F, Regev A (2016) Div-Seq: single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. Science 353:925–928

[41] Harris L, Genovesi LA, Gronostajski RM, Wainwright BJ, Piper M (2015) Nuclear factor one transcription factors: divergent functions in developmental versus adult stem cell populations. Dev Dyn 244:227–238

[42] He G, Luo W, Li P, Remmers C, Netzer WJ, Hendrick J, Bettayeb K, Flajolet M, Gorelick F, Wennogle LP (2010) Gammasecretase activating protein is a therapeutic target for Alzheimer’s disease. Nature 467:95–98

[43] He X, Memczak S, Qu J, Belmonte JCI, Liu GH (2020) Single-cell omics in ageing: a young and growing field. Nat Metab 2:293–302

[44] Head D, Snyder AZ, Girton LE, Morris JC, Buckner RL (2005) Frontal-hippocampal double dissociation between normal aging and Alzheimer’s disease. Cereb Cortex 15:732–739

[45] Herculano-Houzel S (2009) The human brain in numbers: a linearly scaled-up primate brain. Front Hum Neurosci 3:31

[46] Hoppe B, Dorner T (2012) Coagulation and the fibrin network in rheumatic disease: a role beyond haemostasis. Nat Rev Rheumatol 8:738–746

[47] Hou Y, Dan X, Babbar M, Wei Y, Hasselbalch SG, Croteau DL, Bohr VA (2019) Ageing as a risk factor for neurodegenerative disease. Nat Rev Neurol 15:565–581

[48] Hu H, Ji Q, Song M, Ren J, Liu Z, Wang Z, Liu X, Yan K, Hu J, Jing Y (2020) ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin. Nucleic Acids Res 48:6001–6018

[49] Hwang IK, Park JH, Lee TK, Kim DW, Yoo KY, Ahn JH, Kim YH, Cho JH, Kim YM, Won MH (2017) CD74-immunoreactive activated M1 microglia are shown late in the gerbil hippocampal CA1 region following transient cerebral ischemia. Mol Med Rep 15:4148–4154

[50] Ibrayeva A, Bay M, Pu E, Jorg DJ, Peng L, Jun H, Zhang N, Aaron D, Lin C, Resler G (2021) Early stem cell aging in the mature brain. Cell Stem Cell. https://doi.org/10.1016/j.stem.2021.03.018

[51] Jin WN, Shi K, He W, Sun JH, Van Kaer L, Shi FD, Liu Q (2021) Neuroblast senescence in the aged brain augments natural killer cell cytotoxicity leading to impaired neurogenesis and cognition. Nat Neurosci 24:61–73

[52] Kempermann G, Song H, Gage FH (2015) Neurogenesis in the Adult Hippocampus. Cold Spring Harb Perspect Biol 7:a018812

[53] Keren-Shaul H, Spinrad A, Weiner A, Matcovitch-Natan O, Dvir-Szternfeld R, Ulland TK, David E, Baruch K, Lara-Astaiso D, Toth B (2017) A unique microglia type associated with restricting development of Alzheimer’s disease. Cell 169:1276–1290

[54] Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA (2016) Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc 11:499–524

[55] Kruithof EK, Dunoyer-Geindre S (2014) Human tissue-type plasminogen activator. Thromb Haemost 112:243–254

[56] Kuhn HG, Toda T, Gage FH (2018) Adult hippocampal neurogenesis: a coming-of-age story. J Neurosci 38:10401–10410

[57] Leng F, Edison P (2021) Neuroinflammation and microglial activation in Alzheimer disease: where do we go from here? Nat Rev Neurol 17:157–172

[58] Leuner B, Kozorovitskiy Y, Gross CG, Gould E (2007) Diminished adult neurogenesis in the marmoset brain precedes old age. Proc Natl Acad Sci USA 104:17169–17173

[59] Leyns CEG, Ulrich JD, Finn MB, Stewart FR, Koscal LJ, Remolina Serrano J, Robinson GO, Anderson E, Colonna M, Holtzman DM (2017) TREM2 deficiency attenuates neuroinflammation and protects against neurodegeneration in a mouse model of tauopathy. Proc Natl Acad Sci USA 114:11524–11529

[60] Li R, Lindholm K, Yang LB, Yue X, Citron M, Yan R, Beach T, Sue L, Sabbagh M, Cai H(2004) Amyloid beta peptide load is correlated with increased beta-secretase activity in sporadic Alzheimer’s disease patients. Proc Natl Acad Sci USA 101:3632–3637

[61] Li D, Takeda N, Jain R, Manderfield LJ, Liu F, Li L, Anderson SA, Epstein JA (2015) Hopx distinguishes hippocampal from lateral ventricle neural stem cells. Stem Cell Res 15:522–529

[62] Li J, Zheng Y, Yan P, Song M, Wang S, Sun L, Liu Z, Ma S, Belmonte JCI, Chan P(2020) A single-cell transcriptomic atlas of primate pancreatic islet aging. Natl Sci Rev 8(2):127

[63] Liang C, Liu Z, Song M, Li W, Wu Z, Wang Z, Wang Q, Wang S, Yan K, Sun L(2021) Stabilization of heterochromatin by CLOCK promotes stem cell rejuvenation and cartilage regeneration. Cell Res 31:187–205

[64] Linnartz-Gerlach B, Bodea LG, Klaus C, Ginolhac A, Halder R, Sinkkonen L, Walter J, Colonna M, Neumann H (2019) TREM2 triggers microglial density and age-related neuronal loss. Glia 67:539–550

[65] Liu GH, Qu J, Suzuki K, Nivet E, Li M, Montserrat N, Yi F, Xu X, Ruiz S, Zhang W(2012) Progressive degeneration of human neural stem cells caused by pathogenic LRRK2. Nature 491:603–607

[66] Liu X, Liu Z, Sun L, Ren J, Wu Z, Jiang X, Ji Q, Wang Q,Fan Y, Cai Y (2021) Resurrection of human endogenous retroviruses during aging reinforces senescence. bioRxiv. https://doi.org/10. 1101/2021.02.22.432260v1.abstract

[67] Lubbe SJ, Bustos B, Hu J, Krainc D, Joseph T, Hehir J, Tan M, Zhang W, Escott-Price V, Williams NM(2021) Assessing the relationship between monoallelic PRKN mutations and Parkinson’s risk. Human Mol Genet 30:78–86

[68] Ma S, Sun S, Geng L, Song M, Wang W, Ye Y, Ji Q, Zou Z, Wang S, He X (2020a) Caloric restriction reprograms the single-cell transcriptional landscape of rattus norvegicus aging. Cell 180 (984–1001):e1022

[69] Ma S, Sun S, Li J, Fan Y, Qu J, Sun L, Wang S, Zhang Y, Yang S, Liu Z (2020b) Single-cell transcriptomic atlas of primate cardiopulmonary aging. Cell Res 31(4):415–432

[70] Malykhin NV, Bouchard TP, Camicioli R, Coupland NJ (2008) Aging hippocampus and amygdala. NeuroReport 19:543–547

[71] Marcos-Contreras OA, Martinez deLizarrondo S, Bardou I, Orset C, Pruvost M, Anfray A, Frigout Y, Hommet Y, Lebouvier L, Montaner J (2016) Hyperfibrinolysis increases blood-brain barrier permeability by a plasmin- and bradykinin-dependent mechanism. Blood 128:2423–2434

[72] Marques S, Zeisel A, Codeluppi S, van Bruggen D, Mendanha Falcao A, Xiao L, Li H, Haring M, Hochgerner H, Romanov RA (2016) Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Science 352:1326–1329

[73] Martinelli P, Real FX (2019) Mouse models shed light on the SLIT/ ROBO pathway in pancreatic development and cancer. Trends Cancer 5:145–148

[74] Mauffrey P, Tchitchek N, Barroca V, Bemelmans A-P, Firlej V, Allory Y, Roméo P-H, Magnon C (2019) Progenitors from the central nervous system drive neurogenesis in cancer. Nature 569:672–678

[75] McGinnis CS, Murrow LM, Gartner ZJ (2019) DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst 8:329–337.e324

[76] Morrison JH, Baxter MG (2012) The ageing cortical synapse: hallmarks and implications for cognitive decline. Nat Rev Neurosci 13:240–250

[77] Nakamura R, Nakamoto C, Obama H, Durward E, Nakamoto M (2012) Structure-function analysis of Nel, a thrombospondin-1-like glycoprotein involved in neural development and functions. J Biol Chem 287:3282–3291

[78] Navarro Negredo P, Yeo RW, Brunet A (2020) Aging and rejuvenation of neural stem cells and their niches. Cell Stem Cell 27:202–223

[79] Ofengeim D, Yuan J (2013) Regulation of RIP1 kinase signalling at the crossroads of inflammation and cell death. Nat Rev Mol Cell Biol 14:727–736

[80] Ransohoff RM (2016) How neuroinflammation contributes to neurodegeneration. Science 353:777–783

[81] Rivero O, Sich S, Popp S, Schmitt A, Franke B, Lesch KP (2013) Impact of the ADHD-susceptibility gene CDH13 on development and function of brain networks. Eur Neuropsychopharmacol 23:492–507

[82] Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504

[83] Shi Z, Geng Y, Liu J, Zhang H, Zhou L, Lin Q, Yu J, Zhang K, Liu J, Gao X (2018) Single-cell transcriptomics reveals gene signatures and alterations associated with aging in distinct neural stem/progenitor cell subpopulations. Protein Cell 9:351–364

[84] Simon M, Van Meter M, Ablaeva J, Ke Z, Gonzalez RS, Taguchi T, De Cecco M, Leonova KI, Kogan V, Helfand SL (2019) LINE1 derepression in aged wild-type and SIRT6-deficient mice drives inflammation. Cell Metab 29:871–885

[85] Stahl PL, Salmen F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M (2016) Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353:78–82

[86] Su H, Na N, Zhang X, Zhao Y (2017) The biological function and significance of CD74 in immune diseases. Inflamm Res 66:209–216

[87] Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci 102:15545

[88] Sweeney MD, Sagare AP, Zlokovic BV (2018) Blood-brain barrier breakdown in Alzheimer disease and other neurodegenerative disorders. Nat Rev Neurol 14:133–150

[89] Tanaka T, Biancotto A, Moaddel R, Moore AZ, Gonzalez-Freire M, Aon MA, Candia J, Zhang P, Cheung F, Fantoni G(2018) Plasma proteomic signature of age in healthy humans. Aging Cell 17:

[90] Tiensuu H, Haapalainen AM, Karjalainen MK, Pasanen A, Huusko JM, Marttila R, Ojaniemi M, Muglia LJ, Hallman M, Ramet M (2019) Risk of spontaneous preterm birth and fetal growth associates with fetal SLIT2. PLoS Genet 15:e1008107

[91] Tilstra JS, Clauson CL, Niedernhofer LJ, Robbins PD (2011) NFkappaB in aging and disease. Aging Dis 2:449–465

[92] Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL (2014) The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 32:381–386

[93] Ulland TK, Colonna M (2018) TREM2—a key player in microglial biology and Alzheimer disease. Nat Rev Neurol 14:667–675

[94] Vanlandewijck M, He L, Mae MA, Andrae J, Ando K, Del Gaudio F, Nahar K, Lebouvier T, Lavina B, Gouveia L (2018) A molecular atlas of cell types and zonation in the brain vasculature. Nature 554:475–480

[95] Végh MJ, Rausell A, Loos M, Heldring CM, Jurkowski W, van Nierop P, Paliukhovich I, Li KW, del ASol AB, Smit (2014) Hippocampal extracellular matrix levels and stochasticity in synaptic protein expression increase with age and are associated with age-dependent cognitive decline. Mol Cell Proteom 13:2975–2985

[96] Volkman HE, Stetson DB (2014) The enemy within: endogenous retroelements and autoimmune disease. Nat Immunol 15:415–422

[97] Wang L, Song G, Zhang X, Feng T, Pan J, Chen W, Yang M, Bai X, Pang Y, Yu J (2017) PADI2-mediated citrullination promotes prostate cancer progression. Cancer Res 77:5755–5768

[98] Wang S, Zheng Y, Li J, Yu Y, Zhang W, Song M, Liu Z, Min Z, Hu H, Jing Y(2020a) Single-cell transcriptomic atlas of primate ovarian aging. Cell 180(585–600):e519

[99] Wang S, Zheng Y, Li Q, He X, Ren R, Zhang W, Song M, Hu H, Liu F, Sun G(2020b) Deciphering primate retinal aging at singlecell resolution. Protein Cell. https://doi.org/10.1007/s13238-020-00791-x

[100] Wegiel J, Frackowiak J, Mazur-Kolecka B, Schanen NC, Cook EH Jr, Sigman M, Brown WT, Kuchna I, Wegiel J, Nowicki K(2012) Abnormal intracellular accumulation and extracellular Abeta deposition in idiopathic and Dup15q11.2-q13 autism spectrum disorders. PLoS One 7:e35414

[101] Woo MS, Ufer F, Rothammer N, Di Liberto G, Binkle L, Haferkamp U, Sonner JK, Engler JB, Hornig S, Bauer S (2021) Neuronal metabotropic glutamate receptor 8 protects against neurodegeneration in CNS inflammation. J Exp Med. https://doi.org/10.1084/jem.20201290

[102] Wyss-Coray T (2016) Ageing, neurodegeneration and brain rejuvenation. Nature 539:180–186

[103] Yang X, Goh A, Chen SH, Qiu A (2013) Evolution of hippocampal shapes across the human lifespan. Hum Brain Mapp 34:3075–3085

[104] Yang AC, Stevens MY, Chen MB, Lee DP, Stahli D, Gate D, Contrepois K, Chen W, Iram T, Zhang L (2020) Physiological blood-brain transport is impaired with age by a shift in transcytosis. Nature 583:425–430

[105] Young MD, Behjati S (2020) SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. GigaScience 9:giaa151

[106] Yu HC, Tung CH, Huang KY, Huang HB, Lu MC (2020) The essential role of peptidylarginine deiminases 2 for cytokines secretion, apoptosis, and cell adhesion in macrophage. Int J Mol Sci 21:5720

[107] Yuan J, Amin P, Ofengeim D (2019) Necroptosis and RIPK1-mediated neuroinflammation in CNS diseases. Nat Rev Neurosci 20:19–33

[108] Zenker M, Bunt J, Schanze I, Schanze D, Piper M, Priolo M, Gerkes EH, Gronostajski RM, Richards LJ, Vogt J (2019) Variants in nuclear factor I genes influence growth and development. Am J Med Genet C Semin Med Genet 181:611–626

[109] Zhang W, Li J, Suzuki K, Qu J, Wang P, Zhou J, Liu X, Ren R, Xu X, Ocampo A (2015) Aging stem cells. A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging. Science 348:1160–1163

[110] Zhang W, Wan H, Feng G, Qu J, Wang J, Jing Y, Ren R, Liu Z, Zhang L, Chen Z (2018) SIRT6 deficiency results in developmental retardation in cynomolgus monkeys. Nature 560:661–665

[111] Zhang K, Wang Y, Fan T, Zeng C, Sun ZS (2020a) The p21-activated kinases in neural cytoskeletal remodeling and related neurological disorders. Protein Cell. https://doi.org/10.1007/s13238-020-00812-9

[112] Zhang W, Qu J, Liu GH, Belmonte JCI (2020b) The ageing epigenome and its rejuvenation. Nat Rev Mol Cell Biol 21:137–150

[113] Zhang W, Zhang S, Yan P, Ren J, Song M, Li J, Lei J, Pan H, Wang S, Ma X (2020c) A single-cell transcriptomic landscape of primate arterial aging. Nat Commun 11:2202

[114] Zhong S, Ding W, Sun L, Lu Y, Dong H, Fan X, Liu Z, Chen R, Zhang S, Ma Q(2020) Decoding the development of the human hippocampus. Nature 577:531–536

[115] Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, Benner C, Chanda SK (2019) Metascape provides a biologistoriented resource for the analysis of systems-level datasets. Nat Commun 10:1523

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