Al Nimer F, Jelcic I, Kempf C, Pieper T, Budka H, Sospedra M, Martin R (2018) Phenotypic and functional complexity of brain-infiltrating T cells in Rasmussen encephalitis. Neurol Neuroimmunol Neuroinflamm 5:e419. https://doi.org/10.1212/NXI.0000000000000419
Article
PubMed
Google Scholar
Alquicira-Hernandez J, Powell JE (2021) Nebulosa recovers single-cell gene expression signals by kernel density estimation. Bioinformatics 37:2485–2487. https://doi.org/10.1093/bioinformatics/btab003
Article
CAS
Google Scholar
Alsegiani AS, Shah ZA (2020) The role of cofilin in age-related neuroinflammation. Neural Regen Res 15:1451–1459. https://doi.org/10.4103/1673-5374.274330
Article
CAS
PubMed
PubMed Central
Google Scholar
Andoh M, Ikegaya Y, Koyama R (2019) Synaptic pruning by microglia in epilepsy. J Clin Med 8:2170. https://doi.org/10.3390/jcm8122170
Article
CAS
PubMed Central
Google Scholar
Andoh M, Koyama R (2021) Microglia regulate synaptic development and plasticity. Dev Neurobiol 81:568–590. https://doi.org/10.1002/dneu.22814
Article
PubMed
PubMed Central
Google Scholar
Audrito V, Messana VG, Deaglio S (2020) NAMPT and NAPRT: two metabolic enzymes with key roles in inflammation. Front Oncol 10:358. https://doi.org/10.3389/fonc.2020.00358
Article
PubMed
PubMed Central
Google Scholar
Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA et al (2021) Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature 598:111–119. https://doi.org/10.1038/s41586-021-03465-8
Article
CAS
PubMed
PubMed Central
Google Scholar
Barker-Haliski M, White HS (2015) Glutamatergic mechanisms associated with seizures and epilepsy. Cold Spring Harb Perspect Med 5:a022863. https://doi.org/10.1101/cshperspect.a022863
Article
CAS
PubMed
PubMed Central
Google Scholar
Benmamar-Badel A, Owens T, Wlodarczyk A (2020) Protective microglial subset in development, aging, and disease: lessons from transcriptomic studies. Front Immunol 11:430. https://doi.org/10.3389/fimmu.2020.00430
Article
CAS
PubMed
PubMed Central
Google Scholar
Bien CG, Tiemeier H, Sassen R, Kuczaty S, Urbach H, von Lehe M, Becker AJ, Bast T, Herkenrath P, Karenfort M et al (2013) Rasmussen encephalitis: incidence and course under randomized therapy with tacrolimus or intravenous immunoglobulins. Epilepsia 54:543–550. https://doi.org/10.1111/epi.12042
Article
CAS
PubMed
Google Scholar
Cepeda C, Chang JW, Owens GC, Huynh MN, Chen JY, Tran C, Vinters HV, Levine MS, Mathern GW (2015) In Rasmussen encephalitis, hemichannels associated with microglial activation are linked to cortical pyramidal neuron coupling: a possible mechanism for cellular hyperexcitability. CNS Neurosci Ther 21:152–163. https://doi.org/10.1111/cns.12352
Article
PubMed
Google Scholar
Chitnis T, Khoury SJ (2003) Role of costimulatory pathways in the pathogenesis of multiple sclerosis and experimental autoimmune encephalomyelitis. J Allergy Clin Immunol 112(837–849):850. https://doi.org/10.1016/j.jaci.2003.08.025
Article
Google Scholar
Clarner T, Janssen K, Nellessen L, Stangel M, Skripuletz T, Krauspe B, Hess F-M, Denecke B, Beutner C, Linnartz-Gerlach B et al (2015) CXCL10 triggers early microglial activation in the cuprizone model. J Immunol 194:3400–3413. https://doi.org/10.4049/jimmunol.1401459
Article
CAS
PubMed
Google Scholar
Czapski GA, Strosznajder JB (2021) Glutamate and GABA in microglia-neuron cross-talk in Alzheimer’s disease. Int J Mol Sci 22:11677. https://doi.org/10.3390/ijms222111677
Article
CAS
PubMed
PubMed Central
Google Scholar
Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10:48. https://doi.org/10.1186/1471-2105-10-48
Article
PubMed
PubMed Central
Google Scholar
Eyo UB, Peng J, Swiatkowski P, Mukherjee A, Bispo A, Wu LJ (2014) Neuronal hyperactivity recruits microglial processes via neuronal NMDA receptors and microglial P2Y12 receptors after status epilepticus. J Neurosci 34:10528–10540. https://doi.org/10.1523/JNEUROSCI.0416-14.2014
Article
CAS
PubMed
PubMed Central
Google Scholar
Fauser S, Elger CE, Woermann F, Bien CG (2022) Rasmussen encephalitis: Predisposing factors and their potential role in unilaterality. Epilepsia 63:108–119. https://doi.org/10.1111/epi.17131
Article
PubMed
Google Scholar
Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK, Miller HW, McElrath MJ, Prlic M et al (2015) MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol 16:278. https://doi.org/10.1186/s13059-015-0844-5
Article
CAS
PubMed
PubMed Central
Google Scholar
Gerrits E, Brouwer N, Kooistra SM, Woodbury ME, Vermeiren Y, Lambourne M, Mulder J, Kummer M, Moller T, Biber K et al (2021) Distinct amyloid-beta and tau-associated microglia profiles in Alzheimer’s disease. Acta Neuropathol 141:681–696. https://doi.org/10.1007/s00401-021-02263-w
Article
CAS
PubMed
PubMed Central
Google Scholar
Ghaleb AM, Bialkowska AB, Snider AJ, Gnatenko DV, Hannun YA, Yang VW, Schmidt VA (2015) IQ motif-containing GTPase-activating protein 2 (IQGAP2) Is a novel regulator of colonic inflammation in mice. PLoS ONE 10:e0129314. https://doi.org/10.1371/journal.pone.0129314
Article
CAS
PubMed
PubMed Central
Google Scholar
Grajchen E, Hendriks JJA, Bogie JFJ (2018) The physiology of foamy phagocytes in multiple sclerosis. Acta Neuropathol Commun 6:124. https://doi.org/10.1186/s40478-018-0628-8
Article
CAS
PubMed
PubMed Central
Google Scholar
Hafemeister C, Satija R (2019) Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol 20:296. https://doi.org/10.1186/s13059-019-1874-1
Article
CAS
PubMed
PubMed Central
Google Scholar
Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M et al (2021) Integrated analysis of multimodal single-cell data. Cell 184(3573–3587):e3529. https://doi.org/10.1016/j.cell.2021.04.048
Article
CAS
Google Scholar
Janova H, Bottcher C, Holtman IR, Regen T, van Rossum D, Gotz A, Ernst AS, Fritsche C, Gertig U, Saiepour N et al (2016) CD14 is a key organizer of microglial responses to CNS infection and injury. Glia 64:635–649. https://doi.org/10.1002/glia.22955
Article
PubMed
Google Scholar
Kanehisa M, Sato Y, Kawashima M (2022) KEGG mapping tools for uncovering hidden features in biological data. Protein Sci 31:47–53. https://doi.org/10.1002/pro.4172
Article
CAS
PubMed
Google Scholar
Karagiannis TT, Monti S, Sebastiani P (2022) Cell type diversity statistic: an entropy-based metric to compare overall cell type composition across samples. Front Genet 13:855076. https://doi.org/10.3389/fgene.2022.855076
Article
CAS
PubMed
PubMed Central
Google Scholar
Kenkhuis B, Somarakis A, de Haan L, Dzyubachyk O, ME IJ, de Miranda N, Lelieveldt BPF, Dijkstra J, van Roon-Mom WMC, Hollt T, et al (2021) Iron loading is a prominent feature of activated microglia in Alzheimer’s disease patients. Acta Neuropathol Commun 9:27. https://doi.org/10.1186/s40478-021-01126-5
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim JE, Ryu HJ, Kim MJ, Kang TC (2014) LIM kinase-2 induces programmed necrotic neuronal death via dysfunction of DRP1-mediated mitochondrial fission. Cell Death Differ 21:1036–1049. https://doi.org/10.1038/cdd.2014.17
Article
CAS
PubMed
PubMed Central
Google Scholar
Koboldt DC, Miller KE, Miller AR, Bush JM, McGrath S, Leraas K, Crist E, Fair S, Schwind W, Wijeratne S et al (2021) PTEN somatic mutations contribute to spectrum of cerebral overgrowth. Brain 144:2971–2978. https://doi.org/10.1093/brain/awab173
Article
PubMed
PubMed Central
Google Scholar
Kowal K, Silver R, Slawinska E, Bielecki M, Chyczewski L, Kowal-Bielecka O (2011) CD163 and its role in inflammation. Folia Histochem Cytobiol 49:365–374. https://doi.org/10.5603/fhc.2011.0052
Article
CAS
PubMed
Google Scholar
Lee-Sayer SSM, Maeshima N, Dougan MN, Dahiya A, Arif AA, Dosanjh M, Maxwell CA, Johnson P (2018) Hyaluronan-binding by CD44 reduces the memory potential of activated murine CD8 T cells. Eur J Immunol 48:803–814. https://doi.org/10.1002/eji.201747263
Article
CAS
PubMed
Google Scholar
Liu T, Zhang L, Joo D, Sun SC (2017) NF-kappaB signaling in inflammation. Signal Transduct Target Ther 2:17023. https://doi.org/10.1038/sigtrans.2017.23
Article
PubMed
PubMed Central
Google Scholar
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8
Article
CAS
PubMed
PubMed Central
Google Scholar
Luan G, Gao Q, Zhai F, Chen Y, Li T (2016) Upregulation of HMGB1, toll-like receptor and RAGE in human Rasmussen’s encephalitis. Epilepsy Res 123:36–49. https://doi.org/10.1016/j.eplepsyres.2016.03.005
Article
CAS
PubMed
Google Scholar
Manenti S, Orrico M, Masciocchi S, Mandelli A, Finardi A, Furlan R (2022) PD-1/PD-L axis in neuroinflammation: new insights. Front Neurol 13:877936. https://doi.org/10.3389/fneur.2022.877936
Article
PubMed
PubMed Central
Google Scholar
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. https://doi.org/10.1016/j.cels.2019.03.003
Article
CAS
Google Scholar
Muzio L, Viotti A, Martino G (2021) Microglia in Neuroinflammation and neurodegeneration: from understanding to therapy frontiers in neuroscience. Frontiers Media SA, City.
Nguyen TTT, Yoon HK, Kim YT, Choi YH, Lee WK, Jin M (2020) Tryptophanyl-tRNA synthetase 1 signals activate TREM-1 via TLR2 and TLR4. Biomolecules 10:1283. https://doi.org/10.3390/biom10091283
Article
CAS
PubMed Central
Google Scholar
Nguyen VT, Benveniste EN (2002) Critical role of tumor necrosis factor-alpha and NF-kappa B in interferon-gamma -induced CD40 expression in microglia/macrophages. J Biol Chem 277:13796–13803. https://doi.org/10.1074/jbc.M111906200
Article
CAS
PubMed
Google Scholar
Oliveira-Nascimento L, Massari P, Wetzler LM (2012) The role of TLR2 in infection and immunity. Front Immunol 3:79. https://doi.org/10.3389/fimmu.2012.00079
Article
PubMed
PubMed Central
Google Scholar
Orsini A, Foiadelli T, Carli N, Costagliola G, Masini B, Bonuccelli A, Savasta S, Peroni D, Consolini R, Striano P (2020) Rasmussen’s encephalitis: from immune pathogenesis towards targeted-therapy. Seizure 81:76–83. https://doi.org/10.1016/j.seizure.2020.07.023
Article
CAS
PubMed
Google Scholar
Owens GC, Chang JW, Huynh MN, Chirwa T, Vinters HV, Mathern GW (2016) Evidence for resident memory T cells in Rasmussen encephalitis. Front Immunol 7:64. https://doi.org/10.3389/fimmu.2016.00064
Article
CAS
PubMed
PubMed Central
Google Scholar
Owens GC, Huynh MN, Chang JW, McArthur DL, Hickey MJ, Vinters HV, Mathern GW, Kruse CA (2013) Differential expression of interferon-gamma and chemokine genes distinguishes Rasmussen encephalitis from cortical dysplasia and provides evidence for an early Th1 immune response. J Neuroinflammation 10:56. https://doi.org/10.1186/1742-2094-10-56
Article
CAS
PubMed
PubMed Central
Google Scholar
Pardo CA, Vining EP, Guo L, Skolasky RL, Carson BS, Freeman JM (2004) The pathology of Rasmussen syndrome: stages of cortical involvement and neuropathological studies in 45 hemispherectomies. Epilepsia 45:516–526. https://doi.org/10.1111/j.0013-9580.2004.33103.x
Article
PubMed
Google Scholar
Park S, Anderson NL, Canaria DA, Olson MR (2021) Granzyme-producing CD4 T cells in cancer and autoimmune disease. Immunohorizons 5:909–917. https://doi.org/10.4049/immunohorizons.2100017
Article
CAS
PubMed
Google Scholar
Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, Trapnell C (2017) Reversed graph embedding resolves complex single-cell trajectories. Nat Methods 14:979–982. https://doi.org/10.1038/nmeth.4402
Article
CAS
PubMed
PubMed Central
Google Scholar
Rafi-Janajreh AQ, Nagarkatti PS, Nagarkatti M (1998) Role of CD44 in CTL and NK cell activity. Front Biosci 3:d665-671. https://doi.org/10.2741/a311
Article
CAS
PubMed
Google Scholar
Rasmussen T, Olszewski J, Lloydsmith D (1958) Focal seizures due to chronic localized encephalitis. Neurology 8:435–445. https://doi.org/10.1212/wnl.8.6.435
Article
CAS
PubMed
Google Scholar
Rostamzadeh D, Haghshenas MR, Daryanoosh F, Samadi M, Hosseini A, Ghaderi A, Mojtahedi Z, Babaloo Z (2019) Altered frequency of CD8(+) CD11c(+) T cells and expression of immunosuppressive molecules in lymphoid organs of mouse model of colorectal cancer. J Cell Physiol 234:11986–11998. https://doi.org/10.1002/jcp.27856
Article
CAS
PubMed
Google Scholar
Roszer T (2015) Understanding the mysterious M2 macrophage through activation markers and effector mechanisms. Mediators Inflamm 2015:816460. https://doi.org/10.1155/2015/816460
Article
CAS
PubMed
PubMed Central
Google Scholar
Schirmer L, Velmeshev D, Holmqvist S, Kaufmann M, Werneburg S, Jung D, Vistnes S, Stockley JH, Young A, Steindel M et al (2019) Neuronal vulnerability and multilineage diversity in multiple sclerosis. Nature 573:75–82. https://doi.org/10.1038/s41586-019-1404-z
Article
CAS
PubMed
PubMed Central
Google Scholar
Schneider-Hohendorf T, Mohan H, Bien CG, Breuer J, Becker A, Gorlich D, Kuhlmann T, Widman G, Herich S, Elpers C et al (2016) CD8(+) T-cell pathogenicity in Rasmussen encephalitis elucidated by large-scale T-cell receptor sequencing. Nat Commun 7:11153. https://doi.org/10.1038/ncomms11153
Article
CAS
PubMed
PubMed Central
Google Scholar
Schwab N, Bien CG, Waschbisch A, Becker A, Vince GH, Dornmair K, Wiendl H (2009) CD8+ T-cell clones dominate brain infiltrates in Rasmussen encephalitis and persist in the periphery. Brain 132:1236–1246. https://doi.org/10.1093/brain/awp003
Article
PubMed
Google Scholar
Schwabenland M, Bruck W, Priller J, Stadelmann C, Lassmann H, Prinz M (2021) Analyzing microglial phenotypes across neuropathologies: a practical guide. Acta Neuropathol 142:923–936. https://doi.org/10.1007/s00401-021-02370-8
Article
PubMed
PubMed Central
Google Scholar
Squair JW, Gautier M, Kathe C, Anderson MA, James ND, Hutson TH, Hudelle R, Qaiser T, Matson KJE, Barraud Q et al (2021) Confronting false discoveries in single-cell differential expression. Nat Commun 12:5692. https://doi.org/10.1038/s41467-021-25960-2
Article
CAS
PubMed
PubMed Central
Google Scholar
Swanson MEV, Murray HC, Ryan B, Faull RLM, Dragunow M, Curtis MA (2020) Quantitative immunohistochemical analysis of myeloid cell marker expression in human cortex captures microglia heterogeneity with anatomical context. Sci Rep 10:11693. https://doi.org/10.1038/s41598-020-68086-z
Article
CAS
PubMed
PubMed Central
Google Scholar
Syed MM, Phulwani NK, Kielian T (2007) Tumor necrosis factor-alpha (TNF-alpha) regulates Toll-like receptor 2 (TLR2) expression in microglia. J Neurochem 103:1461–1471. https://doi.org/10.1111/j.1471-4159.2007.04838.x
Article
CAS
PubMed
Google Scholar
Tang C, Luan G, Li T (2020) Rasmussen’s encephalitis: mechanisms update and potential therapy target. Ther Adv Chronic Dis 11:2040622320971413. https://doi.org/10.1177/2040622320971413
Article
CAS
PubMed
PubMed Central
Google Scholar
Traag VA, Waltman L, van Eck NJ (2019) From Louvain to Leiden: guaranteeing well-connected communities. Sci Rep 9:5233. https://doi.org/10.1038/s41598-019-41695-z
Article
CAS
PubMed
PubMed Central
Google Scholar
Troscher AR, Wimmer I, Quemada-Garrido L, Kock U, Gessl D, Verberk SGS, Martin B, Lassmann H, Bien CG, Bauer J (2019) Microglial nodules provide the environment for pathogenic T cells in human encephalitis. Acta Neuropathol 137:619–635. https://doi.org/10.1007/s00401-019-01958-5
Article
CAS
PubMed
PubMed Central
Google Scholar
Van der Maaten L, Hinton G (2008) Visualizing data using t-SNE. J Mach Learn Res 9(11):2579–2605. http://jmlr.org/papers/v9/vandermaaten08a.html
Varadkar S, Bien CG, Kruse CA, Jensen FE, Bauer J, Pardo CA, Vincent A, Mathern GW, Cross JH (2014) Rasmussen’s encephalitis: clinical features, pathobiology, and treatment advances. Lancet Neurol 13:195–205. https://doi.org/10.1016/S1474-4422(13)70260-6
Article
PubMed
PubMed Central
Google Scholar
Vinay DS, Kwon BS (2010) CD11c+CD8+ T cells: two-faced adaptive immune regulators. Cell Immunol 264:18–22. https://doi.org/10.1016/j.cellimm.2010.05.010
Article
CAS
PubMed
Google Scholar
Walker DG, Lue LF (2015) Immune phenotypes of microglia in human neurodegenerative disease: challenges to detecting microglial polarization in human brains. Alzheimers Res Ther 7:56. https://doi.org/10.1186/s13195-015-0139-9
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang I, Han SJ, Kaur G, Crane C, Parsa AT (2010) The role of microglia in central nervous system immunity and glioma immunology. J Clin Neurosci 17:6–10. https://doi.org/10.1016/j.jocn.2009.05.006
Article
PubMed
Google Scholar
Yang S, Wang J, Brand DD, Zheng SG (2018) Role of TNF-TNF receptor 2 signal in regulatory T cells and its therapeutic implications. Front Immunol 9:784. https://doi.org/10.3389/fimmu.2018.00784
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou Y, Cui C, Ma X, Luo W, Zheng SG, Qiu W (2020) Nuclear factor kappaB (NF-kappaB)-mediated inflammation in multiple sclerosis. Front Immunol 11:391. https://doi.org/10.3389/fimmu.2020.00391
Article
CAS
PubMed
PubMed Central
Google Scholar
Zierfuss B, Weinhofer I, Buda A, Popitsch N, Hess L, Moos V, Hametner S, Kemp S, Kohler W, Forss-Petter S et al (2020) Targeting foam cell formation in inflammatory brain diseases by the histone modifier MS-275. Ann Clin Transl Neurol 7:2161–2177. https://doi.org/10.1002/acn3.51200
Article
CAS
PubMed
PubMed Central
Google Scholar