Genomic approach to selective vulnerability of the hippocampus in brain ischemia–hypoxia

Aarts, 2003, Novel treatment of excitotoxicity: targeted disruption of intracellular signalling from glutamate receptors, Biochem Pharmacol, 66, 877, 10.1016/S0006-2952(03)00297-1

Abe, 2004, Induced hippocampal neuron protection in an optimized gerbil ischemia model: insult thresholds for tolerance induction and altered gene expression defined by ischemic depolarization, J Cereb Blood Flow Metab, 24, 84, 10.1097/01.WCB.0000098607.42140.4B

Abe, 1995, Ischemic delayed neuronal death. A mitochondrial hypothesis, Stroke, 26, 1478, 10.1161/01.STR.26.8.1478

Adhami, 2007, The roles of autophagy in cerebral ischemia, Autophagy, 3, 42, 10.4161/auto.3412

Allen, 2011, SK2 channels are neuroprotective for ischemia-induced neuronal cell death, J Cereb Blood Flow Metab, 31, 2302, 10.1038/jcbfm.2011.90

Andersen, 2006

Arabadzisz, 1999, Changes in excitatory and inhibitory circuits of the rat hippocampus 12–14months after complete forebrain ischemia, Neuroscience, 92, 27, 10.1016/S0306-4522(98)00736-2

Asai, 2002, Selective proteasomal dysfunction in the hippocampal CA1 region after transient forebrain ischemia, J Cereb Blood Flow Metab, 22, 705, 10.1097/00004647-200206000-00009

Ashton, 1989, Dorsal–ventral gradient in vulnerability of CA1 hippocampus to ischemia: a combined histological and electrophysiological study, Brain Res, 487, 368, 10.1016/0006-8993(89)90842-1

Attwell, 2002, The neural basis of functional brain imaging signals, Trends Neurosci, 25, 621, 10.1016/S0166-2236(02)02264-6

Bano, 2007, Ca2+ signals and neuronal death in brain ischemia, Stroke, 38, 674, 10.1161/01.STR.0000256294.46009.29

Benveniste, 1984, Elevation of the extracellular concentrations of glutamate and aspartate in rat hippocampus during transient cerebral ischemia monitored by intracerebral microdialysis, J Neurochem, 43, 1369, 10.1111/j.1471-4159.1984.tb05396.x

Berger, 1994, Distribution and morphological characteristics of oligodendrocytes in the rat hippocampus in situ and in vitro: an immunocytochemical study with the monoclonal Rip antibody, J Neurocytol, 23, 61, 10.1007/BF01189817

Bernaudin, 1998, Selective neuronal vulnerability and specific glial reactions in hippocampal and neocortical organotypic cultures submitted to ischemia, Exp Neurol, 150, 30, 10.1006/exnr.1997.6728

Bernaudin, 2002, Brain genomic response following hypoxia and re-oxygenation in the neonatal rat. Identification of genes that might contribute to hypoxia-induced ischemic tolerance, J Biol Chem, 277, 39728, 10.1074/jbc.M204619200

Böttiger, 1998, Neuronal stress response and neuronal cell damage after cardiocirculatory arrest in rats, J Cereb Blood Flow Metab, 18, 1077, 10.1097/00004647-199810000-00004

Böttiger, 1999, Global cerebral ischemia due to cardiocirculatory arrest in mice causes neuronal degeneration and early induction of transcription factor genes in the hippocampus, Brain Res Mol Brain Res, 65, 135, 10.1016/S0169-328X(98)00298-8

Bramlett, 2004, Pathophysiology of cerebral ischemia and brain trauma: similarities and differences, J Cereb Blood Flow Metab, 24, 133, 10.1097/01.WCB.0000111614.19196.04

Brierley, 1984, Hypoxia and vascular disorders of the central nervous system, 125

Butler, 2010, Selective vulnerability of hippocampal cornu ammonis 1 pyramidal cells to excitotoxic insult is associated with the expression of polyamine-sensitive N-methyl-d-asparate-type glutamate receptors, Neuroscience, 165, 525, 10.1016/j.neuroscience.2009.10.018

Cao, 2003, Translocation of apoptosis-inducing factor in vulnerable neurons after transient cerebral ischemia and in neuronal cultures after oxygen-glucose deprivation, J Cereb Blood Flow Metab, 23, 1137, 10.1097/01.WCB.0000087090.01171.E7

Cavaglia, 2001, Regional variation in brain capillary density and vascular response to ischemia, Brain Res, 910, 81, 10.1016/S0006-8993(01)02637-3

Chan, 2001, Reactive oxygen radicals in signaling and damage in the ischemic brain, J Cereb Blood Flow Metab, 21, 2, 10.1097/00004647-200101000-00002

Charriaut-Marlangue, 1996, Apoptotic features of selective neuronal death in ischemia, epilepsy and gp 120 toxicity, Trends Neurosci, 19, 109, 10.1016/S0166-2236(96)80039-7

Chaussenot, 2011, Neurologic features and genotype–phenotype correlation in Wolfram syndrome, Ann Neurol, 69, 501, 10.1002/ana.22160

Chen, 1996, Expression of the apoptosis-effector gene, Bax, is up-regulated in vulnerable hippocampal CA1 neurons following global ischemia, J Neurochem, 67, 64, 10.1046/j.1471-4159.1996.67010064.x

Chen, 1998, Induction of caspase-3-like protease may mediate delayed neuronal death in the hippocampus after transient cerebral ischemia, J Neurosci, 18, 4914, 10.1523/JNEUROSCI.18-13-04914.1998

Choi, 1996, Ischemia-induced neuronal apoptosis, Curr Opin Neurobiol, 6, 667, 10.1016/S0959-4388(96)80101-2

Chopp, 1991, Neuronal injury and expression of 72-kDa heat-shock protein after forebrain ischemia in the rat, Acta Neuropathol, 83, 66, 10.1007/BF00294432

Chou, 2013, Genetic susceptibility for ischemic infarction and arteriolosclerosis based on neuropathologic evaluations, Cerebrovasc Dis, 36, 181, 10.1159/000352054

Chu, 2012, Constructing the angiome: a global angiogenesis protein interaction network, Physiol Genomics, 44, 915, 10.1152/physiolgenomics.00181.2011

Colbourne, 1999, Electron microscopic evidence against apoptosis as the mechanism of neuronal death in global ischemia, J Neurosci, 19, 4200, 10.1523/JNEUROSCI.19-11-04200.1999

Coultrap, 2005, Differential expression of NMDA receptor subunits and splice variants among the CA1, CA3 and dentate gyrus of the adult rat, Brain Res Mol Brain Res, 135, 104, 10.1016/j.molbrainres.2004.12.005

Coyle, 1976, Vascular patterns of the rat hippocampal formation, Exp Neurol, 52, 447, 10.1016/0014-4886(76)90216-8

Datson, 2004, Expression profiling in laser-microdissected hippocampal subregions in rat brain reveals large subregion-specific differences in expression, Eur J Neurosci, 20, 2541, 10.1111/j.1460-9568.2004.03738.x

de Oliveira, 2012, Eag1, Eag2, and SK3 potassium channel expression in the rat hippocampus after global transient brain ischemia, J Neurosci Res, 90, 632, 10.1002/jnr.22772

DeGracia, 2007, Irreversible translation arrest in the reperfused brain, J Cereb Blood Flow Metab, 27, 875, 10.1038/sj.jcbfm.9600388

DeGracia, 1997, Effect of brain ischemia and reperfusion on the localization of phosphorylated eukaryotic initiation factor 2 alpha, J Cereb Blood Flow Metab, 17, 1291, 10.1097/00004647-199712000-00004

DeGracia, 2008, Translation arrest and ribonomics in post-ischemic brain: layers and layers of players, J Neurochem, 106, 2288, 10.1111/j.1471-4159.2008.05561.x

Dela Cruz, 2014, Differential distribution of hypoxia-inducible factor 1-beta (ARNT or ARNT2) in mouse substantia nigra and ventral tegmental area, J Chem Neuroanat, 61–62, 64, 10.1016/j.jchemneu.2014.07.001

Dietrich, 1993, Intraischemic but not postischemic brain hypothermia protects chronically following global forebrain ischemia in rats, J Cereb Blood Flow Metab, 13, 541, 10.1038/jcbfm.1993.71

Dmitrieva, 2008, Expression of sphingomyelin synthase 1 gene in rat brain focal ischemia, Brain Res, 1188, 222, 10.1016/j.brainres.2007.10.056

Dong, 2009, Genomic-anatomic evidence for distinct functional domains in hippocampal field CA1, Proc Natl Acad Sci U S A, 106, 11794, 10.1073/pnas.0812608106

Duvernoy, 2013

Fanselow, 2010, Are the dorsal and ventral hippocampus functionally distinct structures?, Neuron, 65, 7, 10.1016/j.neuron.2009.11.031

Ferrand-Drake, 1999, The time-course of DNA fragmentation in the choroid plexus and the CA1 region following transient global ischemia in the rat brain. The effect of intra-ischemic hypothermia, Neuroscience, 93, 537, 10.1016/S0306-4522(99)00181-5

Ferrer, 2003, Signaling of cell death and cell survival following focal cerebral ischemia: life and death struggle in the penumbra, J Neuropathol Exp Neurol, 62, 329, 10.1093/jnen/62.4.329

Fiskum, 2000, Mitochondrial participation in ischemic and traumatic neural cell death, J Neurotrauma, 17, 843, 10.1089/neu.2000.17.843

Forder, 2009, Postsynaptic mechanisms of excitotoxicity: involvement of postsynaptic density proteins, radicals, and oxidant molecules, Neuroscience, 158, 293, 10.1016/j.neuroscience.2008.10.021

Friberg, 1999, Differences in the activation of the mitochondrial permeability transition among brain regions in the rat correlate with selective vulnerability, J Neurochem, 72, 2488, 10.1046/j.1471-4159.1999.0722488.x

Gao, 2002, Decreased large conductance Ca(2+)-activated K(+) channel activity in dissociated CA1 hippocampal neurons in rats exposed to perinatal and postnatal hypoxia, Neurosci Lett, 332, 163, 10.1016/S0304-3940(02)00946-1

Ghorbel, 2003, Cross-talk between hypoxic and circadian pathways: cooperative roles for hypoxia-inducible factor 1alpha and CLOCK in transcriptional activation of the vasopressin gene, Mol Cell Neurosci, 22, 396, 10.1016/S1044-7431(02)00019-2

Giannakopoulos, 2009, Pathological substrates of cognitive decline in Alzheimer’s disease, Front Neurol Neurosci, 24, 20, 10.1159/000197881

Gidday, 2006, Cerebral preconditioning and ischaemic tolerance, Nat Rev Neurosci, 7, 437, 10.1038/nrn1927

Gilbert, 2003, DNA microarray analysis of hippocampal gene expression measured twelve hours after hypoxia-ischemia in the mouse, J Cereb Blood Flow Metab, 23, 1195, 10.1097/01.WCB.0000088763.02615.79

Gillardon, 1997, Activation of CPP-32 protease in hippocampal neurons following ischemia and epilepsy, Brain Res Mol Brain Res, 50, 16, 10.1016/S0169-328X(97)00162-9

Gillardon, 1999, Expression of cell death-associated phospho-c-Jun and p53-activated gene 608 in hippocampal CA1 neurons following global ischemia, Brain Res Mol Brain Res, 73, 138, 10.1016/S0169-328X(99)00251-X

Ginsberg, 2008, Neuroprotection for ischemic stroke: past, present and future, Neuropharmacology, 55, 363, 10.1016/j.neuropharm.2007.12.007

Ginsberg, 2005, Expression profile analysis within the human hippocampus: comparison of CA1 and CA3 pyramidal neurons, J Comp Neurol, 487, 107, 10.1002/cne.20535

Gorter, 1997, Global ischemia induces downregulation of Glur2 mRNA and increases AMPA receptor-mediated Ca2+ influx in hippocampal CA1 neurons of gerbil, J Neurosci, 17, 6179, 10.1523/JNEUROSCI.17-16-06179.1997

Graham, 2001, Programmed cell death in cerebral ischemia, J Cereb Blood Flow Metab, 21, 99, 10.1097/00004647-200102000-00001

Greene, 2009, Quantitative transcriptional neuroanatomy of the rat hippocampus: evidence for wide-ranging, pathway-specific heterogeneity among three principal cell layers, Hippocampus, 19, 253, 10.1002/hipo.20502

Gubits, 1993, Immediate early gene induction after neonatal hypoxia-ischemia, Brain Res Mol Brain Res, 18, 228, 10.1016/0169-328X(93)90194-T

Hall, 2014, Capillary pericytes regulate cerebral blood flow in health and disease, Nature, 508, 55, 10.1038/nature13165

Hallmayer, 1985, Low dose of barbiturates for prevention of hippocampal lesions after brief ischemic episodes, Acta Neuropathol, 68, 27, 10.1007/BF00688952

Harb, 2013, In vivo imaging of cerebral microvascular plasticity from birth to death, J Cereb Blood Flow Metab, 33, 146, 10.1038/jcbfm.2012.152

Hardingham, 2009, Coupling of the NMDA receptor to neuroprotective and neurodestructive events, Biochem Soc Trans, 37, 1147, 10.1042/BST0371147

Hawrylycz, 2012, An anatomically comprehensive atlas of the adult human brain transcriptome, Nature, 489, 391, 10.1038/nature11405

Hayashi, 2003, Temporal profile of angiogenesis and expression of related genes in the brain after ischemia, J Cereb Blood Flow Metab, 23, 166, 10.1097/00004647-200302000-00004

Hedtjärn, 2004, Global gene expression in the immature brain after hypoxia–ischemia, J Cereb Blood Flow Metab, 24, 1317, 10.1097/01.WCB.0000141558.40491.75

Hill, 2012, Intracerebral chondroitinase ABC and heparan sulfate proteoglycan glypican improve outcome from chronic stroke in rats, Proc Natl Acad Sci U S A, 109, 9155, 10.1073/pnas.1205697109

Honkaniemi, 1996, Global ischemia induces apoptosis-associated genes in hippocampus, Brain Res Mol Brain Res, 42, 79, 10.1016/S0169-328X(96)00121-0

Honkaniemi, 1997, Expression of zinc finger immediate early genes in rat brain after permanent middle cerebral artery occlusion, J Cereb Blood Flow Metab, 17, 636, 10.1097/00004647-199706000-00005

Hou, 2002, Molecular mechanisms of cerebral ischemia-induced neuronal death, Int Rev Cytol, 221, 93, 10.1016/S0074-7696(02)21011-6

Hsu, 1993, Vulnerability of mossy fiber targets in the rat hippocampus to forebrain ischemia, J Neurosci, 13, 3964, 10.1523/JNEUROSCI.13-09-03964.1993

Huang, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat Protoc, 4, 44, 10.1038/nprot.2008.211

Huang, 2013, Loss of cell adhesion molecule CHL1 improves homeostatic adaptation and survival in hypoxic stress, Cell Death Dis, 4, e768, 10.1038/cddis.2013.284

Ide, 1999, Ubiquitin stress response in postischemic hippocampal neurons under nontolerant and tolerant conditions, J Cereb Blood Flow Metab, 19, 750, 10.1097/00004647-199907000-00004

Iliff, 2012, A paravascular pathway facilitates CSF flow through the brain parenchyma and the clearance of interstitial solutes, including amyloid β, Sci Transl Med, 4, 10.1126/scitranslmed.3003748

Ingraham, 2008, Aging reduces hypoxia-induced microvascular growth in the rodent hippocampus, J Gerontol A Biol Sci Med Sci, 63, 12, 10.1093/gerona/63.1.12

Ito, 1975, Experimental cerebral ischemia in mongolian gerbils. I. Light microscopic observations, Acta Neuropathol, 32, 209, 10.1007/BF00696570

Iwabuchi, 2014, Characterization of the ubiquitin-modified proteome regulated by transient forebrain ischemia, J Cereb Blood Flow Metab, 34, 425, 10.1038/jcbfm.2013.210

Jamison, 2008, Persistent redistribution of poly-adenylated mRNAs correlates with translation arrest and cell death following global brain ischemia and reperfusion, Neuroscience, 154, 504, 10.1016/j.neuroscience.2008.03.057

Jin, 1999, In situ detection of neuronal DNA strand breaks using the Klenow fragment of DNA polymerase I reveals different mechanisms of neuron death after global cerebral ischemia, J Neurochem, 72, 1204, 10.1046/j.1471-4159.1999.0721204.x

Jin, 2000, Induction of vascular endothelial growth factor and hypoxia-inducible factor-1alpha by global ischemia in 7rat brain, Neuroscience, 99, 577, 10.1016/S0306-4522(00)00207-4

Jin, 2001, Microarray analysis of hippocampal gene expression in global cerebral ischemia, Ann Neurol, 50, 93, 10.1002/ana.1073

Jørgensen, 1993, Microglial and astroglial reactions to ischemic and kainic acid-induced lesions of the adult rat hippocampus, Exp Neurol, 120, 70, 10.1006/exnr.1993.1041

Kamme, 2003, Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity, J Neurosci, 23, 3607, 10.1523/JNEUROSCI.23-09-03607.2003

Kang, 2015, Proteogenomics of the human hippocampus: the road ahead, Biochim Biophys Acta, 1854, 788, 10.1016/j.bbapap.2015.02.010

Kato, 1995, An immunohistochemical study of heat shock protein-27 in the hippocampus in a gerbil model of cerebral ischemia and ischemic tolerance, Neuroscience, 68, 65, 10.1016/0306-4522(95)00141-5

Kawahara, 2004, Genome-wide gene expression analysis for induced ischemic tolerance and delayed neuronal death following transient global ischemia in rats, J Cereb Blood Flow Metab, 24, 212, 10.1097/01.WCB.0000106012.33322.A2

Kawai, 1992, Global cerebral ischemia associated with cardiac arrest in the rat: I. Dynamics of early neuronal changes, J Cereb Blood Flow Metab, 12, 238, 10.1038/jcbfm.1992.34

Kindy, 1992, Transient ischemia stimulates glial fibrillary acid protein and vimentin gene expression in the gerbil neocortex, striatum and hippocampus, Brain Res Mol Brain Res, 13, 199, 10.1016/0169-328X(92)90027-9

Kirino, 2002, Ischemic tolerance, J Cereb Blood Flow Metab, 22, 1283, 10.1097/00004647-200211000-00001

Kirino, 1991, Induced tolerance to ischemia in gerbil hippocampal neurons, J Cereb Blood Flow Metab, 11, 299, 10.1038/jcbfm.1991.62

Kleinfeld, 2011, Large-scale automated histology in the pursuit of connectomes, J Neurosci, 31, 16125, 10.1523/JNEUROSCI.4077-11.2011

Kokaia, 1999, GDNF family ligands and receptors are differentially regulated after brain insults in the rat, Eur J Neurosci, 11, 1202, 10.1046/j.1460-9568.1999.00513.x

Kovalenko, 2006, Ischemia-induced modifications in hippocampal CA1 stratum radiatum excitatory synapses, Hippocampus, 16, 814, 10.1002/hipo.20211

Krajewski, 1995, Upregulation of bax protein levels in neurons following cerebral ischemia, J Neurosci, 15, 6364, 10.1523/JNEUROSCI.15-10-06364.1995

Kristián, 1996, Calcium-related damage in ischemia, Life Sci, 59, 357, 10.1016/0024-3205(96)00314-1

Kumar, 2001, Brain ischemia and reperfusion activates the eukaryotic initiation factor 2alpha kinase, PERK, J Neurochem, 77, 1418, 10.1046/j.1471-4159.2001.00387.x

Kunizuka, 1999, Activation of Arc gene, a dendritic immediate early gene, by middle cerebral artery occlusion in rat brain, NeuroReport, 10, 1717, 10.1097/00001756-199906030-00017

Langhauser, 2014, Blocking of α4 integrin does not protect from acute ischemic stroke in mice, Stroke, 45, 1799, 10.1161/STROKEAHA.114.005000

Larsson, 2001, Stereological assessment of vulnerability of immunocytochemically identified striatal and hippocampal neurons after global cerebral ischemia in rats, Brain Res, 913, 117, 10.1016/S0006-8993(01)02762-7

Lee, 1999, The changing landscape of ischaemic brain injury mechanisms, Nature, 399, A7, 10.1038/399a007

Lein, 2004, Defining a molecular atlas of the hippocampus using DNA microarrays and high-throughput in situ hybridization, J Neurosci, 24, 3879, 10.1523/JNEUROSCI.4710-03.2004

Lein, 2007, Genome-wide atlas of gene expression in the adult mouse brain, Nature, 445, 168, 10.1038/nature05453

Lindvall, 1992, Differential regulation of mRNAs for nerve growth factor, brain-derived neurotrophic factor, and neurotrophin 3 in the adult rat brain following cerebral ischemia and hypoglycemic coma, Proc Natl Acad Sci U S A, 89, 648, 10.1073/pnas.89.2.648

Lipton, 1999, Ischemic cell death in brain neurons, Physiol Rev, 79, 1431, 10.1152/physrev.1999.79.4.1431

Liverman, 2004, Response of the brain to oligemia: gene expression, c-Fos, and Nrf2 localization, Brain Res Mol Brain Res, 126, 57, 10.1016/j.molbrainres.2004.02.028

Løkkegaard, 2001, Stereological estimates of number and length of capillaries in subdivisions of the human hippocampal region, Hippocampus, 11, 726, 10.1002/hipo.1088

Lu, 2003, Genomics of the periinfarction cortex after focal cerebral ischemia, J Cereb Blood Flow Metab, 23, 786, 10.1097/01.WCB.0000062340.80057.06

Luuk, 2008, Distribution of Wfs1 protein in the central nervous system of the mouse and its relation to clinical symptoms of the Wolfram syndrome, J Comp Neurol, 509, 642, 10.1002/cne.21777

MacManus, 1997, Gene expression induced by cerebral ischemia: an apoptotic perspective, J Cereb Blood Flow Metab, 17, 815, 10.1038/aj.jcbfm.9590266

MacManus, 1995, Differences in DNA fragmentation following transient cerebral or decapitation ischemia in rats, J Cereb Blood Flow Metab, 15, 728, 10.1038/jcbfm.1995.93

Martin, 1998, Neurodegeneration in excitotoxicity, global cerebral ischemia, and target deprivation: a perspective on the contributions of apoptosis and necrosis, Brain Res Bull, 46, 281, 10.1016/S0361-9230(98)00024-0

Martone, 1999, Modification of postsynaptic densities after transient cerebral ischemia: a quantitative and three-dimensional ultrastructural study, J Neurosci, 19, 1988, 10.1523/JNEUROSCI.19-06-01988.1999

Mattiasson, 2003, Flow cytometric analysis of mitochondria from CA1 and CA3 regions of rat hippocampus reveals differences in permeability transition pore activation, J Neurochem, 87, 532, 10.1046/j.1471-4159.2003.02026.x

Mattson, 2000, Apoptotic and antiapoptotic mechanisms in stroke, Cell Tissue Res, 301, 173, 10.1007/s004419900154

McGahan, 1998, Ischemia-induced CA1 neuronal death is preceded by elevated FosB and Jun expression and reduced NGFI-A and JunB levels, Brain Res Mol Brain Res, 56, 146, 10.1016/S0169-328X(98)00039-4

Mengozzi, 2012, Erythropoietin-induced changes in brain gene expression reveal induction of synaptic plasticity genes in experimental stroke, Proc Natl Acad Sci U S A, 109, 9617, 10.1073/pnas.1200554109

Mies, 1990, Cerebral blood flow, glucose utilization, regional glucose, and ATP content during the maturation period of delayed ischemic injury in gerbil brain, J Cereb Blood Flow Metab, 10, 638, 10.1038/jcbfm.1990.116

Mies, 1993, Cardiac arrest-induced complete cerebral ischaemia in the rat: dynamics of postischaemic in vivo calcium uptake and protein synthesis, Neurol Res, 15, 253, 10.1080/01616412.1993.11740145

Miettinen, 1996, Specific induction of protein kinase C delta subspecies after transient middle cerebral artery occlusion in the rat brain: inhibition by MK-801, J Neurosci, 16, 6236, 10.1523/JNEUROSCI.16-19-06236.1996

Miyamoto, 2000, Hypoxia, hyperoxia, ischemia, and brain necrosis, Neurology, 54, 362, 10.1212/WNL.54.2.362

Morioka, 1991, The microglial reaction in the rat dorsal hippocampus following transient forebrain ischemia, J Cereb Blood Flow Metab, 11, 966, 10.1038/jcbfm.1991.162

Morioka, 1992, Progressive expression of immunomolecules on microglial cells in rat dorsal hippocampus following transient forebrain ischemia, Acta Neuropathol, 83, 149, 10.1007/BF00308474

Moser, 2003, Brain capillaries and cholinergic neurons persist in organotypic brain slices in the absence of blood flow, Eur J Neurosci, 18, 85, 10.1046/j.1460-9568.2003.02728.x

Müller, 2004, Ischemia leads to apoptosis–and necrosis-like neuron death in the ischemic rat hippocampus, Brain Pathol, 14, 415, 10.1111/j.1750-3639.2004.tb00085.x

Müller, 2007, Anti-apoptotic signaling and failure of apoptosis in the ischemic rat hippocampus, Neurobiol Dis, 25, 582, 10.1016/j.nbd.2006.11.009

Nagayama, 2000, Activation of poly(ADP-ribose) polymerase in the rat hippocampus may contribute to cellular recovery following sublethal transient global ischemia, J Neurochem, 74, 1636, 10.1046/j.1471-4159.2000.0741636.x

Nellgård, 1992, Postischemic blockade of AMPA but not NMDA receptors mitigates neuronal damage in the rat brain following transient severe cerebral ischemia, J Cereb Blood Flow Metab, 12, 2, 10.1038/jcbfm.1992.2

Ng, 2009, An anatomic gene expression atlas of the adult mouse brain, Nat Neurosci, 12, 356, 10.1038/nn.2281

Ni, 1998, Transient global forebrain ischemia induces a prolonged expression of the caspase-3 mRNA in rat hippocampal CA1 pyramidal neurons, J Cereb Blood Flow Metab, 18, 248, 10.1097/00004647-199803000-00003

Nikonenko, 2009, Structural features of ischemic damage in the hippocampus, Anat Rec, 292, 1914, 10.1002/ar.20969

Nishino, 2004, Time course and cellular distribution of hsp27 and hsp72 stress protein expression in a quantitative gerbil model of ischemic injury and tolerance: thresholds for hsp72 induction and hilar lesioning in the context of ischemic preconditioning, J Cereb Blood Flow Metab, 24, 167, 10.1097/01.WCB.0000100853.67976.8B

Nitatori, 1995, Delayed neuronal death in the CA1 pyramidal cell layer of the gerbil hippocampus following transient ischemia is apoptosis, J Neurosci, 15, 1001, 10.1523/JNEUROSCI.15-02-01001.1995

Noh, 2005, Blockade of calcium-permeable AMPA receptors protects hippocampal neurons against global ischemia-induced death, Proc Natl Acad Sci U S A, 102, 12230, 10.1073/pnas.0505408102

Northington, 2011, Neuronal cell death in neonatal hypoxia-ischemia, Ann Neurol, 69, 743, 10.1002/ana.22419

Nowak, 1991, Localization of 70 kDa stress protein mRNA induction in gerbil brain after ischemia, J Cereb Blood Flow Metab, 11, 432, 10.1038/jcbfm.1991.84

Obach, 2004, 6-Phosphofructo-2-kinase (pfkfb3) gene promoter contains hypoxia-inducible factor-1 binding sites necessary for transactivation in response to hypoxia, J Biol Chem, 279, 53562, 10.1074/jbc.M406096200

Olsson, 2003, Brain damage in a mouse model of global cerebral ischemia. Effect of NMDA receptor blockade, Brain Res, 982, 260, 10.1016/S0006-8993(03)03014-2

Ordy, 1993, Selective vulnerability and early progression of hippocampal CA1 pyramidal cell degeneration and GFAP-positive astrocyte reactivity in the rat four-vessel occlusion model of transient global ischemia, Exp Neurol, 119, 128, 10.1006/exnr.1993.1014

Ouyang, 2004, Cellular neuroprotective mechanisms in cerebral ischemia: Bcl-2 family proteins and protection of mitochondrial function, Cell Calcium, 36, 303, 10.1016/j.ceca.2004.02.015

Ouyang, 1999, Survival- and death-promoting events after transient cerebral ischemia: phosphorylation of Akt, release of cytochrome C and Activation of caspase-like proteases, J Cereb Blood Flow Metab, 19, 1126, 10.1097/00004647-199910000-00009

Ouyang, 2007, Selective dysfunction of hippocampal CA1 astrocytes contributes to delayed neuronal damage after transient forebrain ischemia, J Neurosci, 27, 4253, 10.1523/JNEUROSCI.0211-07.2007

Pagliarini, 2008, A mitochondrial protein compendium elucidates complex I disease biology, Cell, 134, 112, 10.1016/j.cell.2008.06.016

Paşca, 2014, Generating human neurons in vitro and using them to understand neuropsychiatric disease, Annu Rev Neurosci, 37, 479, 10.1146/annurev-neuro-062012-170328

Paschen, 2003, Shutdown of translation: lethal or protective? Unfolded protein response versus apoptosis, J Cereb Blood Flow Metab, 23, 773, 10.1097/01.WCB.0000075009.47474.F9

Paschen, 2003, Mechanisms of neuronal cell death: diverse roles of calcium in the various subcellular compartments, Cell Calcium, 34, 305, 10.1016/S0143-4160(03)00138-6

Paschen, 2003, Transient cerebral ischemia activates processing of xbp1 messenger RNA indicative of endoplasmic reticulum stress, J Cereb Blood Flow Metab, 23, 449, 10.1097/00004647-200304000-00009

Paschen, 2004, GADD34 protein levels increase after transient ischemia in the cortex but not in the CA1 subfield: implications for post-ischemic recovery of protein synthesis in ischemia-resistant cells, J Neurochem, 90, 694, 10.1111/j.1471-4159.2004.02555.x

Pellegrini-Giampietro, 1992, Switch in glutamate receptor subunit gene expression in CA1 subfield of hippocampus following global ischemia in rats, Proc Natl Acad Sci U S A, 89, 10499, 10.1073/pnas.89.21.10499

Petito, 1987, Delayed hippocampal damage in humans following cardiorespiratory arrest, Neurology, 37, 1281, 10.1212/WNL.37.8.1281

Petito, 1990, The two patterns of reactive astrocytosis in postischemic rat brain, J Cereb Blood Flow Metab, 10, 850, 10.1038/jcbfm.1990.141

Petito, 1997, DNA fragmentation follows delayed neuronal death in CA1 neurons exposed to transient global ischemia in the rat, J Cereb Blood Flow Metab, 17, 967, 10.1097/00004647-199709000-00006

Petito, 1998, Selective glial vulnerability following transient global ischemia in rat brain, J Neuropathol Exp Neurol, 57, 231, 10.1097/00005072-199803000-00004

Pulsinelli, 1982, Temporal profile of neuronal damage in a model of transient forebrain ischemia, Ann Neurol, 11, 491, 10.1002/ana.410110509

Reimer, 2011, Rapid disruption of axon-glial integrity in response to mild cerebral hypoperfusion, J Neurosci, 31, 18185, 10.1523/JNEUROSCI.4936-11.2011

Reis, 2011, Striatal neurons expressing full-length mutant huntingtin exhibit decreased N-cadherin and altered neuritogenesis, Hum Mol Genet, 20, 2344, 10.1093/hmg/ddr127

Rickhag, 2006, Comprehensive regional and temporal gene expression profiling of the rat brain during the first 24h after experimental stroke identifies dynamic ischemia-induced gene expression patterns, and reveals a biphasic activation of genes in surviving tissue, J Neurochem, 96, 14, 10.1111/j.1471-4159.2005.03508.x

Ruan, 2006, Dendritic plasticity of CA1 pyramidal neurons after transient global ischemia, Neuroscience, 140, 191, 10.1016/j.neuroscience.2006.01.039

Ruan, 2007, Morphological heterogeneity of CA1 pyramidal neurons in response to ischemia, J Neurosci Res, 85, 193, 10.1002/jnr.21101

Ruan, 2009, Diversity and fluctuation of spine morphology in CA1 pyramidal neurons after transient global ischemia, J Neurosci Res, 87, 61, 10.1002/jnr.21816

Ruan, 2012, Remodeling of synapses in the CA1 area of the hippocampus after transient global ischemia, Neuroscience, 218, 268, 10.1016/j.neuroscience.2012.05.035

Rytter, 2003, Mouse hippocampal organotypic tissue cultures exposed to in vitro “ischemia” show selective and delayed CA1 damage that is aggravated by glucose, J Cereb Blood Flow Metab, 23, 23, 10.1097/00004647-200301000-00003

Salazar-Colocho, 2008, Involvement of the vascular wall in regenerative processes after CA1 ischemic neuronal death, Int J Dev Neurosci, 26, 541, 10.1016/j.ijdevneu.2008.05.008

Sarajärvi, 2012, Bepridil decreases Aβ and calcium levels in the thalamus after middle cerebral artery occlusion in rats, J Cell Mol Med, 16, 2754, 10.1111/j.1582-4934.2012.01599.x

Schmidt-Kastner, 1988, Distribution of ischemic neuronal damage in the dorsal hippocampus of rat, Acta Neuropathol, 76, 411, 10.1007/BF00686979

Schmidt-Kastner, 2006, Neuroglobin mRNA expression after transient global brain ischemia and prolonged hypoxia in cell culture, Brain Res, 1103, 173, 10.1016/j.brainres.2006.05.047

Schmidt-Kastner, 2008, Hypoxia-regulated components of the U4/U6.U5 tri-small nuclear riboprotein complex: possible role in autosomal dominant retinitis pigmentosa, Mol Vis, 14, 125

Schmidt-Kastner, 2012, An environmental analysis of genes associated with schizophrenia: hypoxia and vascular factors as interacting elements in the neurodevelopmental model, Mol Psychiatry, 17, 1194, 10.1038/mp.2011.183

Schneider, 2004, Identification of regulated genes during transient cortical ischemia in mice by restriction-mediated differential display (RMDD), Brain Res Mol Brain Res, 124, 20, 10.1016/j.molbrainres.2004.02.002

Schneider, 2004, Identification of regulated genes during permanent focal cerebral ischaemia: characterization of the protein kinase 9b5/MARKL1/MARK4, J Neurochem, 88, 1114, 10.1046/j.1471-4159.2003.02228.x

Schobel, 2013, Imaging patients with psychosis and a mouse model establishes a spreading pattern of hippocampal dysfunction and implicates glutamate as a driver, Neuron, 78, 81, 10.1016/j.neuron.2013.02.011

Scholefield, 2013, Hypothermia for neuroprotection in children after cardiopulmonary arrest, Cochrane Database Syst Rev, 2, 10.1002/14651858.CD009442.pub2

Semenza, 2012, Hypoxia-inducible factors in physiology and medicine, Cell, 148, 399, 10.1016/j.cell.2012.01.021

Siesjö, 1995, Mechanisms of secondary brain damage in global and focal ischemia: a speculative synthesis, J Neurotrauma, 12, 943, 10.1089/neu.1995.12.943

Simon, 1984, Blockade of N-methyl-d-aspartate receptors may protect against ischemic damage in the brain, Science, 226, 850, 10.1126/science.6093256

Simon, 1991, The temporal profile of 72-kDa heat-shock protein expression following global ischemia, J Neurosci, 11, 881, 10.1523/JNEUROSCI.11-03-00881.1991

Small, 2011, A pathophysiological framework of hippocampal dysfunction in ageing and disease, Nat Rev Neurosci, 12, 585, 10.1038/nrn3085

Smith, 1984, The density and distribution of ischemic brain injury in the rat following 2–10min of forebrain ischemia, Acta Neuropathol, 64, 319, 10.1007/BF00690397

Soriano, 2000, Parallel gene expression monitoring using oligonucleotide probe arrays of multiple transcripts with an animal model of focal ischemia, J Cereb Blood Flow Metab, 20, 1045, 10.1097/00004647-200007000-00004

Stenman, 2008, Canonical Wnt signaling regulates organ-specific assembly and differentiation of CNS vasculature, Science, 322, 1247, 10.1126/science.1164594

Sugawara, 1999, Mitochondrial release of cytochrome c corresponds to the selective vulnerability of hippocampal CA1 neurons in rats after transient global cerebral ischemia, J Neurosci, 19, 10.1523/JNEUROSCI.19-22-j0002.1999

Sugawara, 2002, Effects of global ischemia duration on neuronal, astroglial, oligodendroglial, and microglial reactions in the vulnerable hippocampal CA1 subregion in rats, J Neurotrauma, 19, 85, 10.1089/089771502753460268

Sun, 2001, Neuroglobin is up-regulated by and protects neurons from hypoxic-ischemic injury, Proc Natl Acad Sci U S A, 98, 15306, 10.1073/pnas.251466698

Sunkin, 2013, Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system, Nucleic Acids Res, 41, D996, 10.1093/nar/gks1042

Takeda, 2001, WFS1 (Wolfram syndrome 1) gene product: predominant subcellular localization to endoplasmic reticulum in cultured cells and neuronal expression in rat brain, Hum Mol Genet, 10, 477, 10.1093/hmg/10.5.477

Tanaka, 1992, Reaction of astrocytes in the gerbil hippocampus following transient ischemia: immunohistochemical observations with antibodies against glial fibrillary acidic protein, glutamine synthetase, and S-100 protein, Exp Neurol, 116, 264, 10.1016/0014-4886(92)90006-C

Tang, 2002, Genomic responses of the brain to ischemic stroke, intracerebral haemorrhage, kainate seizures, hypoglycemia, and hypoxia, Eur J Neurosci, 15, 1937, 10.1046/j.1460-9568.2002.02030.x

Timsit, 1999, Increased cyclin D1 in vulnerable neurons in the hippocampus after ischaemia and epilepsy: a modulator of in vivo programmed cell death?, Eur J Neurosci, 11, 263, 10.1046/j.1460-9568.1999.00434.x

Tomasevic, 1999, Activation of p53 and its target genes p21(WAF1/Cip1) and PAG608/Wig-1 in ischemic preconditioning, Brain Res Mol Brain Res, 70, 304, 10.1016/S0169-328X(99)00146-1

Torres-Muñoz, 2004, Gene expression profiles in microdissected neurons from human hippocampal subregions, Brain Res Mol Brain Res, 127, 105, 10.1016/j.molbrainres.2004.05.017

Uchino, 1995, Cyclosporin A dramatically ameliorates CA1 hippocampal damage following transient forebrain ischaemia in the rat, Acta Physiol Scand, 155, 469, 10.1111/j.1748-1716.1995.tb09999.x

Ueda, 2005, Protective preconditioning by transient global ischemia in the rat: components of delayed injury progression and lasting protection distinguished by comparisons of depolarization thresholds for cell loss at long survival times, J Cereb Blood Flow Metab, 25, 949, 10.1038/sj.jcbfm.9600107

Vivien, 1998, Evidence of type I and type II transforming growth factor-beta receptors in central nervous tissues: changes induced by focal cerebral ischemia, J Neurochem, 70, 2296, 10.1046/j.1471-4159.1998.70062296.x

Wang, 2005, High intrinsic oxidative stress may underlie selective vulnerability of the hippocampal CA1 region, Brain Res Mol Brain Res, 140, 120, 10.1016/j.molbrainres.2005.07.018

Wang, 2007, Genome-wide transcriptome profiling of region-specific vulnerability to oxidative stress in the hippocampus, Genomics, 90, 201, 10.1016/j.ygeno.2007.03.007

Wang, 2009, Genomic and biochemical approaches in the discovery of mechanisms for selective neuronal vulnerability to oxidative stress, BMC Neurosci, 10, 12, 10.1186/1471-2202-10-12

Wang, 2011, Dynamic variation of genes profiles and pathways in the hippocampus of ischemic mice: a genomic study, Brain Res, 1372, 13, 10.1016/j.brainres.2010.11.099

Wang, 2012, O-GlcNAc cycling mutants modulate proteotoxicity in Caenorhabditis elegans models of human neurodegenerative diseases, Proc Natl Acad Sci U S A, 109, 17669, 10.1073/pnas.1205748109

Widmann, 1991, [14C]leucine incorporation into brain proteins in gerbils after transient ischemia: relationship to selective vulnerability of hippocampus, J Neurochem, 56, 789, 10.1111/j.1471-4159.1991.tb01993.x

Wolf, 1996, NeuN: a useful neuronal marker for diagnostic histopathology, J Histochem Cytochem, 44, 1167, 10.1177/44.10.8813082

Xu, 1997, Elevation of neuronal expression of NAIP reduces ischemic damage in the rat hippocampus, Nat Med, 3, 997, 10.1038/nm0997-997

Yang, 2015, SUMO proteomics to decipher the SUMO-modified proteome regulated by various diseases, Proteomics, 15, 1181, 10.1002/pmic.201400298

Yang, 2008, Transient global cerebral ischemia induces a massive increase in protein sumoylation, J Cereb Blood Flow Metab, 28, 269, 10.1038/sj.jcbfm.9600523

Yang, 2015, Semaphorin-3C signals through Neuropilin-1 and PlexinD1 receptors to inhibit pathological angiogenesis, EMBO Mol Med, 10.15252/emmm.201404922

Yeh, 1998, Upregulation of pleiotrophin gene expression in developing microvasculature, macrophages, and astrocytes after acute ischemic brain injury, J Neurosci, 18, 3699, 10.1523/JNEUROSCI.18-10-03699.1998

Yenari, 2012, Neuroprotective mechanisms of hypothermia in brain ischaemia, Nat Rev Neurosci, 13, 267, 10.1038/nrn3174

Yenari, 2008, Metabolic downregulation: a key to successful neuroprotection?, Stroke, 39, 2910, 10.1161/STROKEAHA.108.514471

Yonekura, 2006, P53 potentiates hippocampal neuronal death caused by global ischemia, J Cereb Blood Flow Metab, 26, 1332, 10.1038/sj.jcbfm.9600293

Yoshida, 2009, Hypoxia enhances the generation of induced pluripotent stem cells, Cell Stem Cell, 5, 237, 10.1016/j.stem.2009.08.001

Zhao, 2001, Transcriptional profiling reveals strict boundaries between hippocampal subregions, J Comp Neurol, 441, 187, 10.1002/cne.1406

Zola-Morgan, 1986, Human amnesia and the medial temporal region: enduring memory impairment following a bilateral lesion limited to field CA1 of the hippocampus, J Neurosci, 6, 2950, 10.1523/JNEUROSCI.06-10-02950.1986