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Int. J. Mol. Sci. 2014, 15(4), 5596-5622; doi:10.3390/ijms15045596
Published: 1 April 2014
Abstract: Apoptosis triggered by exogenous or endogenous stimuli is a crucial phenomenon to determine the fate of neurons, both in physiological and in pathological conditions. Our previous study established that gastric inhibitory polypeptide (Gip) is a neurotrophic factor capable of preventing apoptosis of cerebellar granule neurons (CGNs), during its pre-commitment phase. In the present study, we conducted whole-genome expression profiling to obtain a comprehensive view of the transcriptional program underlying the rescue effect of Gip in CGNs. By using DNA microarray technology, we identified 65 genes, we named survival related genes, whose expression is significantly de-regulated following Gip treatment. The expression levels of six transcripts were confirmed by real-time quantitative polymerase chain reaction. The proteins encoded by the survival related genes are functionally grouped in the following categories: signal transduction, transcription, cell cycle, chromatin remodeling, cell death, antioxidant activity, ubiquitination, metabolism and cytoskeletal organization. Our data outline that Gip supports CGNs rescue via a molecular framework, orchestrated by a wide spectrum of gene actors, which propagate survival signals and support neuronal viability.
Neuronal apoptosis represents a distinctive mode of programmed cell death that is characterized by an intrinsic suicide program, by which a neuron orchestrates its own destruction. It is characterized by specific biochemical and morphological events, including fragmentation of nuclear DNA, breakdown of the cellular cytoskeleton, cell shrinkage and pyknosis, and the bulging out of the plasma membrane (blebbing) leading to the formation of apoptotic bodies [1,2]. During normal nervous system development, physiologically appropriate neuronal loss contributes to a sculpting process that removes approximately one-half of all neurons born during neurogenesis . Neuronal loss subsequent to this developmental window is physiologically inappropriate for most systems and can contribute to neurological deficits, e.g., neurodegenerative diseases such as Alzheimer’s and Parkinson disease [2,4,5]. Elucidating the molecular mechanisms underlying neuronal apoptosis hence may contribute to our understanding of basic developmental biology and human neuropathology .
Cerebellar granule neurons (CGNs) represent, both in vivo and in vitro, a common model for the study of neuronal apoptosis [7–10]. Primary cultures of CGNs have been extensively utilized to examine the signal transduction mechanisms underlying neuronal apoptosis [11–13]. In this in vitro paradigm, CGNs undergo rapid apoptotic cell death within 24 h after removal of serum and lowering of extracellular potassium from 25 to 5 mM . Apoptosis requires transcription and protein synthesis and becomes irreversible during the first six hours following induction. Before this “commitment point”, CGNs can be rescued by the activation of specific signal transduction pathways or by the treatment with specific neurotrophic factors [8,14–16]. Among these, we have recently showed that gastric inhibitory polypeptide (Gip) exerts a potent anti-apoptotic effect in cultured CGNs .
Gip is a 42-amino acid hormone, belonging to the glucagon superfamily of polypeptides and deriving from a 153-amino acid precursor [17–19]. In addition to its ability to regulate insulin secretion, Gip is known to exert a range of pleiotropic and extra-pancreatic actions [20–30]. Gip and its receptor show a widespread distribution in the central nervous system and have been implicated with neurogenesis, survival, synaptic plasticity and cognitive function [16,31–35]. The ability of Gip to regulate cell viability and apoptosis has been demonstrated in hippocampal and cerebellar granule neurons [16,36,37], as well as in β-cells [38–46] and osteoblasts . Although the survival effects of Gip are initiated by a G-protein-coupled receptor and activate a variety of intracellular second messengers [48–50], these signaling pathways converge into the nucleus and regulate a transcriptional program governing cell life and death, which is still largely unknown. In this study we have used whole-genome expression analysis by DNA microarray technology to identify the complete spectrum of genes and pathways activated by Gip during the commitment phase of apoptosis of CGNs.
2. Results and Discussion
2.1. Whole-Genome Expression Changes Underlying Apoptosis Rescue by Gip
CGNs undergo apoptotic cell death after removal of serum and lowering of extracellular potassium from 25 to 5 mM  and can be rescued by Gip treatment. By using whole-genome oligonucleotide microarrays, we monitored whole gene expression profiles of CGNs six hours after induction of apoptosis or following rescue by a maximal effective dose (100 nM) of Gip.
When gene expression profiles in CGNs 6 h after induction of apoptosis (K5) were compared to those of apoptosis rescued CGNs (K5 + GIP), 65 genes showed significant changes of gene expression. The majority (53/65) of genes differently expressed during rescue by Gip (K5 vs. K5 + Gip) were also differentially expressed following induction of apoptosis (K25 vs. K5). Figure 1 shows the gene expression patterns of rescue genes organized in a hierarchical cluster. Although our data represent the average gene expression from four replicates, we confirmed the reliability of the microarray data by real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR). The expression pattern of four genes (Egr1, Nipal2, Fam171a2, Nptx1; differentially expressed in K5 or K5 + GIP) observed by microarrays closely paralleled the pattern observed using real-time PCR (Table 1).
In the following paragraphs, transcriptional changes implicated in the present study will be discussed within the framework of deregulated gene groups and are represented in Figure 2.
2.2. Deregulated Gene Groups
2.2.1. Signal Transduction
The most numerous group of differentially expressed genes, after treatment of CGNs with Gip, encodes proteins involved in signal transduction, which are mostly up-regulated. To facilitate understanding of how the neuroprotective effect of the Gip could be converted into appropriate cellular responses, we divided the translated products by this gene group into subcellular compartments, including extracellular, transmembrane, cytoplasmic and nuclear molecules (Figure 2).
The extracellular proteins include two neuropeptides, Apelin (Apln) and Chemokine C-X3-C motif ligand 1 (Cx3cl1), and two secretory proteins, Cysteine-rich secretory protein LCCL domain containing 2 (Crispld2) and WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1 (Wfikkn1), which are all up-regulated by Gip treatment.
Apln is a neuropeptide, known to prevent apoptosis in cortical neurons  and protect hippocampal neurons against NMDA receptor-mediated excitotoxicity [52–54]. Apln also enhances the protective effect of VEGF on H2O2-induced motor neuron death, whereas its deficiency accelerates motor neuron degeneration in the SOD1 (G93A) ALS mouse model . Cx3cl1 is a neuron associated chemokine with neuroprotective effects in several in vivo and in vitro models of CNS pathology, including Parkinson’s disease [56–59]. Cx3cl1 attenuates excito-neurotoxicity and inhibits Fas-mediated cell death signaling [60–63]. Crispld2 is involved in neurogenesis, formation of normal neural crest cells and craniofacial development . Wiffkn1 is a key inhibitor of Myostatin, which induces mitochondria-dependent apoptosis in the neuroblastoma cell line SH-SY5Y and slows muscle atrophy in the SOD1 (G93A) mice, an animal model of ALS [65–67].
A large group of transmembrane proteins is differentially expressed following Gip rescue. This group includes one over-expressed transmembrane adaptor protein, Shisa family member 8 (Shisa8), and six metabotropic receptors: Sema domain immunoglobulin domain transmembrane domain and short cytoplasmic domain (Sema4f), Interleukin 17 receptor E (Il-17re), Parathyroid hormone receptor 1 (Pthr1), Olfactory receptor 1462 (Olr1462) and Olfactory receptor 6 (Olr6) and Olfactory receptor 883 (Olr883). All of these metabotropic receptors are over-expressed, with the exception of Olr6 and Olr883.
Antagonizing Wnt and FGF signaling, Shisa8 is necessary for brain development [68,69], whereas interacting with Shisa9 it promotes short-term plasticity . Sema4f, which is a member of the class IV subgroup of the semaphorin family, plays a role in neural development and glutamatergic synaptic plasticity in cultured hippocampal neurons [70,71]. The cytokine membrane receptor Il-17re exerts a great influence on adaptive immune cell recruitment in cases of CNS bacterial infection. High expression levels of Il-17re regulate the cellular mitogenesis via the RAS/MAPK signaling pathway, whereas a deficiency can induce CNS autoimmune disease [72–75]. Activation of the G-protein-coupled receptor Pthr1 elicits neuroprotective effects in rat cerebellar granule cells [76,77], regulating the l-type calcium channel and inhibiting kainic acid-induced excitotoxicity [78,79]. Similarly, Pthr1 expression in medulloblastoma protects from apoptosis . Olr1462, Olr6 and Olr883 are members of the olfactory receptor family and as such play a role in the embryonic development of the human brain. Dysregulation of some cortical olfactory receptors has been associated with Parkinson disease .
Different genes, encoding for cytoplasmic proteins, are up-regulated following Gip treatment. This group includes two members of the phosphatidylinositol signaling pathway, Inositol polyphosphate-4-phosphatase type II (Inpp4b) and Pleckstrin homology domain containing, family O member 1 (Plekho1), one member of the type IV cyclic nucleotide phosphodiesterase (PDE) family, Phosphodiesterase 4B, cAMP-specific (Pde4b) and one serine and threonine-specific protein kinase Zinc finger, MYND-type containing 8 (Zmynd8). Inpp4b plays a neuro-proliferative effect against neurotoxicity induced by aluminium chloride AlCl3 in the experimental model of Crocus sativus L. . High expression levels of Plekho1 appear to play a novel anti-apoptotic role against TNF reverse signaling in THP-1 and HEK293 cells . Conversely low expression levels of Pde4b promote apoptosis in non-neuronal cells, such as the 3-D colonic-crypt  and B-cell model , as well as in the microglial cell line BV-2 . In addition, deregulation in intracellular signaling mediated by PDE4B has been reported in schizophrenia and bipolar disorder . Interacting with a member of the REST co-repressors group (RCOR2), Zmynd8 inhibits neural differentiation in Xenopus embryos .
It is interesting to note that a splice-variant of the Zmynd8 gene, called Protein kinase C-beta2 (PKCbeta2), regulates several cellular functions, including the inhibition of apoptosis .
In the cytoplasmic proteins subcategory, Gip induces two genes encoding synaptic proteins, SH3 and multiple ankyrin repeat domains 2 (Shank2) and Discs, large (Drosophila) homolog-associated protein 1 (Dlgap1) [90–93]. They both represent scaffolding proteins of excitatory synapses inside the CNS [93–95]. An increase in Shank2 expression and mutations of Shank2 have been reported in Alzheimer’s disease and in Plena McDermid Syndrome, respectively , whereas genetic variants in the Dlgap1 gene can induce schizophrenia .
Microarray screening of genes up-regulated in CGNs following Gip rescue highlighted four members of the nuclear proteins category: Prickle homolog 1 Drosophila (Prickle1), Pleckstrin homology-like domain, family A, member 1 (Phlda1), Coiled-coil domain containing 89 (Ccdc89) and Testis specific protein Y-linked 4 (Tspyl4).
Prickle1 is a nuclear receptor, which positively regulates planar cell polarity (PCP), both in CNS neurons  and in murine neuroblastoma (C1300) cells [99,100], and facilitates cortical neurogenesis . Depletion in Prickle1 expression has been reported in human progressive myoclonus epilepsy (PME) [98,101]. Phlda1 (Tdag51) is a member of the pleckstrin homology-like domain family and although its anti-apoptotic role has not yet been found in neuronal cells, its protective effect has been shown in NWTb3 fibroblast mouse  and in the oral cancer cell line Ca9-22 . Moreover, deficiency of Phlda1 expression promotes oxidative stress induced-apoptosis in MEFs, a mouse model of embryonic fibroblasts . In contrast, high expression levels of Phlda1 are correlated with the evolution of intractable epilepsy (IE) . Ccdc89 is a potential regulator of neurogenesis, interacting with the orange domain of the hairy-related transcription factor (HRT/Hey1) in Xenopus and mouse . The nuclear protein Tspy4 is a member of the Tspy (testis-specific protein Y-encoded) family and, as such, is a sperm-specific biomarker in human cervico-vaginal fluids . However the recent discovery that Tspy1 is found together with the multi-domain adapter protein CASK in neuronal axon fibers in the brain  could be the starting point to further investigate the role of Tspy4 in the development of the brain.
Microarray analysis showed that the Gip rescue regulates the expression of a considerable fraction of genes encoding proteins involved in transcriptional regulation, which can be divided into immediate-early and secondary-response genes.
The first subgroup includes the up-regulated Immediate early response 5 (Ier5) and Immediate early response 5-like (Ier5l). Ier5 regulates the cellular response to mitogenic signals . Its expression increases in rat cerebral cortex after sleep deprivation or spontaneous waking  and may also be considered a regulator of circadian rhythms. Ier5l is related to cellular and embryonic development .
The secondary response genes subgroup includes three transcription factors, Neuronal differentiation 2 (NeuroD2), Ets variant gene 1 (Etv1), Taf5 RNA polymerase II TATA box binding protein (TBP)-associated factor, 100 kDa (Taf5), and two transcriptional regulators, Immunoglobulin helicase μ-binding protein 2 (Ighmbp2) and LIM domain only 2 (rhombotin-like 1) (Lmo2). All of these molecules are over-expressed by Gip treatment, with the exception of Taf5.
NeuroD2 is a basic helix-loop-helix (bHLH) protein, a member of the NeuroD family, which has pleiotropic functions, including neurogenesis, neuronal differentiation, development, connectivity and synaptic maturation [112–117]. Its over-expression, in particular, has been related to the survival of cerebellar and hippocampal neurons . Deficiency of NeuroD2 in mice has been linked to amygdala dysfunction  and ataxia [117,118]. Similarly, a member of the ETS (E twenty-six) family, Etv1, controls a broad array of neuronal processes, including dopamine neuronal differentiation, maturation of granule cells by means of gene regulation (Nrc2, Tiam2 genes and more others) and Bdnf cascade signaling [119–122]. Etv1 induction also promotes sensory motor-circuitry , whereas Etv1 deficiency has been reported in Spinal muscular atrophy . Although the Etv1 anti-apoptotic role in neurons has not been previously reported, its protective role has been demonstrated in the human breast cancer cell line MDA-MB-23 . Taf5 is an integral subunit of the TFIID transcription complex that is known to stabilize the interaction with Taf6 , a pro-apoptotic protein which controls p53-apoptosis in human cells . Down-regulation of Taf5 following Gip treatment, therefore, may induce a rescue effect by interfering with Taf6.
The transcriptional regulator Ighmbp2, which is over-expressed by Gip treatment, is a member of the helicase superfamily. Its encoded protein regulates replication, recombination and repair processes . Defects in DNA repair are very often involved in cell death and a lack of Ighmbp2 may underlie altered DNA repair. In addition, several mutations of Ighmbp2 have been reportedin Distal Spinal Muscolar Atrofy type 1 (DMSA) [129,130]. Lmo2 controls cerebellum and hippocampal development and plays a role in neurogenesis, interacting with the pro-survival factors Slc and Gata2 [131,132].
2.2.3. Cell Cycle
The Gip neuroprotective effect regulates the expression of two genes involved in cell cycle checkpoints: Pds5, regulator of cohesion maintenance, homolog B (S. cerevisiae) (Pds5b) and Ino80 complex subunit (Ino80). These two genes are both up-regulated following Gip treatment. Pds5b is a cohesion protein, known to pair replicated sister chromatids during cohesion in the S phase of the cell cycle [133,134]. Precise missense mutations of Pds5b have been associated to apoptosis in saccharomyces cerevisiae during early meiosis  and with the onset of Cornelia de Lange Syndrome (CdLS) . Ino80 is a member of the chromatin remodeler family, which plays an efficient role in DNA synthesis, S-phase progression and chromosome segregation during the normal cell division cycle . In yeast, Ino80 enhances chromatin mobility in response to DNA damage, acting downstream from the checkpoint factor Mec , whereas it suppresses genome instability, modulating chromatin remodelling complexes and repairing DNA double-strand breaks via the expression of Rad54B and XRCC3 genes .
2.2.4. Chromatin Remodelling
Two genes encoding proteins involved in chromatin remodelling are up-regulated by Gip during rescue of CGNs apoptosis: Chromodomain protein Y-like 2 (Cdyl2) and TEN1 CST complex subunit (Ten1).
Cdyl2 is a member of the chromodomain Y chromosome (CDY) family and plays several roles, including histone modification and genome imprinting . Ten1 is a member of the trimeric CTS complex (telomere-capping complex), which is essential for genome stability [141–143]. Insufficient telomeric DNA length or deficiency of key telomere-associated factors is known to elicit a DNA damage response, resulting in cellular senescence or apoptosis .
2.2.5. Cell Death
Microarray analysis showed down-regulation of Caspase 8 associated protein 2 (Casp8ap2) following Gip treatment. This gene encodes a multifunctional protein of the cysteine proteases family, which orchestrates the formation of the death complex [145,146], interacting with caspase-8 and activating Fas-mediated apoptosis and histone mRNA 3′ end processing [147,148].
2.2.6. Antioxidant Activity
Gip rescue was associated with the up-regulation of a gene, Cytoglobin (Cygb), involved in the antioxidant defense system. The protein encoded by this gene is a member of the globin molecule family with a double functional nature: antioxidant activity, inducing superoxide dismutase, and anti-apoptotic activity, inhibiting the apoptotic effects of caspase-2 and caspase-3 [149–152]. In particular, Cygb plays a protective role against hypoxia-ischemia (HI) in rat brains  and safeguards cerebellar cells against chronic exposure to carbon monoxide (CO) during pre- and post-natal development .
During Gip rescue we observed the over-expression of two members of the CGNs ubiquitin-proteasome system: Zinc and ring finger 1 E3 ubiquitin protein ligase (Znrf1) and Ubiquitin specific peptidase 10 (Usp10).
Znrf1 is a member of the ZNRF-E3 ubiquitin ligase family, which plays an important role in neuronal development, transmission, plasticity and also neuritogenesis by interacting with tubulin and glutamine synthetase (GS) [154–156]. Relevant to the present study is the previous demonstration that up-regulation of the Znrf1 gene induces an anti-apoptotic effect in MOLT-4 leukemia cells . Usp10 is an ubiquitin-specific protease, which contributes to the formation of the stress granules interacting with GTPase-activating protein SH3 domain binding protein 1 (G3BP1) . Stress granules are essential sites for translating stress-inducible genes and for reducing reactive oxygen species production .
Microarray analysis showed an over-expression of five genes, encoding respectively two members of the serine protease subgroup, Rhomboid 5 homolog 2 (Rhbdf2) and Dipeptidyl-peptidase 3 (Dpp3), one aminoacyl-tRNAsynthetase, Leucyl-tRNAsynthetase 2, mitochondrial (Lars2), one mitochondrial protein carrier, Solute carrier family 25 member 42 (Slc25a42) and one adipogenic protein, Mesenteric estrogen dependent adipogenesis (Medag).
Rhbdf2 is a catalytically inactive member of the rhomboid family, which was recently reported as a key regulator of the anti-apoptotic TNF-alpha convertase enzyme (Adam17 or Tace) [160,161] that activates the transcription factor NF-kappa B in rat cortical neuron cultures after exposure to oxygen-glucose and glutamate deprivation [160–162]. Dpp3 is a member of the S9B peptidase family that is known to inhibit four pro-apoptotic genes, BCL2-like 10 (apoptosis facilitator) (BCL2L10), Tumor necrosis factor (ligand) superfamily, member 10 (TNFSF10), Tumor necrosis factor receptor superfamily, member 25 (TNFRSF25) and Tumor necrosis factor (ligand) superfamily, member 8 (TNFSF8) . Dpp3 also activates the antioxidant response element (ARE) in primary mouse-derived cortical neurons, inducing NF-E2-related factor 2 (NRF2) nuclear translocation and NAD(P)H: quinoneoxidoreductase 1 . Lars2 is a nuclear gene encoding the enzyme catalyzing the aminoacylation of mitochondrial tRNA (Leu) and its over-expression may represent an additional mechanism whereby CGNs contrast the induction of apoptosis and the partial inactivation of vital tRNALeu molecules . In addition, over-expression of Lars2 in the human brain is a hallmark of a mitochondrial DNA point mutation (3243A > G) and may have a pathophysiological role in bipolar disorder and schizophrenia . Slc25a42 is a novel member of the mitochondrial carrier family for coenzyme A (CoA) and adenosine 3′,5′-diphosphate [167,168] and is involved in the Stanley syndrome and Amish microcephaly . Medag promotes adipogenesis and glucose uptake, interacting with several mediators, such as the fatty acid transporter CD36 that is involved in the uptake of the apoptotic material [170,171].
2.2.9. Cytoskeletal Organization
Following Gip treatment, we observed the differential expression of a number of genes whose encoded proteins are involved with cytoskeletal rearrangements, cell shape, and motility, as well as dendritic spines . These genes segregate into three groups: cytoplasmic actin isoforms, actin-binding proteins and other manipulators of the cytoskeletal organization.
The group of cytoplasmic actin includes two genes over-expressed by Gip: Actin beta (Actb) and Actin, gamma 2, smooth muscle, enteric (Actg2). Actb is one of the six different actin isoforms in humans and regulates synaptic formation and neuronal plasticity, interacting with the RNA-binding protein Sam68 [173,174]. Actb also plays a neuroprotective effect in propriospinal neurons after axotomy and in the MCF-7 breast cancer cells following treatment with salicylic acid . A deficit in Actb gene expression alters cytoplasmic actin dynamicity and clinically induces Baraitser-Winter pathology and fragile X tremor/ataxia syndrome [173,176]. Consistent with the functions of other actin isoforms, Actg2 regulates the maintenance of the cytoskeleton, including actin-based motility in neurons . Induction of Actg2, in particular, was found to rescue cardiac alpha-actin-deficient mice , whereas Actg2 repression contributes to cell cycle arrest following cadmium treatment of human lung fibroblast .
The group of actin-binding proteins includes the over-expressed Coronin, actin binding protein, 2A (Coro2a) and Enah/Vasp-like (Evl). Coro2a is a member of the WD repeat protein family, which regulates motile processes, neuronal actin organization and focal-adhesion turnover through the cofilin signaling pathway [180,181]. Evl is a member of the Ena/VASP protein family, which enhances axon guidance, lamellipodial and filopodial dynamics in migrating cells, specifically binding the Sema6A-1 [182–184].
The group of manipulators of the cytoskeletal organization includes Leucine rich repeat containing 8 family, member D (Lrrc8d), PDZ and LIM domain 5 (Pdlim5), Epsin 3 (Epn3), Transmembrane protein 47 (Tmem47) and SH3 and PX domains 2A (Sh3pxd2a). All of these, with the exception of Sh3pxd2a, are over-expressed following Gip treatment.
Lrrc8d, a member of the leucine-rich repeat protein family, is involved in B-cell development  and regulates cell adhesion and cellular trafficking. Pdlim5 is a LIM domain protein, which is involved in cytoskeleton organization, synaptic development and plasticity . Epn3, a member of the Epsin family, stimulates neurite outgrowth and brain development interacting with Epn1 . Tmem47 is a member of the PMP22/EMP/claudin protein family , which is required in the formation and sealing capacity of cell junctions mostly in the kidney . Up-regulation of Tmem47 inhibits neurite outgrowth and regulates neuronal differentiation . The human TMEM47 is considered a likely candidate for X-linked mental retardation . Sh3pxd2a is an adapter protein, which regulates the outgrowth of podosomes, a type of actin-rich structure involved in tumor invasion and in pro-apoptotic signals. Interacting with the metalloprotease ADAM12, Sh3pxd2a may confer susceptibility to late-onset Alzheimer’s disease [191–193].
3. Experimental Section
All the substances were obtained from Sigma Aldrich (Milano, Italy) unless otherwise specified.
3.2. Neuronal Cultures
CGNs were obtained from dissociated cerebella of eight-day-old Wistar rats (Charles River, Lecco, Italy) (P8) and cultured as previously described . Cells were plated in basal Eagle’s medium supplemented with 10% fetal calf serum, 25 mM KCl, 2 mM glutamine and 100 μg/mL gentamycin in poly-l-lysine coated 24-well clusters (NUNC, VWR International PBI s.r.l., Milano, Italy). Granule neurons were plated at 0.5 × 106 cells/well in BME.
3.3. Microarray Experiments
After six days “in vitro” (DIV), extracellular KCl of CGNs was shifted from 25 to 5 mM for neuronal apoptotic death induction. After two washes with serum-free BME containing 5 mM KCl, neurons were incubated with the same medium for 6 h (K5), while control neurons were incubated with serum free medium supplemented with 25 mM KCl (K25). K5 neurons were also treated with a maximal effective dose of GIP. After six hours of incubation, total RNA was extracted with Trizol (Life Technologies, Monza, Italy) from four biological replicates (derived from the same litter) for each of the experimental conditions (K25, K5, K5 + GIP). RNA integrity was confirmed by using a RNA chip and a 2100 Bioanalyzer (Agilent Technologies, Milano, Italy) with the protocol outlined by the manufacturer. Complementary RNAs (cRNAs) labeled with Cy3-CTP were synthesized from 1 μg of total RNA of each sample using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Milano, Italy) following the manufacturer’s protocol. Aliquots (750 ng) of Cy3 labeled cRNA targets were hybridized on Whole Rat Genome Oligo Microarrays (Agilent Technologies, Milano, Italy). Microarray hybridization and washing were performed using reagents and instruments (hybridization chambers and rotating oven) as indicated by the manufacturer. Microarrays were scanned at 5-μm resolution using a GenePix Personal 4100A microarray scanner and the GenePix Pro 6.0 acquisition and data-extraction software (Molecular Devices, Sunnyvale, CA, USA). Raw data were processed and analyzed with GeneSpringGX 12.5 (Agilent Technologies, Milano, Italy). To remove unreliable data, all genes from all samples were filtered for quality to include only probe data fulfilling all of the following criteria in all replicates of at least one out of four experimental conditions: the spot had <3% of saturated pixels at 532 nm; the spot was not flagged “bad”, “not found” or “absent”; the spot was detectable well above background (signal-to-noise ratios at 532 nm were >10). Filtering data by quality control criteria short-listed 29,892 genes as our complete data set, out of a total of 41,012 probes present on the microarray. Genes in our quality-filtered data set were screened by a one-way ANOVA using Welch’s t-test, followed by the Benjamini and Hochberg False Discovery Rate procedure as a multiple testing correction and the Tukey’s Post Hoc test. Genes with a corrected p value <0.05 were selected as differentially expressed genes.
3.4. Real Time Quantitative PCR
Following extraction, total RNA samples (three/experimental condition) were reverse transcribed with an oligo(dT)12–18 and SuperScript II Rnase H-reverse transcriptase (Life Technologies, Milano, Italy). Aliquots of cDNA (0.1 and 0.2 mg) and known amounts of external standard (purified PCR product, 102 to 108 copies) were amplified in parallel reactions using primers indicated in Table 1. To control for the integrity of RNA and for differences attributable to errors in experimental manipulation, mRNA levels of mouse ribosomal S18 and phosphoglycerate kinase 1 were measured in similar reactions. Each PCR reaction (final volume 20 mL) contained 0.5 mM of primers, 2.5 mM Mg2+ and 1× DNA SYBR Green master mix (Roche Diagnostics, Monza, Italy). PCR amplifications were performed with a Light-Cycler (Roche Diagnostics, Monza, Italy) using the following four cycle programs: (i) denaturation of cDNA (1 cycle: 95 °C for 1 min); (ii) amplification (40 cycles: 95 °C for 0 s, 57 °C for 5 s, 72 °C for 10 s); (iii) melting curve analysis (1 cycle: 95 °C for 0 s, 67 °C for 10 s, 95 °C for 0 s); (iv) cooling (1 cycle: 40 °C for 3 min). Temperature transition rate was 20 °C/s except for the third segment of the melting curve analysis where it was 0.2 °C/s. Fluorimeter gain value was 7. The sequence of forward and reverse gene specific primers is shown in Table 1. Real-time detection of fluorimetric intensity of SYBR Green I, indicating the amount of PCR product formed, was measured at the end of each elongation phase. Quantification was performed by comparing the fluorescence of PCR products of unknown concentration with the fluorescence of the external standards. For this analysis, fluorescence values measured in the log-linear phase of amplification were considered using the second derivative maximum method of the Light Cycler Data Analysis software (Roche Diagnostics, Monza, Italy). Specificity of PCR products obtained was characterized by melting curve analysis followed by gel electrophoresis and DNA sequencing.
In the last years, the advent of full genome sequencing and high-throughput technologies are revolutionizing our ability to decode the underlying mechanisms of neuronal apoptosis and survival by offering a new approach based on systems biology. In this study we report for the first time a whole-genome analysis of these processes in CGNs following rescue by Gip. The results reveal the existence of a previously unknown transcriptional program associated with neuronal survival. The exact role and functional relationships of the genes implicated by gene expression profiling are mostly unknown and will require further studies. Systematic characterization of expression patterns associated to different rescue factors and in distinct temporal domains will also provide a framework for interpreting the biological significance of the expression patterns observed. Genetic or pharmacological exploitation of potential targets will help to determine their cause-relationship and identify new clues for neuroprotective drugs.
We gratefully acknowledge Cristina Calì, Alfia Corsino, Maria Patrizia D’Angelo and Francesco Marino for their administrative and technical support.
Conflicts of Interest
The authors declare no conflict of interest.
- Author ContributionsB.M. carried out microarray and RT-PCR analysis, and drafted the manuscript; M.T.C. performed all neuronal cultures experiments, P.C. and S.C. conceived and designed the study. S.C. performed microarray data analysis.
- Jellinger, K.A. Challenges in neuronal apoptosis. Curr. Alzheimer Res 2006, 3, 377–391. [Google Scholar]
- Arends, M.J.; Wyllie, A.H. Apoptosis: Mechanisms and roles in pathology. Internatl. Rev. Exp. Pathol 1991, 32, 223–254. [Google Scholar]
- Oppenheim, R.W. Cell death during development of the nervous system. Annu. Rev. Neurosci 1991, 14, 453–501. [Google Scholar]
- Pettmann, B.; Henderson, C.E. Neuronal cell death. Neuron 1998, 20, 633–647. [Google Scholar]
- Mattson, M.P. Neuronal life-and-death signaling, apoptosis, and neurodegenerative disorders. Antioxid. Redox Signal 2006, 8, 1997–2006. [Google Scholar]
- D’Mello, S.R.; Chin, P.C. Treating neurodegenerative conditions through the understanding of neuronal apoptosis. Curr. Drug Targets 2005, 4, 3–23. [Google Scholar]
- Contestabile, A. Cerebellar granule cells as a model to study mechanisms of neuronal apoptosis or survival in vivo and in vitro. Cerebellum 2002, 1, 41–55. [Google Scholar]
- D’Mello, S.R.; Galli, C.; Ciotti, T.; Calissano, P. Induction of apoptosis in cerebellar granule neurons by low potassium: Inhibition of death by insulin-like growth factor i and camp. Proc. Natl. Acad. Sci. USA 1993, 90, 10989–10993. [Google Scholar]
- Gallo, V.; Ciotti, M.T.; Coletti, A.; Aloisi, F.; Levi, G. Selective release of glutamate from cerebellar granule cells differentiating in culture. Proc. Natl. Acad. Sci. USA 1982, 79, 7919–7923. [Google Scholar]
- Isaev, N.K.; Stelmashook, E.V.; Halle, A.; Harms, C.; Lautenschlager, M.; Weih, M.; Dirnagl, U.; Victorov, I.V.; Zorov, D.B. Inhibition of Na+, K+-atpase activity in cultured rat cerebellar granule cells prevents the onset of apoptosis induced by low potassium. Neurosci. Lett 2000, 283, 41–44. [Google Scholar]
- Wood, K.A.; Dipasquale, B.; Youle, R.J. In situ labeling of granule cells for apoptosis-associated DNA fragmentation reveals different mechanisms of cell loss in developing cerebellum. Neuron 1993, 11, 621–632. [Google Scholar]
- Tanaka, M.; Marunouchi, T. Immunohistochemical analysis of developmental stage of external granular layer neurons which undergo apoptosis in postnatal rat cerebellum. Neurosci. Lett 1998, 242, 85–88. [Google Scholar]
- Nikolic, M.; Gardner, H.A.; Tucker, K.L. Postnatal neuronal apoptosis in the cerebral cortex: Physiological and pathophysiological mechanisms. Neuroscience 2013, 254, 369–378. [Google Scholar]
- Galli, C.; Meucci, O.; Scorziello, A.; Werge, T.M.; Calissano, P.; Schettini, G. Apoptosis in cerebellar granule cells is blocked by high kcl, forskolin, and igf-1 through distinct mechanisms of action: The involvement of intracellular calcium and rna synthesis. J. Neurosci 1995, 15, 1172–1179. [Google Scholar]
- Cavallaro, S.; Copani, A.; D’Agata, V.; Musco, S.; Petralia, S.; Ventra, C.; Stivala, F.; Travali, S.; Canonico, P.L. Pituitary adenylate cyclase activating polypeptide prevents apoptosis in cultured cerebellar granule neurons. Mol. Pharmacol 1996, 50, 60–66. [Google Scholar]
- Paratore, S.; Ciotti, M.T.; Basille, M.; Vaudry, D.; Gentile, A.; Parenti, R.; Calissano, P.; Cavallaro, S. Gastric inhibitory polypeptide and its receptor are expressed in the central nervous system and support neuronal survival. Cent. Nerv. Syst. Agent Med. Chem 2011, 11, 210–222. [Google Scholar]
- Inagaki, N.; Seino, Y.; Takeda, J.; Yano, H.; Yamada, Y.; Bell, G.I.; Eddy, R.L.; Fukushima, Y.; Byers, M.G.; Shows, T.B.; et al. Gastric inhibitory polypeptide: Structure and chromosomal localization of the human gene. Mol. Endocrinol 1989, 3, 1014–1021. [Google Scholar]
- Tseng, C.C.; Jarboe, L.A.; Landau, S.B.; Williams, E.K.; Wolfe, M.M. Glucose-dependent insulinotropic peptide: Structure of the precursor and tissue-specific expression in rat. Proc. Natl. Acad. Sci. USA 1993, 90, 1992–1996. [Google Scholar]
- Ojima, A.; Matsui, T.; Maeda, S.; Takeuchi, M.; Yamagishi, S. Glucose-dependent insulinotropic polypeptide (gip) inhibits signaling pathways of advanced glycation end products (ages) in endothelial cells via its antioxidative properties. Horm. Metab. Res 2012, 44, 501–505. [Google Scholar]
- Harada, N. Structure and function of incretin receptor. Nihon Rinsho 2011, 69, 813–820. (in Japanese). [Google Scholar]
- Yamada, Y.; Hayami, T.; Nakamura, K.; Kaisaki, P.J.; Someya, Y.; Wang, C.Z.; Seino, S.; Seino, Y. Human gastric inhibitory polypeptide receptor: Cloning of the gene (gipr) and cdna. Genomics 1995, 29, 773–776. [Google Scholar]
- Gremlich, S.; Porret, A.; Hani, E.H.; Cherif, D.; Vionnet, N.; Froguel, P.; Thorens, B. Cloning, functional expression, and chromosomal localization of the human pancreatic islet glucose-dependent insulinotropic polypeptide receptor. Diabetes 1995, 44, 1202–1208. [Google Scholar]
- Hauner, H.; Glatting, G.; Kaminska, D.; Pfeiffer, E.F. Effects of gastric inhibitory polypeptide on glucose and lipid metabolism of isolated rat adipocytes. Ann. Nutr. Metab 1988, 32, 282–288. [Google Scholar]
- Kogire, M.; Inoue, K.; Sumi, S.; Doi, R.; Yun, M.; Kaji, H.; Tobe, T. Effects of gastric inhibitory polypeptide and glucagon on portal venous and hepatic arterial flow in conscious dogs. Digest. Dis. Sci 1992, 37, 1666–1670. [Google Scholar]
- Holst, J.J. On the physiology of gip and glp-1. Horm. Metab. Res 2004, 36, 747–754. [Google Scholar]
- Hansotia, T.; Drucker, D.J. Gip and glp-1 as incretin hormones: Lessons from single and double incretin receptor knockout mice. Regul. Pept 2005, 128, 125–134. [Google Scholar]
- Gault, V.A.; Harriott, P.; Flatt, P.R.; O’Harte, F.P. Cyclic amp production and insulin releasing activity of synthetic fragment peptides of glucose-dependent insulinotropic polypeptide. Biosci. Rep 2002, 22, 523–528. [Google Scholar]
- Ehses, J.A.; Lee, S.S.; Pederson, R.A.; McIntosh, C.H. A new pathway for glucose-dependent insulinotropic polypeptide (gip) receptor signaling: Evidence for the involvement of phospholipase a2 in gip-stimulated insulin secretion. J. Biol. Chem 2001, 276, 23667–23673. [Google Scholar]
- Volz, A.; Goke, R.; Lankat-Buttgereit, B.; Fehmann, H.C.; Bode, H.P.; Goke, B. Molecular cloning, functional expression, and signal transduction of the gip-receptor cloned from a human insulinoma. FEBS Lett 1995, 373, 23–29. [Google Scholar]
- Brubaker, P.L.; Drucker, D.J. Structure-function of the glucagon receptor family of g protein-coupled receptors: The glucagon, gip, glp-1, and glp-2 receptors. Recept. Channels 2002, 8, 179–188. [Google Scholar]
- Kaplan, A.M.; Vigna, S.R. Gastric inhibitory polypeptide (gip) binding sites in rat brain. Peptides 1994, 15, 297–302. [Google Scholar]
- Gault, V.A.; Holscher, C. Protease-resistant glucose-dependent insulinotropic polypeptide agonists facilitate hippocampal ltp and reverse the impairment of ltp induced by beta-amyloid. J. Neurophysiol 2008, 99, 1590–1595. [Google Scholar]
- Figueiredo, C.P.; Pamplona, F.A.; Mazzuco, T.L.; Aguiar, A.S., Jr.; Walz, R.; Prediger, R.D. Role of the glucose-dependent insulinotropic polypeptide and its receptor in the central nervous system: Therapeutic potential in neurological diseases. Behav. Pharmacol 2010, 21, 394–408. [Google Scholar]
- Faivre, E.; Gault, V.A.; Thorens, B.; Holscher, C. Glucose-dependent insulinotropic polypeptide receptor knockout mice are impaired in learning, synaptic plasticity, and neurogenesis. J. Neurophysiol 2011, 105, 1574–1580. [Google Scholar]
- Buhren, B.A.; Gasis, M.; Thorens, B.; Muller, H.W.; Bosse, F. Glucose-dependent insulinotropic polypeptide (gip) and its receptor (gipr): Cellular localization, lesion-affected expression, and impaired regenerative axonal growth. J. Neurosci. Res 2009, 87, 1858–1870. [Google Scholar]
- Nyberg, J.; Jacobsson, C.; Anderson, M.F.; Eriksson, P.S. Immunohistochemical distribution of glucose-dependent insulinotropic polypeptide in the adult rat brain. J. Neurosci. Res 2007, 85, 2099–2119. [Google Scholar]
- Nyberg, J.; Anderson, M.F.; Meister, B.; Alborn, A.M.; Strom, A.K.; Brederlau, A.; Illerskog, A.C.; Nilsson, O.; Kieffer, T.J.; Hietala, M.A.; et al. Glucose-dependent insulinotropic polypeptide is expressed in adult hippocampus and induces progenitor cell proliferation. J. Neurosci 2005, 25, 1816–1825. [Google Scholar]
- Kim, S.J.; Ao, Z.; Warnock, G.; McIntosh, C.H. Incretin-stimulated interaction between beta-cell kv1.5 and kvbeta2 channel proteins involves acetylation/deacetylation by cbp/sirt1. Biochem. J 2013, 451, 227–234. [Google Scholar]
- Yabe, D.; Seino, Y. Two incretin hormones glp-1 and gip: Comparison of their actions in insulin secretion and beta cell preservation. Prog. Biophys. Mol. Biol 2011, 107, 248–256. [Google Scholar]
- Campbell, R.K. Fate of the beta-cell in the pathophysiology of type 2 diabetes. J. Am. Pharm. Assoc 2009, 49, S10–S15. [Google Scholar]
- Maida, A.; Hansotia, T.; Longuet, C.; Seino, Y.; Drucker, D.J. Differential importance of glucose-dependent insulinotropic polypeptide vs. glucagon-like peptide 1 receptor signaling for beta cell survival in mice. Gastroenterology 2009, 137, 2146–2157. [Google Scholar]
- Widenmaier, S.B.; Ao, Z.; Kim, S.J.; Warnock, G.; McIntosh, C.H. Suppression of p38 mapk and jnk via akt-mediated inhibition of apoptosis signal-regulating kinase 1 constitutes a core component of the beta-cell pro-survival effects of glucose-dependent insulinotropic polypeptide. J. Biol. Chem 2009, 284, 30372–30382. [Google Scholar]
- Kim, S.J.; Nian, C.; Widenmaier, S.; McIntosh, C.H. Glucose-dependent insulinotropic polypeptide-mediated up-regulation of beta-cell antiapoptotic bcl-2 gene expression is coordinated by cyclic amp (camp) response element binding protein (creb) and camp-responsive creb coactivator 2. Mol. Cell. Biol 2008, 28, 1644–1656. [Google Scholar]
- Trumper, A.; Trumper, K.; Horsch, D. Mechanisms of mitogenic and anti-apoptotic signaling by glucose-dependent insulinotropic polypeptide in beta(ins-1)-cells. J. Endocrinol 2002, 174, 233–246. [Google Scholar]
- Kim, S.J.; Winter, K.; Nian, C.; Tsuneoka, M.; Koda, Y.; McIntosh, C.H. Glucose-dependent insulinotropic polypeptide (gip) stimulation of pancreatic beta-cell survival is dependent upon phosphatidylinositol 3-kinase (pi3k)/protein kinase b (pkb) signaling, inactivation of the forkhead transcription factor foxo1, and down-regulation of bax expression. J. Biol. Chem 2005, 280, 22297–22307. [Google Scholar]
- Lyssenko, V.; Eliasson, L.; Kotova, O.; Pilgaard, K.; Wierup, N.; Salehi, A.; Wendt, A.; Jonsson, A.; de Marinis, Y.Z.; Berglund, L.M.; et al. Pleiotropic effects of gip on islet function involve osteopontin. Diabetes 2011, 60, 2424–2433. [Google Scholar]
- Tsukiyama, K.; Yamada, Y.; Yamada, C.; Harada, N.; Kawasaki, Y.; Ogura, M.; Bessho, K.; Li, M.; Amizuka, N.; Sato, M.; et al. Gastric inhibitory polypeptide as an endogenous factor promoting new bone formation after food ingestion. Mol. Endocrinol 2006, 20, 1644–1651. [Google Scholar]
- Kubota, A.; Yamada, Y.; Yasuda, K.; Someya, Y.; Ihara, Y.; Kagimoto, S.; Watanabe, R.; Kuroe, A.; Ishida, H.; Seino, Y. Gastric inhibitory polypeptide activates map kinase through the wortmannin-sensitive and -insensitive pathways. Biochem. Biophys. Res. Commun 1997, 235, 171–175. [Google Scholar]
- Ehses, J.A.; Casilla, V.R.; Doty, T.; Pospisilik, J.A.; Winter, K.D.; Demuth, H.U.; Pederson, R.A.; McIntosh, C.H. Glucose-dependent insulinotropic polypeptide promotes beta-(ins-1) cell survival via cyclic adenosine monophosphate-mediated caspase-3 inhibition and regulation of p38 mitogen-activated protein kinase. Endocrinology 2003, 144, 4433–4445. [Google Scholar]
- Yasuda, K.; Inagaki, N.; Yamada, Y.; Kubota, A.; Seino, S.; Seino, Y. Hamster gastric inhibitory polypeptide receptor expressed in pancreatic islets and clonal insulin-secreting cells: Its structure and functional properties. Biochem. Biophys. Res. Commun 1994, 205, 1556–1562. [Google Scholar]
- Zeng, X.J.; Yu, S.P.; Zhang, L.; Wei, L. Neuroprotective effect of the endogenous neural peptide apelin in cultured mouse cortical neurons. Exp. Cell Res 2010, 316, 1773–1783. [Google Scholar]
- O’Donnell, L.A.; Agrawal, A.; Sabnekar, P.; Dichter, M.A.; Lynch, D.R.; Kolson, D.L. Apelin, an endogenous neuronal peptide, protects hippocampal neurons against excitotoxic injury. J. Neurochem 2007, 102, 1905–1917. [Google Scholar]
- Reaux, A.; de Mota, N.; Skultetyova, I.; Lenkei, Z.; El Messari, S.; Gallatz, K.; Corvol, P.; Palkovits, M.; Llorens-Cortes, C. Physiological role of a novel neuropeptide, apelin, and its receptor in the rat brain. J. Neurochem 2001, 77, 1085–1096. [Google Scholar]
- Cook, D.R.; Gleichman, A.J.; Cross, S.A.; Doshi, S.; Ho, W.; Jordan-Sciutto, K.L.; Lynch, D.R.; Kolson, D.L. Nmda receptor modulation by the neuropeptide apelin: Implications for excitotoxic injury. J. Neurochem 2011, 118, 1113–1123. [Google Scholar]
- Kasai, A.; Kinjo, T.; Ishihara, R.; Sakai, I.; Ishimaru, Y.; Yoshioka, Y.; Yamamuro, A.; Ishige, K.; Ito, Y.; Maeda, S. Apelin deficiency accelerates the progression of amyotrophic lateral sclerosis. PLoS One 2011, 6, e23968. [Google Scholar]
- Morganti, J.M.; Nash, K.R.; Grimmig, B.A.; Ranjit, S.; Small, B.; Bickford, P.C.; Gemma, C. The soluble isoform of cx3cl1 is necessary for neuroprotection in a mouse model of parkinson’s disease. J. Neurosci 2012, 32, 14592–14601. [Google Scholar]
- Hao, F.; Zhang, N.N.; Zhang, D.M.; Bai, H.Y.; Piao, H.; Yuan, B.; Zhu, H.Y.; Yu, H.; Xiao, C.S.; Li, A.P. Chemokine fractalkine attenuates overactivation and apoptosis of bv-2 microglial cells induced by extracellular atp. Neurochem. Res 2013, 38, 1002–1012. [Google Scholar]
- Cipriani, R.; Villa, P.; Chece, G.; Lauro, C.; Paladini, A.; Micotti, E.; Perego, C.; de Simoni, M.G.; Fredholm, B.B.; Eusebi, F.; et al. Cx3cl1 is neuroprotective in permanent focal cerebral ischemia in rodents. J. Neurosci 2011, 31, 16327–16335. [Google Scholar]
- Lauro, C.; Cipriani, R.; Catalano, M.; Trettel, F.; Chece, G.; Brusadin, V.; Antonilli, L.; van Rooijen, N.; Eusebi, F.; Fredholm, B.B.; et al. Adenosine a1 receptors and microglial cells mediate cx3cl1-induced protection of hippocampal neurons against glu-induced death. Neuropsychopharmacology 2010, 35, 1550–1559. [Google Scholar]
- Noda, M.; Doi, Y.; Liang, J.; Kawanokuchi, J.; Sonobe, Y.; Takeuchi, H.; Mizuno, T.; Suzumura, A. Fractalkine attenuates excito-neurotoxicity via microglial clearance of damaged neurons and antioxidant enzyme heme oxygenase-1 expression. J. Biol. Chem 2011, 286, 2308–2319. [Google Scholar]
- Boehme, S.A.; Lio, F.M.; Maciejewski-Lenoir, D.; Bacon, K.B.; Conlon, P.J. The chemokine fractalkine inhibits fas-mediated cell death of brain microglia. J. Immunol 2000, 165, 397–403. [Google Scholar]
- Cook, A.; Hippensteel, R.; Shimizu, S.; Nicolai, J.; Fatatis, A.; Meucci, O. Interactions between chemokines: Regulation of fractalkine/cx3cl1 homeostasis by sdf/cxcl12 in cortical neurons. J. Biol. Chem 2010, 285, 10563–10571. [Google Scholar]
- Catalano, M.; Lauro, C.; Cipriani, R.; Chece, G.; Ponzetta, A.; di Angelantonio, S.; Ragozzino, D.; Limatola, C. Cx3cl1 protects neurons against excitotoxicity enhancing glt-1 activity on astrocytes. J. Neuroimmunol 2013, 263, 75–82. [Google Scholar]
- Yuan, Q.; Chiquet, B.T.; Devault, L.; Warman, M.L.; Nakamura, Y.; Swindell, E.C.; Hecht, J.T. Craniofacial abnormalities result from knock down of nonsyndromic clefting gene, crispld2, in zebrafish. Genesis 2012, 50, 871–881. [Google Scholar]
- Szlama, G.; Kondas, K.; Trexler, M.; Patthy, L. Wfikkn1 and wfikkn2 bind growth factors tgfbeta1, bmp2 and bmp4 but do not inhibit their signalling activity. FEBS J 2010, 277, 5040–5050. [Google Scholar]
- Liu, Y.; Cheng, H.; Zhou, Y.; Zhu, Y.; Bian, R.; Chen, Y.; Li, C.; Ma, Q.; Zheng, Q.; Zhang, Y.; et al. Myostatin induces mitochondrial metabolic alteration and typical apoptosis in cancer cells. Cell Death Dis 2013, 4, e494. [Google Scholar]
- Holzbaur, E.L.; Howland, D.S.; Weber, N.; Wallace, K.; She, Y.; Kwak, S.; Tchistiakova, L.A.; Murphy, E.; Hinson, J.; Karim, R.; et al. Myostatin inhibition slows muscle atrophy in rodent models of amyotrophic lateral sclerosis. Neurobiol. Dis 2006, 23, 697–707. [Google Scholar]
- Filipe, M.; Goncalves, L.; Bento, M.; Silva, A.C.; Belo, J.A. Comparative expression of mouse and chicken shisa homologues during early development. Dev. Dyn 2006, 235, 2567–2573. [Google Scholar]
- Pei, J.; Grishin, N.V. Unexpected diversity in shisa-like proteins suggests the importance of their roles as transmembrane adaptors. Cell Signal 2012, 24, 758–769. [Google Scholar]
- Schultze, W.; Eulenburg, V.; Lessmann, V.; Herrmann, L.; Dittmar, T.; Gundelfinger, E.D.; Heumann, R.; Erdmann, K.S. Semaphorin4f interacts with the synapse-associated protein sap90/psd-95. J. Neurochem 2001, 78, 482–489. [Google Scholar]
- Barrette, B.; Calvo, E.; Vallieres, N.; Lacroix, S. Transcriptional profiling of the injured sciatic nerve of mice carrying the Wld(s) mutant gene: Identification of genes involved in neuroprotection, neuroinflammation, and nerve regeneration. Brain Behav. Immun 2010, 24, 1254–1267. [Google Scholar]
- Li, T.S.; Li, X.N.; Chang, Z.J.; Fu, X.Y.; Liu, L. Identification and functional characterization of a novel interleukin 17 receptor: A possible mitogenic activation through ras/mitogen-activated protein kinase signaling pathway. Cell Signal 2006, 18, 1287–1298. [Google Scholar]
- Moseley, T.A.; Haudenschild, D.R.; Rose, L.; Reddi, A.H. Interleukin-17 family and il-17 receptors. Cytokine Growth Factor Rev 2003, 14, 155–174. [Google Scholar]
- Vidlak, D.; Kielian, T. Differential effects of interleukin-17 receptor signaling on innate and adaptive immunity during central nervous system bacterial infection. J. Neuroinflam 2012, 9, 128. [Google Scholar]
- Bonni, A.; Brunet, A.; West, A.E.; Datta, S.R.; Takasu, M.A.; Greenberg, M.E. Cell survival promoted by the ras-mapk signaling pathway by transcription-dependent and independent mechanisms. Science 1999, 286, 1358–1362. [Google Scholar]
- Holt, E.H.; Broadus, A.E.; Brines, M.L. Parathyroid hormone-related peptide is produced by cultured cerebellar granule cells in response to l-type voltage-sensitive Ca2+ channel flux via a Ca2+/calmodulin-dependent kinase pathway. J. Biol. Chem 1996, 271, 28105–28111. [Google Scholar]
- Ono, T.; Inokuchi, K.; Ogura, A.; Ikawa, Y.; Kudo, Y.; Kawashima, S. Activity-dependent expression of parathyroid hormone-related protein (pthrp) in rat cerebellar granule neurons. Requirement of pthrp for the activity-dependent survival of granule neurons. J. Biol. Chem 1997, 272, 14404–14411. [Google Scholar]
- Chatterjee, O.; Nakchbandi, I.A.; Philbrick, W.M.; Dreyer, B.E.; Zhang, J.P.; Kaczmarek, L.K.; Brines, M.L.; Broadus, A.E. Endogenous parathyroid hormone-related protein functions as a neuroprotective agent. Brain Res 2002, 930, 58–66. [Google Scholar]
- Brines, M.L.; Ling, Z.; Broadus, A.E. Parathyroid hormone-related protein protects against kainic acid excitotoxicity in rat cerebellar granule cells by regulating l-type channel calcium flux. Neurosci. Lett 1999, 274, 13–16. [Google Scholar]
- Gessi, M.; Monego, G.; Calviello, G.; Lanza, P.; Giangaspero, F.; Silvestrini, A.; Lauriola, L.; Ranelletti, F.O. Human parathyroid hormone-related protein and human parathyroid hormone receptor type 1 are expressed in human medulloblastomas and regulate cell proliferation and apoptosis in medulloblastoma-derived cell lines. Acta Neuropathol 2007, 114, 135–145. [Google Scholar]
- Garcia-Esparcia, P.; Schluter, A.; Carmona, M.; Moreno, J.; Ansoleaga, B.; Torrejon-Escribano, B.; Gustincich, S.; Pujol, A.; Ferrer, I. Functional genomics reveals dysregulation of cortical olfactory receptors in parkinson disease: Novel putative chemoreceptors in the human brain. J. Neuropathol. Exp. Neurol 2013, 72, 524–539. [Google Scholar]
- Shati, A.A.; Elsaid, F.G.; Hafez, E.E. Biochemical and molecular aspects of aluminium chloride-induced neurotoxicity in mice and the protective role of crocus sativus l. Extraction and honey syrup. Neuroscience 2011, 175, 66–74. [Google Scholar]
- Juhasz, K.; Zvara, A.; Lipp, A.M.; Nimmervoll, B.; Sonnleitner, A.; Balogi, Z.; Duda, E. Casein kinase 2-interacting protein-1, an inflammatory signaling molecule interferes with tnf reverse signaling in human model cells. Immunol. Lett 2013, 152, 55–64. [Google Scholar]
- Tsunoda, T.; Ota, T.; Fujimoto, T.; Doi, K.; Tanaka, Y.; Yoshida, Y.; Ogawa, M.; Matsuzaki, H.; Hamabashiri, M.; Tyson, D.R.; et al. Inhibition of phosphodiesterase-4 (pde4) activity triggers luminal apoptosis and akt dephosphorylation in a 3-d colonic-crypt model. Mol. Cancer 2012, 11, 46. [Google Scholar]
- Kim, S.W.; Rai, D.; McKeller, M.R.; Aguiar, R.C. Rational combined targeting of phosphodiesterase 4b and syk in dlbcl. Blood 2009, 113, 6153–6160. [Google Scholar]
- Svoboda, N.; Zierler, S.; Kerschbaum, H.H. Camp mediates ammonia-induced programmed cell death in the microglial cell line bv-2. Eur. J. Neurosci 2007, 25, 2285–2295. [Google Scholar]
- Fatemi, S.H.; King, D.P.; Reutiman, T.J.; Folsom, T.D.; Laurence, J.A.; Lee, S.; Fan, Y.T.; Paciga, S.A.; Conti, M.; Menniti, F.S. Pde4b polymorphisms and decreased pde4b expression are associated with schizophrenia. Schizophr. Res 2008, 101, 36–49. [Google Scholar]
- Zeng, W.; Kong, Q.; Li, C.; Mao, B. Xenopus rcor2 (rest corepressor 2) interacts with zmynd8, which is involved in neural differentiation. Biochem. Biophys. Res. Commun 2010, 394, 1024–1029. [Google Scholar]
- Lee, S.H.; Chen, T.; Zhou, J.; Hofmann, J.; Bepler, G. Protein kinase c-beta gene variants, pathway activation, and enzastaurin activity in lung cancer. Clin. Lung Cancer 2010, 11, 169–175. [Google Scholar]
- Lim, S.; Naisbitt, S.; Yoon, J.; Hwang, J.I.; Suh, P.G.; Sheng, M.; Kim, E. Characterization of the shank family of synaptic proteins. Multiple genes, alternative splicing, and differential expression in brain and development. J. Biol. Chem 1999, 274, 29510–29518. [Google Scholar]
- Boeckers, T.M.; Bockmann, J.; Kreutz, M.R.; Gundelfinger, E.D. Prosap/shank proteins—A family of higher order organizing molecules of the postsynaptic density with an emerging role in human neurological disease. J. Neurochem 2002, 81, 903–910. [Google Scholar]
- Park, E.; Na, M.; Choi, J.; Kim, S.; Lee, J.R.; Yoon, J.; Park, D.; Sheng, M.; Kim, E. The shank family of postsynaptic density proteins interacts with and promotes synaptic accumulation of the beta pix guanine nucleotide exchange factor for rac1 and cdc42. J. Biol. Chem 2003, 278, 19220–19229. [Google Scholar]
- Naisbitt, S.; Kim, E.; Weinberg, R.J.; Rao, A.; Yang, F.C.; Craig, A.M.; Sheng, M. Characterization of guanylate kinase-associated protein, a postsynaptic density protein at excitatory synapses that interacts directly with postsynaptic density-95/synapse-associated protein 90. J. Neurosci 1997, 17, 5687–5696. [Google Scholar]
- Boeckers, T.M.; Winter, C.; Smalla, K.H.; Kreutz, M.R.; Bockmann, J.; Seidenbecher, C.; Garner, C.C.; Gundelfinger, E.D. Proline-rich synapse-associated proteins prosap1 and prosap2 interact with synaptic proteins of the sapap/gkap family. Biochem. Biophys. Res. Commun 1999, 264, 247–252. [Google Scholar]
- Moutin, E.; Raynaud, F.; Fagni, L.; Perroy, J. Gkap-dlc2 interaction organizes the postsynaptic scaffold complex to enhance synaptic nmda receptor activity. J. Cell Sci 2012, 125, 2030–2040. [Google Scholar]
- Grabrucker, A.M. A role for synaptic zinc in prosap/shank psd scaffold malformation in autism spectrum disorders. Dev. Neurobiol 2014, 74, 136–146. [Google Scholar]
- Li, J.M.; Lu, C.L.; Cheng, M.C.; Luu, S.U.; Hsu, S.H.; Chen, C.H. Genetic analysis of the dlgap1 gene as a candidate gene for schizophrenia. Psychiatry Res 2013, 205, 13–17. [Google Scholar]
- Liu, C.; Lin, C.; Whitaker, D.T.; Bakeri, H.; Bulgakov, O.V.; Liu, P.; Lei, J.; Dong, L.; Li, T.; Swaroop, A. Prickle1 is expressed in distinct cell populations of the central nervous system and contributes to neuronal morphogenesis. Hum. Mol. Genet 2013, 22, 2234–2246. [Google Scholar]
- Fujimura, L.; Hatano, M. Role of prickle1 and prickle2 in neurite outgrowth in murine neuroblastoma cells. Methods Mol. Biol 2012, 839, 173–185. [Google Scholar]
- Fujimura, L.; Watanabe-Takano, H.; Sato, Y.; Tokuhisa, T.; Hatano, M. Prickle promotes neurite outgrowth via the dishevelled dependent pathway in c1300 cells. Neurosci. Lett 2009, 467, 6–10. [Google Scholar]
- Bassuk, A.G.; Wallace, R.H.; Buhr, A.; Buller, A.R.; Afawi, Z.; Shimojo, M.; Miyata, S.; Chen, S.; Gonzalez-Alegre, P.; Griesbach, H.L.; et al. A homozygous mutation in human prickle1 causes an autosomal-recessive progressive myoclonus epilepsy-ataxia syndrome. Am. J. Hum. Genet 2008, 83, 572–581. [Google Scholar]
- Toyoshima, Y.; Karas, M.; Yakar, S.; Dupont, J.; Lee, H.; LeRoith, D. Tdag51 mediates the effects of insulin-like growth factor i (igf-i) on cell survival. J. Biol. Chem 2004, 279, 25898–25904. [Google Scholar]
- Murata, T.; Sato, T.; Kamoda, T.; Moriyama, H.; Kumazawa, Y.; Hanada, N. Differential susceptibility to hydrogen sulfide-induced apoptosis between phlda1-overexpressing oral cancer cell lines and oral keratinocytes: Role of phlda1 as an apoptosis suppressor. Exp. Cell Res 2014, 320, 247–257. [Google Scholar]
- Park, E.S.; Kim, J.; Ha, T.U.; Choi, J.S.; Soo Hong, K.; Rho, J. Tdag51 deficiency promotes oxidative stress-induced apoptosis through the generation of reactive oxygen species in mouse embryonic fibroblasts. Exp. Mol. Med 2013, 45, e35. [Google Scholar]
- Xi, Z.Q.; Wang, L.Y.; Sun, J.J.; Liu, X.Z.; Zhu, X.; Xiao, F.; Guan, L.F.; Li, J.M.; Wang, L.; Wang, X.F. Tdag51 in the anterior temporal neocortex of patients with intractable epilepsy. Neurosci. Lett 2007, 425, 53–58. [Google Scholar]
- Van Wayenbergh, R.; Taelman, V.; Pichon, B.; Fischer, A.; Kricha, S.; Gessler, M.; Christophe, D.; Bellefroid, E.J. Identification of boip, a novel cdna highly expressed during spermatogenesis that encodes a protein interacting with the orange domain of the hairy-related transcription factor hrt1/hey1 in xenopus and mouse. Dev. Dyn 2003, 228, 716–725. [Google Scholar]
- Jacot, T.A.; Zalenskaya, I.; Mauck, C.; Archer, D.F.; Doncel, G.F. Tspy4 is a novel sperm-specific biomarker of semen exposure in human cervicovaginal fluids; potential use in hiv prevention and contraception studies. Contraception 2013, 88, 387–395. [Google Scholar]
- Kido, T.; Schubert, S.; Schmidtke, J.; Chris Lau, Y.F. Expression of the human tspy gene in the brains of transgenic mice suggests a potential role of this y chromosome gene in neural functions. Yi Chuan Xue Bao 2011, 38, 181–191. (in Chinese). [Google Scholar]
- Williams, M.; Lyu, M.S.; Yang, Y.L.; Lin, E.P.; Dunbrack, R.; Birren, B.; Cunningham, J.; Hunter, K. Ier5, a novel member of the slow-kinetics immediate-early genes. Genomics 1999, 55, 327–334. [Google Scholar]
- Cirelli, C.; Tononi, G. Gene expression in the brain across the sleep-waking cycle. Brain Res 2000, 885, 303–321. [Google Scholar]
- Baye, T.M.; Wilke, R.A.; Olivier, M. Genomic and geographic distribution of private snps and pathways in human populations. Personal. Med 2009, 6, 623–641. [Google Scholar]
- Konishi, Y.; Aoki, T.; Ohkawa, N.; Matsu-Ura, T.; Mikoshiba, K.; Tamura, T. Identification of the C-terminal activation domain of the neurod-related factor (ndrf). Nucleic Acids Res 2000, 28, 2406–2412. [Google Scholar]
- Bormuth, I.; Yan, K.; Yonemasu, T.; Gummert, M.; Zhang, M.; Wichert, S.; Grishina, O.; Pieper, A.; Zhang, W.; Goebbels, S.; et al. Neuronal basic helix-loop-helix proteins neurod2/6 regulate cortical commissure formation before midline interactions. J. Neurosci 2013, 33, 641–651. [Google Scholar]
- Schwab, M.H.; Bartholomae, A.; Heimrich, B.; Feldmeyer, D.; Druffel-Augustin, S.; Goebbels, S.; Naya, F.J.; Zhao, S.; Frotscher, M.; Tsai, M.J.; et al. Neuronal basic helix-loop-helix proteins (nex and beta2/neuro d) regulate terminal granule cell differentiation in the hippocampus. J. Neurosci 2000, 20, 3714–3724. [Google Scholar]
- Konishi, Y.; Matsu-ura, T.; Mikoshiba, K.; Tamura, T. Stimulation of gene expression of neurod-related factor in the mouse brain following pentylenetetrazol-induced seizures. Brain Res 2001, 97, 129–136. [Google Scholar]
- Lin, C.H.; Hansen, S.; Wang, Z.; Storm, D.R.; Tapscott, S.J.; Olson, J.M. The dosage of the neurod2 transcription factor regulates amygdala development and emotional learning. Proc. Natl. Acad. Sci. USA 2005, 102, 14877–14882. [Google Scholar]
- Lin, C.H.; Stoeck, J.; Ravanpay, A.C.; Guillemot, F.; Tapscott, S.J.; Olson, J.M. Regulation of neurod2 expression in mouse brain. Dev. Biol 2004, 265, 234–245. [Google Scholar]
- Olson, J.M.; Asakura, A.; Snider, L.; Hawkes, R.; Strand, A.; Stoeck, J.; Hallahan, A.; Pritchard, J.; Tapscott, S.J. Neurod2 is necessary for development and survival of central nervous system neurons. Dev. Biol 2001, 234, 174–187. [Google Scholar]
- Flames, N.; Hobert, O. Gene regulatory logic of dopamine neuron differentiation. Nature 2009, 458, 885–889. [Google Scholar]
- Abe, H.; Okazawa, M.; Nakanishi, S. The etv1/er81 transcription factor orchestrates activity-dependent gene regulation in the terminal maturation program of cerebellar granule cells. Proc. Natl. Acad. Sci. USA 2011, 108, 12497–12502. [Google Scholar]
- Abe, H.; Okazawa, M.; Nakanishi, S. Gene regulation via excitation and bdnf is mediated by induction and phosphorylation of the etv1 transcription factor in cerebellar granule cells. Proc. Natl. Acad. Sci. USA 2012, 109, 8734–8739. [Google Scholar]
- Tuoc, T.C.; Stoykova, A. Er81 is a downstream target of pax6 in cortical progenitors. BMC Dev. Biol 2008, 8, 23. [Google Scholar]
- Arber, S.; Ladle, D.R.; Lin, J.H.; Frank, E.; Jessell, T.M. Ets gene er81 controls the formation of functional connections between group ia sensory afferents and motor neurons. Cell 2000, 101, 485–498. [Google Scholar]
- Zhang, Z.; Pinto, A.M.; Wan, L.; Wang, W.; Berg, M.G.; Oliva, I.; Singh, L.N.; Dengler, C.; Wei, Z.; Dreyfuss, G. Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy. Proc. Natl. Acad. Sci. USA 2013, 110, 19348–19353. [Google Scholar]
- Chen, Y.; Zou, H.; Yang, L.Y.; Li, Y.; Wang, L.; Hao, Y.; Yang, J.L. Er81-shrna inhibits growth of triple-negative human breast cancer cell line mda-mb-231 in vivo and in vitro. Asian Pac. J. Cancer Prev. 2012, 13, 2385–2392. [Google Scholar]
- Scheer, E.; Delbac, F.; Tora, L.; Moras, D.; Romier, C. Tfiid taf6–taf9 complex formation involves the heat repeat-containing C-terminal domain of taf6 and is modulated by taf5 protein. J. Biol. Chem 2012, 287, 27580–27592. [Google Scholar]
- Wilhelm, E.; Kornete, M.; Targat, B.; Vigneault-Edwards, J.; Frontini, M.; Tora, L.; Benecke, A.; Bell, B. Taf6delta orchestrates an apoptotic transcriptome profile and interacts functionally with p53. BMC Mol. Biol 2010, 11, 10. [Google Scholar]
- Mizuta, T.R.; Fukita, Y.; Miyoshi, T.; Shimizu, A.; Honjo, T. Isolation of cdna encoding a binding protein specific to 5′-phosphorylated single-stranded DNA with g-rich sequences. Nucleic Acids Res 1993, 21, 1761–1766. [Google Scholar]
- Krieger, F.; Elflein, N.; Ruiz, R.; Guerra, J.; Serrano, A.L.; Asan, E.; Tabares, L.; Jablonka, S. Fast motor axon loss in smard1 does not correspond to morphological and functional alterations of the NMJ. Neurobiol. Dis 2013, 54, 169–182. [Google Scholar]
- Tachi, N.; Kikuchi, S.; Kozuka, N.; Nogami, A. A new mutation of ighmbp2 gene in spinal muscular atrophy with respiratory distress type 1. Pediatr. Neurol 2005, 32, 288–290. [Google Scholar]
- Hinks, G.L.; Shah, B.; French, S.J.; Campos, L.S.; Staley, K.; Hughes, J.; Sofroniew, M.V. Expression of lim protein genes lmo1, lmo2, and lmo3 in adult mouse hippocampus and other forebrain regions: Differential regulation by seizure activity. J. Neurosci 1997, 17, 5549–5559. [Google Scholar]
- Herberth, B.; Minko, K.; Csillag, A.; Jaffredo, T.; Madarasz, E. Scl, gata-2 and lmo2 expression in neurogenesis. Int. J. Dev. Neurosci 2005, 23, 449–463. [Google Scholar]
- Kulemzina, I.; Schumacher, M.R.; Verma, V.; Reiter, J.; Metzler, J.; Failla, A.V.; Lanz, C.; Sreedharan, V.T.; Ratsch, G.; Ivanov, D. Cohesin rings devoid of scc3 and pds5 maintain their stable association with the DNA. PLoS Genet 2012, 8, e1002856. [Google Scholar]
- Chan, K.L.; Gligoris, T.; Upcher, W.; Kato, Y.; Shirahige, K.; Nasmyth, K.; Beckouet, F. Pds5 promotes and protects cohesin acetylation. Proc. Natl. Acad. Sci. USA 2013, 110, 13020–13025. [Google Scholar]
- Ren, Q.; Yang, H.; Rosinski, M.; Conrad, M.N.; Dresser, M.E.; Guacci, V.; Zhang, Z. Mutation of the cohesin related gene pds5 causes cell death with predominant apoptotic features in saccharomyces cerevisiae during early meiosis. Mutat. Res 2005, 570, 163–173. [Google Scholar]
- Zhang, B.; Chang, J.; Fu, M.; Huang, J.; Kashyap, R.; Salavaggione, E.; Jain, S.; Kulkarni, S.; Deardorff, M.A.; Uzielli, M.L.; et al. Dosage effects of cohesin regulatory factor pds5 on mammalian development: Implications for cohesinopathies. PLoS One 2009, 4, e5232. [Google Scholar]
- Hur, S.K.; Park, E.J.; Han, J.E.; Kim, Y.A.; Kim, J.D.; Kang, D.; Kwon, J. Roles of human ino80 chromatin remodeling enzyme in DNA replication and chromosome segregation suppress genome instability. Cell. Mol. Life Sci 2010, 67, 2283–2296. [Google Scholar]
- Seeber, A.; Dion, V.; Gasser, S.M. Checkpoint kinases and the ino80 nucleosome remodeling complex enhance global chromatin mobility in response to DNA damage. Genes Dev 2013, 27, 1999–2008. [Google Scholar]
- Park, E.J.; Hur, S.K.; Kwon, J. Human ino80 chromatin-remodelling complex contributes to DNA double-strand break repair via the expression of rad54b and xrcc3 genes. Biochem. J 2010, 431, 179–187. [Google Scholar]
- Fischle, W.; Franz, H.; Jacobs, S.A.; Allis, C.D.; Khorasanizadeh, S. Specificity of the chromodomain y chromosome family of chromodomains for lysine-methylated ark(s/t) motifs. J. Biol. Chem 2008, 283, 19626–19635. [Google Scholar]
- Gu, P.; Min, J.N.; Wang, Y.; Huang, C.; Peng, T.; Chai, W.; Chang, S. Ctc1 deletion results in defective telomere replication, leading to catastrophic telomere loss and stem cell exhaustion. EMBO J 2012, 31, 2309–2321. [Google Scholar]
- Chen, L.Y.; Redon, S.; Lingner, J. The human cst complex is a terminator of telomerase activity. Nature 2012, 488, 540–544. [Google Scholar]
- Kasbek, C.; Wang, F.; Price, C.M. Human ten1 maintains telomere integrity and functions in genome-wide replication restart. J. Biol. Chem 2013, 288, 30139–30150. [Google Scholar]
- Gramatges, M.M.; Bertuch, A.A. Short telomeres: From dyskeratosis congenita to sporadic aplastic anemia and malignancy. Transl. Res 2013, 162, 353–363. [Google Scholar]
- Lee, K.D.; Pai, M.Y.; Hsu, C.C.; Chen, C.C.; Chen, Y.L.; Chu, P.Y.; Lee, C.H.; Chen, L.T.; Chang, J.Y.; Huang, T.H.; et al. Targeted casp8ap2 methylation increases drug resistance in mesenchymal stem cells and cancer cells. Biochem. Biophys. Res. Commun 2012, 422, 578–585. [Google Scholar]
- Kumral, A.; Tuzun, F.; Tugyan, K.; Ozbal, S.; Yilmaz, O.; Yesilirmak, C.D.; Duman, N.; Ozkan, H. Role of epigenetic regulatory mechanisms in neonatal hypoxic-ischemic brain injury. Early Hum. Dev 2013, 89, 165–173. [Google Scholar]
- Imai, Y.; Kimura, T.; Murakami, A.; Yajima, N.; Sakamaki, K.; Yonehara, S. The ced-4-homologous protein flash is involved in fas-mediated activation of caspase-8 during apoptosis. Nature 1999, 398, 777–785. [Google Scholar]
- Yang, X.C.; Burch, B.D.; Yan, Y.; Marzluff, W.F.; Dominski, Z. Flash, a proapoptotic protein involved in activation of caspase-8, is essential for 3′ end processing of histone pre-mrnas. Mol. Cell 2009, 36, 267–278. [Google Scholar]
- Burmester, T.; Ebner, B.; Weich, B.; Hankeln, T. Cytoglobin: A novel globin type ubiquitously expressed in vertebrate tissues. Mol. Biol. Evolut 2002, 19, 416–421. [Google Scholar]
- Ascenzi, P.; Marino, M.; Polticelli, F.; Coletta, M.; Gioia, M.; Marini, S.; Pesce, A.; Nardini, M.; Bolognesi, M.; Reeder, B.J.; et al. Non-covalent and covalent modifications modulate the reactivity of monomeric mammalian globins. Biochim. Biophys. Acta 2013, 1834, 1750–1756. [Google Scholar]
- Tian, S.F.; Yang, H.H.; Xiao, D.P.; Huang, Y.J.; He, G.Y.; Ma, H.R.; Xia, F.; Shi, X.C. Mechanisms of neuroprotection from hypoxia-ischemia (hi) brain injury by up-regulation of cytoglobin (cygb) in a neonatal rat model. J. Biol. Chem 2013, 288, 15988–16003. [Google Scholar]
- Hundahl, C.A.; Elfving, B.; Muller, H.K.; Hay-Schmidt, A.; Wegener, G. A gene-environment study of cytoglobin in the human and rat hippocampus. PLoS One 2013, 8, e63288. [Google Scholar]
- Beltran-Parrazal, L.; Acuna, D.; Ngan, A.M.; Kim, E.; Ngan, A.; Kawakami, K.; Edmond, J.; Lopez, I.A. Neuroglobin, cytoglobin, and transcriptional profiling of hypoxia-related genes in the rat cerebellum after prenatal chronic very mild carbon monoxide exposure (25 ppm). Brain Res 2010, 1330, 61–71. [Google Scholar]
- Araki, T.; Milbrandt, J. Znrf proteins constitute a family of presynaptic e3 ubiquitin ligases. J. Neurosci 2003, 23, 9385–9394. [Google Scholar]
- Yoshida, K.; Watanabe, M.; Hatakeyama, S. Znrf1 interacts with tubulin and regulates cell morphogenesis. Biochem. Biophys. Res. Commun 2009, 389, 506–511. [Google Scholar]
- Saitoh, F.; Araki, T. Proteasomal degradation of glutamine synthetase regulates schwann cell differentiation. J. Neurosci 2010, 30, 1204–1212. [Google Scholar]
- Tidd, D.M.; Broughton, C.M.; Clark, R.E. Cpg oligodeoxynucleotide 5mer-induced apoptosis in molt-4 leukaemia cells does not require caspase 3 or new protein synthesis. Nucleic Acids Res 2003, 31, 2297–2304. [Google Scholar]
- Matsuki, H.; Takahashi, M.; Higuchi, M.; Makokha, G.N.; Oie, M.; Fujii, M. Both g3bp1 and g3bp2 contribute to stress granule formation. Genes Cells 2013, 18, 135–146. [Google Scholar]
- Takahashi, M.; Higuchi, M.; Matsuki, H.; Yoshita, M.; Ohsawa, T.; Oie, M.; Fujii, M. Stress granules inhibit apoptosis by reducing reactive oxygen species production. Mol. Cell. Biol 2013, 33, 815–829. [Google Scholar]
- Maretzky, T.; McIlwain, D.R.; Issuree, P.D.; Li, X.; Malapeira, J.; Amin, S.; Lang, P.A.; Mak, T.W.; Blobel, C.P. Irhom2 controls the substrate selectivity of stimulated adam17-dependent ectodomain shedding. Proc. Natl. Acad. Sci. USA 2013, 110, 11433–11438. [Google Scholar]
- Christova, Y.; Adrain, C.; Bambrough, P.; Ibrahim, A.; Freeman, M. Mammalian irhoms have distinct physiological functions including an essential role in tace regulation. EMBO Rep 2013, 14, 884–890. [Google Scholar]
- Hurtado, O.; Lizasoain, I.; Fernandez-Tome, P.; Alvarez-Barrientos, A.; Leza, J.C.; Lorenzo, P.; Moro, M.A. Tace/adam17-tnf-alpha pathway in rat cortical cultures after exposure to oxygen-glucose deprivation or glutamate. J. Cereb. Blood Flow Metab 2002, 22, 576–585. [Google Scholar]
- Meliopoulos, V.A.; Andersen, L.E.; Brooks, P.; Yan, X.; Bakre, A.; Coleman, J.K.; Tompkins, S.M.; Tripp, R.A. Microrna regulation of human protease genes essential for influenza virus replication. PLoS One 2012, 7, e37169. [Google Scholar]
- Liu, Y.; Kern, J.T.; Walker, J.R.; Johnson, J.A.; Schultz, P.G.; Luesch, H. A genomic screen for activators of the antioxidant response element. Proc. Natl. Acad. Sci. USA 2007, 104, 5205–5210. [Google Scholar]
- Staneviciene, I.; Sadauskiene, I.; Lesauskaite, V.; Ivanoviene, L.; Kasauskas, A.; Ivanov, L. Subacute effects of cadmium and zinc ions on protein synthesis and cell death in mouse liver. Medicina 2008, 44, 131–138. [Google Scholar]
- Munakata, K.; Iwamoto, K.; Bundo, M.; Kato, T. Mitochondrial DNA 3243A > G mutation and increased expression of lars2 gene in the brains of patients with bipolar disorder and schizophrenia. Biol. Psychiatry 2005, 57, 525–532. [Google Scholar]
- Haitina, T.; Lindblom, J.; Renstrom, T.; Fredriksson, R. Fourteen novel human members of mitochondrial solute carrier family 25 (slc25) widely expressed in the central nervous system. Genomics 2006, 88, 779–790. [Google Scholar]
- Fiermonte, G.; Paradies, E.; Todisco, S.; Marobbio, C.M.; Palmieri, F. A novel member of solute carrier family 25 (slc25a42) is a transporter of coenzyme a and adenosine 3′,5′-diphosphate in human mitochondria. J. Biol. Chem 2009, 284, 18152–18159. [Google Scholar]
- Palmieri, F. The mitochondrial transporter family (slc25): Physiological and pathological implications. Pflugers Arch 2004, 447, 689–709. [Google Scholar]
- Zhang, H.; Chen, X.; Sairam, M.R. Novel genes of visceral adiposity: Identification of mouse and human mesenteric estrogen-dependent adipose (meda)-4 gene and its adipogenic function. Endocrinology 2012, 153, 2665–2676. [Google Scholar]
- Stolzing, A.; Grune, T. Neuronal apoptotic bodies: Phagocytosis and degradation by primary microglial cells. FASEB J 2004, 18, 743–745. [Google Scholar]
- Prager-Khoutorsky, M.; Spira, M.E. Neurite retraction and regrowth regulated by membrane retrieval, membrane supply, and actin dynamics. Brain Res 2009, 1251, 65–79. [Google Scholar]
- Klein, M.E.; Younts, T.J.; Castillo, P.E.; Jordan, B.A. Rna-binding protein sam68 controls synapse number and local beta-actin mrna metabolism in dendrites. Proc. Natl. Acad. Sci. USA 2013, 110, 3125–3130. [Google Scholar]
- Ghosh, T.; Soni, K.; Scaria, V.; Halimani, M.; Bhattacharjee, C.; Pillai, B. Microrna-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic β-actin gene. Nucleic Acids Res 2008, 36, 6318–6332. [Google Scholar]
- Ferreira, E.; Cronje, M.J. Selection of suitable reference genes for quantitative real-time PCR in apoptosis-induced mcf-7 breast cancer cells. Mol. Biotechnol 2012, 50, 121–128. [Google Scholar]
- Riviere, J.B.; van Bon, B.W.; Hoischen, A.; Kholmanskikh, S.S.; O’Roak, B.J.; Gilissen, C.; Gijsen, S.; Sullivan, C.T.; Christian, S.L.; Abdul-Rahman, O.A.; et al. De novo mutations in the actin genes actb and actg1 cause baraitser-winter syndrome. Nat. Genet 2012, 44, 440–444. [Google Scholar]
- Miwa, T.; Manabe, Y.; Kurokawa, K.; Kamada, S.; Kanda, N.; Bruns, G.; Ueyama, H.; Kakunaga, T. Structure, chromosome location, and expression of the human smooth muscle (enteric type) γ-actin gene: Evolution of six human actin genes. Mol. Cell. Biol 1991, 11, 3296–3306. [Google Scholar]
- Kumar, A.; Crawford, K.; Close, L.; Madison, M.; Lorenz, J.; Doetschman, T.; Pawlowski, S.; Duffy, J.; Neumann, J.; Robbins, J.; et al. Rescue of cardiac alpha-actin-deficient mice by enteric smooth muscle gamma-actin. Proc. Natl. Acad. Sci. USA 1997, 94, 4406–4411. [Google Scholar]
- Li, G.Y.; Kim, M.; Kim, J.H.; Lee, M.O.; Chung, J.H.; Lee, B.H. Gene expression profiling in human lung fibroblast following cadmium exposure. Food Chem. Toxicol 2008, 46, 1131–1137. [Google Scholar]
- Marshall, T.W.; Aloor, H.L.; Bear, J.E. Coronin 2a regulates a subset of focal-adhesion-turnover events through the cofilin pathway. J. Cell Sci 2009, 122, 3061–3069. [Google Scholar]
- Huang, W.; Ghisletti, S.; Saijo, K.; Gandhi, M.; Aouadi, M.; Tesz, G.J.; Zhang, D.X.; Yao, J.; Czech, M.P.; Goode, B.L.; et al. Coronin 2a mediates actin-dependent de-repression of inflammatory response genes. Nature 2011, 470, 414–418. [Google Scholar]
- Franco, D.L.; Rezaval, C.; Caceres, A.; Schinder, A.F.; Ceriani, M.F. Ena/vasp downregulation triggers cell death by impairing axonal maintenance in hippocampal neurons. Mol. Cell. Neurosci 2010, 44, 154–164. [Google Scholar]
- Krause, M.; Leslie, J.D.; Stewart, M.; Lafuente, E.M.; Valderrama, F.; Jagannathan, R.; Strasser, G.A.; Rubinson, D.A.; Liu, H.; Way, M.; et al. Lamellipodin, an ena/vasp ligand, is implicated in the regulation of lamellipodial dynamics. Dev. Cell 2004, 7, 571–583. [Google Scholar]
- Klostermann, A.; Lutz, B.; Gertler, F.; Behl, C. The orthologous human and murine semaphorin 6a-1 proteins (sema6a-1/sema6a-1) bind to the enabled/vasodilator-stimulated phosphoprotein-like protein (evl) via a novel carboxyl-terminal zyxin-like domain. J. Biol. Chem 2000, 275, 39647–39653. [Google Scholar]
- Kubota, K.; Kim, J.Y.; Sawada, A.; Tokimasa, S.; Fujisaki, H.; Matsuda-Hashii, Y.; Ozono, K.; Hara, J. Lrrc8 involved in b cell development belongs to a novel family of leucine-rich repeat proteins. FEBS Lett 2004, 564, 147–152. [Google Scholar]
- Herrick, S.; Evers, D.M.; Lee, J.Y.; Udagawa, N.; Pak, D.T. Postsynaptic pdlim5/enigma homolog binds spar and causes dendritic spine shrinkage. Mol. Cell. Neurosci 2010, 43, 188–200. [Google Scholar]
- Hussain, N.K.; Yamabhai, M.; Bhakar, A.L.; Metzler, M.; Ferguson, S.S.; Hayden, M.R.; McPherson, P.S.; Kay, B.K. A role for epsin n-terminal homology/ap180 n-terminal homology (enth/anth) domains in tubulin binding. J. Biol. Chem 2003, 278, 28823–28830. [Google Scholar]
- Romanitan, M.O.; Popescu, B.O.; Spulber, S.; Bajenaru, O.; Popescu, L.M.; Winblad, B.; Bogdanovic, N. Altered expression of claudin family proteins in alzheimer’s disease and vascular dementia brains. J. Cell. Mol. Med 2010, 14, 1088–1100. [Google Scholar]
- Bruggeman, L.A.; Martinka, S.; Simske, J.S. Expression of tm4sf10, a claudin/emp/pmp22 family cell junction protein, during mouse kidney development and podocyte differentiation. Dev. Dyn 2007, 236, 596–605. [Google Scholar]
- Laketa, V.; Simpson, J.C.; Bechtel, S.; Wiemann, S.; Pepperkok, R. High-content microscopy identifies new neurite outgrowth regulators. Mol. Biol. Cell 2007, 18, 242–252. [Google Scholar]
- Laumet, G.; Petitprez, V.; Sillaire, A.; Ayral, A.M.; Hansmannel, F.; Chapuis, J.; Hannequin, D.; Pasquier, F.; Scarpini, E.; Galimberti, D.; et al. A study of the association between the adam12 and sh3pxd2a (sh3md1) genes and Alzheimer’s disease. Neurosci. Lett 2010, 468, 1–2. [Google Scholar]
- Harold, D.; Jehu, L.; Turic, D.; Hollingworth, P.; Moore, P.; Summerhayes, P.; Moskvina, V.; Foy, C.; Archer, N.; Hamilton, B.A.; et al. Interaction between the adam12 and sh3md1 genes may confer susceptibility to late-onset alzheimer’s disease. Am. J. Med. Genet. B 2007, 144B, 448–452. [Google Scholar]
- Malinin, N.L.; Wright, S.; Seubert, P.; Schenk, D.; Griswold-Prenner, I. Amyloid-β neurotoxicity is mediated by fish adapter protein and adam12 metalloprotease activity. Proc. Natl. Acad. Sci. USA 2005, 102, 3058–3063. [Google Scholar]
- Levi, G.; Aloisi, F.; Ciotti, M.T.; Gallo, V. Autoradiographic localization and depolarization-induced release of acidic amino acids in differentiating cerebellar granule cell cultures. Brain Res 1984, 290, 77–86. [Google Scholar]
|Table 1. Validation of microarray data by real-time quantitative RT-PCR. Real-time PCR was used to validate the change in gene expression detected by microarray and to support the survival effects of Gip on CGNs.|
|Name||Genbank||K25||K5||K5 + GIP||Forward primer||Reverse primer|
|Early growth response protein 1 (Egr1)||U75397||−0.94||0.11||1.58||5′-GTTGGAATGCTGTGGTTACC-3′||5′-GCCAAACAAGTCACTTTGTTTA-3′|
|1475 ± 85||3019 ± 108||3361 ± 102|
|NIPA-like domain containing 2 (Nipal2)||NM_001130559||−1.26||−0.22||0.71||5′-ACATGGAGAAGCAACCTCTG-3′||5′-CTCCGTAATTGTCAGCAGCT-3′|
|667 ± 16||2011 ± 91||4065 ± 133|
|Family with sequence similarity 171, member A2 (Fam171a2)||XM_001081512||0.11||−0.63||−1.58||5′-AGGACAACGTGTACCGCAAT-3′||5′-TGGGGATCAGGTTGAGGGAA-3′|
|2877 ± 128||1136 ± 92||871 ± 65|
|DEAD (Asp-Glu-Ala-Asp) box helicase 56 (Ddx56)||NM_0010042112||0.35||−0.53||0.18||5′-TCTTAGGCTGTCACCGACTT-3′||5′-ATTAGCCACTCTCACATCGC-3′|
|2493 ± 106||163 ± 12||2166 ± 77|
|Zinc finger protein 423 (Zfp423)||XM_001081512||−1.23||−0.27||0.59||5′-GAAGACAGGAACAGCGTGAC-3′||5′-GTCGTCATCACCATCTCCAG-3′|
|277 ± 31||856 ± 35||3184 ± 69|
|Neuronalpentraxin I (Nptx1)||NM_153735||−1.50||−0.39||1.14||5′-GGAGCTGAATGGTTACATGG-3′||5′-ATAAGTCCACTGCGCACAGA-3′|
|781 ± 32||2630 ± 85||4502 ± 181|
Microarray (upper row): mean normalized value (Log scale); Quantitative RT-PCR (lower row): mean ± SEM of copies/100 pg RT-RNA.
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