Spatio-temporal expression of a novel neuron-derived neurotrophic factor (NDNF) in mouse brains during development
© Kuang et al; licensee BioMed Central Ltd. 2010
Received: 25 February 2010
Accepted: 25 October 2010
Published: 25 October 2010
Neuron-derived neurotrophic factor (NDNF) is evolutionarily well conserved, being present in invertebrate animals such as the nematode, Caenorhabditis elegans, as well as in the fruit fly, Drosophila melanogaster. Multiple cysteines are conserved between species and secondary structure prediction shows that NDNF is mainly composed of beta-strands. In this study, we aimed to investigate the function of NDNF.
NDNF is a glycosylated, disulfide-bonded secretory protein that contains a fibronectin type III domain. NDNF promoted migration and growth and elicited neurite outgrowth of mouse hippocampal neurons in culture. NDNF also protected cultured hippocamal neurons against excitotoxicity and amyloid beta-peptide toxicity. Western blotting showed that NDNF was exclusively expressed in the brain and spinal cord. Immunostaining indicated that NDNF was expressed by neurons and not by astrocytes. Cajal-Retzius cells, cortex neurons, hippocampus neurons, olfactory mitral cells, cerebellar purkinje cells, cerebellar granular cells and spinal neurons were found to be NDNF-positive. NDNF expression was observed in the neurons during development.
The results of this study indicated that NDNF is a novel neurotrophic factor derived from neurons that may be useful in the treatment of neuronal degeneration diseases and nerve injuries.
Extracellular signal molecules play an important role in the development of distinct patterns of neuronal growth, migration, differentiation and function. Neurotrophic factors (NTFs) are a large class of secreted trophic factors that have been shown to play a critical role in the development and function of the nervous system [1, 2]. NTFs induce differentiation, support the activity of neurons and prevent neuron death in neurodegenerative disorders and nervous lesions [3–5]. Since the discovery of nerve growth factor (NGF), many NTFs that are able to affect neurons in primary culture, during normal development and in experimental neuron lesions have been found, including neurotrophins, ciliar neurotrophic factor and members of the glial cell-derived neurotrophic factor (GDNF) family. Our group is currently trying to identify new neurotrophic factors.
The fly nord gene, which is primarily expressed in the mushroom body, is involved in olfactory learning . If fly cells use the same molecules and genes as humans, then there is a good chance that the pathway is conserved among organisms. The human ortholog of the nord gene is c4orf31, which encodes a fibronectin type-III domain-containing protein and belongs to a conserved protein family (Pfam10179: DUF2369) found from elegans to humans. C4orf31 is highly expressed in layer 1 cells of neocortex, potentially Cajal-Retzius (CR) neurons . CR cells are early-developing cells that are important in cortical lamination . Protein sequence analysis indicated that c4orf31 protein contains a putative signal peptide and may be secreted by CR cells. As a fibronectin type-III domain-containing protein and a putative secreted protein by CR cells, c4orf31 may participate in the regulation of neural development, migration and differentiation.
In this study, c4orf31 was engineered to be expressed in mammalian cells and identified as secreted glycosylated protein. C4orf31 promotes hippocampal neuron migration and axons outgrowth in culture. Western blotting and immunochemistry studies indicated that c4orf31 is exclusively expressed in the brain and specifically expressed in neurons. Based on these findings, c4orf31 is defined as neuron-derived neurotrophic factor (NDNF). Additionally, we evaluated the distribution of c4orf31 in the mouse brain during development.
Protein sequence analysis
Human (NP_078850), mouse (NP_765987), bovine (XP_597721), chicken (XP_420627), frog (NP_001085901), fly (NP_611900) and nematode (NP_500282) protein sequences were used in this study. In addition, the rat NDNF protein sequence was acquired by homology comparison. A sequence alignment software program, Clustalw 2.0, was used to align these protein sequences . A program for displaying phylogenies, Treeview, was used to display the protein phylogeny . The signal peptide sequence was predicted using SignalP3.0 . The protein secondary structure, N-glycosylation sites, disulfide bonds and globularity were analyzed using the PredictProtein program package [12–15].
Generation of pNDNF plasmid and transfection
The target gene fragment encoding the full protein was RT-PCR amplified from human brain tissue using the following primers: forward primer (5'-CCGCTCGAGAGGATGGTGCTGCTCCACTGGT-3'); reverse primer (5'-CCCAAGCTTACAGAACTTTCTAGTTTTCACAACC-3'). The products were then inserted between the XhoI and HindIII restriction sites of pcDNA3.1 (-)/myc-His A, named pNDNF and verified by sequencing. Next, control and pNDNF plasmids were introduced into HEK293 and COS7 cells using the phosphate calcium method described by Jordan et al. . Transfected HEK293 cells were then used to observe the intracellular distribution and the NDNF secreted into the culture medium was detected by western blotting. G418-resistant COS7 clones were screened for NDNF expression by immunofluorescence and the conditioned medium was used to conduct a transwell chemotaxis assay.
Antibodies used and western blotting
Rabbit polyclonal antibody against the NDNF C-terminal peptide SVKYQSKIVKTRK was prepared (Abmart, Shanghai). The specificity of NDNF antibody was tested by peptide blocking and overexpression. Mouse monoclonal antibody to neuN (Chemicon, MAB377), mouse anti-reelin monoclonal antibody (Chemicon, MAB5364), mouse monoclonal [GF5] antibody to GFAP (abcam, ab10062), rabbit anti-ERGIC-53/p58-Cy3 (Sigma, E6782), mouse monoclonal antibody to beta-actin and Myc tag (Santa Cruz) were used. The conditioned medium was concentrated by cold acetone precipitation. Tissue proteins were extracted with RIPA buffer and then separated by SDS/PAGE. The nitrocellulose membrane signals were detected by chemiluminescence. NDNF protein was immunoprecipitated from mouse brain extracts and then digested with N-Glycosidase F (PNGase F) according to the manufacturer's protocols (New England Biolabs).
Immunostaining of cultured cells
Cells were fixed with 4% paraformaldehyde (PFA) containing 0.4% sucrose for 30 minutes, permeabilized with 0.1% Triton X-100 in phosphate-buffered saline (PBS) for 5 minutes and then blocked with 5% fetal calf serum in PBS at room temperature for 45 minutes. After blocking, the cells were incubated at room temperature for 2 hours with NDNF antibody and anti-ERGIC-53/p58-Cy3, and then with Alex488-conjugated anti-mouse secondary antibody for 1 hour. DAPI was used to stain the nuclei.
Histology and immunohistochemistry
All procedures used by our facility are conducted in accordance with the National Institutes of Health guidelines and are subject to annual review by the Animal Care and Use Committee at Henan University. C57BL/6 mice (Model Animal Research Center, Nanjing) were maintained on a chow diet. Postnatal mouse brains were fixed by vascular perfusion with 4% PFA in PBS at pH 7.4 at physiological pressures (75-85 mm/Hg for the anesthetized mice). Mouse embryos were fixed in 4% PFA overnight at 4°C. Serial sections (5 μm) were used for HE staining, Nissl staining and immunostaining. After blocking with 5% goat serum in PBST (Blocking buffer) for 30 minutes, the sections were incubated with NDNF, reelin, neuN and GFAP antibody in blocking buffer for 2 hours. The samples were then probed with secondary antibody, Alex488 or Alex568-conjugated anti-mouse or rabbit IgG (Molecular probes). All samples were then evaluated using a BX61 fluorescence microscope (Olympus).
Hippocampal neuron culture
The method used for neuronal culture has been described previously . Briefly, cover slips were treated overnight with nitric acid. The cover slips were then coated with poly-D-lysine (Sigma, P0899) in boric acid buffer for at least 5 hours, followed by laminin (Sigma, L2020) in PBS for 2 hours before plating cells. The neonatal wistar rats were then decapitated and their heads were collected into a dish with chilled HBSS (Sigma, H4385). Next, the skull was opened and the brain was removed and transferred into a new dish with chilled HBSS. The meninges were then removed and the hippocampus was isolated and removed. The hippocampus was then digested in warmed 0.25% trypsin (Invitrogen) in HEPES buffer (pH7.2) with 1 mM EDTA for 20 minutes at 37°C. A fire-polished Pasteur pipette was then used to homogenize the hippocampus in DMEM with 10% horse serum (Gibco, 16050130), after which the dissociated cells were centrifuged at 80 g for 5 min. The supernatants were then removed and the cell pellets were resuspended in neural basal medium (Gibco, 21103-049) with 1/50 B27 supplement (Invitrogen, 17504-044) and then plated on the cover slips within a 24-well plate at the designated cell density (25,000 cells/cm2). EGFP expression and neuN co-staining were conducted to verify the culture method.
Transwell chemotaxis assay
Transwell (Costar) 24-well inserts with 8 μm pores were coated with poly-D-lysine and laminin as described above. Hippocampal neurons were plated on the supports, while the bottom chamber contained control medium from empty vector-transfected COS7 cells (600 ul), the conditioned medium from pNDNF plasmid-transfected COS7 cells (600 ul) or BDNF (20 ng/ml). After 2 days, the inserts were fixed in methyl alcohol at room temperature for 20 min and then stained with 0.1% crystal violet for 20 minutes, after which the upper cells were carefully removed. The migrated neurons were then photographed with a BX61 microscope and the number of cells was calculated using the Image Pro program. The number of migratory neurons, soma area and neurite length were counted or measured and statistically analyzed by performing student's t-test in SPSS 12.0 program. A significance level was accepted for p = 0.05. The experiment was repeated three times.
Analysis neuronal survival
Cells were plated at a density of 400 cells/mm2 of culture surface, and experiments were performed in 3-day-old cultures. Aβ25-35 and glutamate were purchased from Sigma and 1 mM stocks were prepared in sterile water 2 h before use. Vehicle, NDNF and BDNF, as in the transwell chemotaxis assay, were added to cultures 2 h before addition of glutamate (10 uM) or Aβ (5 uM). Twenty-four hours later, neuron viability was analyzed by incubating cells with the mitochondrial dye MTT for 3 hr and then assessed by quantitation of colorimetric conversion in triplicate. Percent survival is expressed relative to control (100%). Student's t-test was used for statistical comparisons.
Protein sequence analysis of NDNF
Intracellular localization and secretory characterization of NDNF
NDNF promotes neuron migration and neurite growth
NDNF supports the survival of hippocampal neurons
NDNF is exclusively expressed in neurons
Western blot analysis was conducted to detect the expression pattern of NDNF in mouse tissues, including the brain, spinal cord, heart, liver and kidney. The results showed that NDNF protein was only found in the brain and spinal cord (Figure 4B). Subsequently, immunofluorescence was used to reveal the expression of NDNF in the nervous system in greater detail.
Expression pattern of NDNF during mouse brain development
Neurotrophic factors play essential roles in the developing and mature nervous system [2, 4, 22, 23]. Accordingly, the neurotrophic factors and the genes encoding them have been studied in various developmental disorders, birth defects and neurodegenerative diseases [24–26]. In this study, we identified a novel, conserved and potent neuron-derived neurotrophic factor that may be useful for the treatment of neural degeneration diseases. NDNF didn't resemble the members of the neurotrophin family. The expression level varied among different neurons and during brain development.
Prototypic neurotrophic factors such as nerve growth factor (NGF) are secreted target-derived molecules that bind to transmembrane receptors on the cell surface . The receptor then dimerizes and is activated by transphosphorylation of the catalytic intracellular domain, which starts a complex intracellular signaling cascade that leads to immediate, early and late transcriptional changes in the target cell . Some neurotrophic factors are secreted, but not derived from a distant target tissue. These molecules, which include ciliary neurotrophic factor (CNTF), have an auto- or paracrine effect on neuronal cells [3, 29]. NDNF is exclusively expressed in neurons and may act through an auto- or paracrine loop.
Fibronectin type III domain is one of three types of internal repeats found in the plasma protein fibronectin . Approximately 2% of all animal proteins contain the FnIII repeat, including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors and adhesion molecules. FnIII-like domains are also found in bacterial glycosyl hydrolases . The FnIII region has a fold similar to that of immunoglobulin domains, with seven beta strands forming two antiparallel beta sheets that are packed against each other [32, 33]. FnIII-like domains of NDNF are distant from other members of FnIII superfamily, especially the conserved cysteines.
CR cells are transient neurons that contribute to construction of the cerebral cortex at specific developmental stages, and its axons appear to establish synaptic contacts on the apical dendrites of pyramidal cells . Our results indicated that CR cells also express NDNF protein at high levels, which may nourish CR cells and promote the migration and differentiation of neurons. The findings presented here also suggest that NDNF might play an essential role in cortical lamination.
NDNF is a novel neurotrophic factor derived from neurons that may be useful in the treatment of neuronal degeneration diseases and nerve injuries.
brain-derived neurotrophic factor
fibronectin type III
glial fibrillary acidic protein
glial cell-derived neurotrophic factor
Hank's buffered salt solution
neuron-derived neurotrophic factor
nerve growth factor
We thank Xiao-bing Yuan for providing BDNF protein. This work was supported by grants from the National Natural Science Foundation of China (30800175, 30771140) and by Faculty Research Grant of Henan University (07YBZR011).
- Levi-Montalcini R: The nerve growth factor 35 years later. Science. 1987, 237: 1154-1162. 10.1126/science.3306916.View ArticlePubMedGoogle Scholar
- Klein R: Role of neurotrophins in mouse neuronal development. FASEB J. 1994, 8: 738-744.PubMedGoogle Scholar
- Sendtner M, Schmalbruch H, Stöckli KA, Carroll P, Kreutzberg GW, Thoenen H: Ciliary neurotrophic factor prevents degeneration of motor neurons in mouse mutant progressive motor neuronopathy. Nature. 1992, 358: 502-504. 10.1038/358502a0.View ArticlePubMedGoogle Scholar
- Jaaro H, Beck G, Conticello SG, Fainzilber M: Evolving better brains: a need for neurotrophins?. Trends Neurosci. 2001, 24: 79-85. 10.1016/S0166-2236(00)01690-8.View ArticlePubMedGoogle Scholar
- Nagahara AH, Merrill DA, Coppola G, Tsukada S, Schroeder BE, Shaked GM, Wang L, Blesch A, Kim A, Conner JM, Rockenstein E, Chao MV, Koo EH, Geschwind D, Masliah E, Chiba AA, Tuszynski MH: Neuroprotective effects of brain-derived neurotrophic factor in rodent and primate models of Alzheimer's disease. Nat Med. 2009, 15: 331-337. 10.1038/nm.1912.PubMed CentralView ArticlePubMedGoogle Scholar
- Dubnau J, Chiang AS, Grady L, Barditch J, Gossweiler S, McNeil J, Smith P, Buldoc F, Scott R, Certa U, Broger C, Tully T: The staufen/pumilio pathway is involved in Drosophila long-term memory. Curr Biol. 2003, 13: 286-296. 10.1016/S0960-9822(03)00064-2.View ArticlePubMedGoogle Scholar
- Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, Desaki AL, Desta T, Diep E, Dolbeare TA, Donelan MJ, Dong HW, Dougherty JG, Duncan BJ, Ebbert AJ, Eichele G, et al, et al.: Genome-wide atlas of gene expression in the adult mouse brain. Nature. 2007, 445: 168-176. 10.1038/nature05453.View ArticlePubMedGoogle Scholar
- Soriano E, Del Río JA: The cells of cajal-retzius: still a mystery one century after. Neuron. 2005, 46: 389-394. 10.1016/j.neuron.2005.04.019.View ArticlePubMedGoogle Scholar
- Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673.PubMed CentralView ArticlePubMedGoogle Scholar
- Page RD: TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci. 1996, 12: 357-358.PubMedGoogle Scholar
- Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004, 340: 783-795. 10.1016/j.jmb.2004.05.028.View ArticlePubMedGoogle Scholar
- Rost B, Sander C: Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol. 1993, 232: 584-599. 10.1006/jmbi.1993.1413.View ArticlePubMedGoogle Scholar
- Bairoch A, Bucher P, Hofmann K: The PROSITE database, its status in 1997. Nucleic Acids Res. 1997, 25: 217-221. 10.1093/nar/25.1.217.PubMed CentralView ArticlePubMedGoogle Scholar
- Rost B, Yachdav G, Liu J: The PredictProtein server. Nucleic Acids Res. 2004, 32: W321-W326. 10.1093/nar/gkh377.PubMed CentralView ArticlePubMedGoogle Scholar
- Vullo A, Frasconi P: Disulfide connectivity prediction using recursive neural networks and evolutionary information. Bioinformatics. 2004, 20: 653-659. 10.1093/bioinformatics/btg463.View ArticlePubMedGoogle Scholar
- Jordan M, Schallhorn A, Wurm FM: Transfecting mammalian cells: Optimization of critical parameters affecting calcium-phosphate precipitate formation. Nucleic Acids Res. 1996, 24: 596-601. 10.1093/nar/24.4.596.PubMed CentralView ArticlePubMedGoogle Scholar
- Segura I, Essmann CL, Weinges S, Acker-Palmer A: Grb4 and GIT1 transduce ephrinB reverse signals modulating spine morphogenesis and synapse formation. Nat Neurosci. 2007, 10: 301-310. 10.1038/nn1858.View ArticlePubMedGoogle Scholar
- Robertson NG, Hamaker SA, Patriub V, Aster JC, Morton CC: Subcellular localisation, secretion, and post-translational processing of normal cochlin, and of mutants causing the sensorineural deafness and vestibular disorder, DFNA9. J Med Genet. 2003, 40: 479-486. 10.1136/jmg.40.7.479.PubMed CentralView ArticlePubMedGoogle Scholar
- Atwal JK, Massie B, Miller FD, Kaplan DR: The TrkB-Shc site signals neuronal survival and local axon growth via MEK and P13-kinase. Neuron. 2000, 27: 265-277. 10.1016/S0896-6273(00)00035-0.View ArticlePubMedGoogle Scholar
- Hirotsune S, Takahara T, Sasaki N, Hirose K, Yoshiki A, Ohashi T, Kusakabe M, Murakami Y, Muramatsu M, Watanabe S, Nakao K, Katsuki M, Hayashizaki Y: The reeler gene encodes a protein with an EGF-like motif expressed by pioneer neurons. Nat Genet. 1995, 10: 77-83. 10.1038/ng0595-77.View ArticlePubMedGoogle Scholar
- Pesold C, Impagnatiello F, Pisu MG, Uzunov DP, Costa E, Guidotti A, Caruncho HJ: Reelin is preferentially expressed in neurons synthesizing γ-aminobutyric acid in cortex and hippocampus of adult rats. Proc Natl Acad Sci USA. 1998, 95: 3221-3226. 10.1073/pnas.95.6.3221.PubMed CentralView ArticlePubMedGoogle Scholar
- Bibel M, Barde YA: Neurotrophins: key regulators of cell fate and cell shape in the vertebrate nervous system. Genes Dev. 2000, 14: 2919-2937. 10.1101/gad.841400.View ArticlePubMedGoogle Scholar
- Zhu B, Pennack J, McQuilton P, Forero MG, Mizuguchi K, Sutcliffe B, Gu CJ, Fenton JC, Hidalgo A: Drosophila neurotrophins reveal a common mechanism for nervous system formation. PLoS Biology. 2008, 6: e284-10.1371/journal.pbio.0060284.PubMed CentralView ArticlePubMedGoogle Scholar
- Phillips HS, Hains JM, Laramee GR, Rosenthal A, Winslow JW: Widespread expression of BDNF but not NT3 by target areas of basal forebrain cholinergic neurons. Science. 1990, 250: 290-294. 10.1126/science.1688328.View ArticlePubMedGoogle Scholar
- Scott SA, Mufson EJ, Weingartner JA, Skau KA, Crutcher KA: Nerve growth factor in Alzheimer's disease: increased levels throughout the brain coupled with declines in nucleus basalis. J Neurosci. 1995, 15: 6213-6221.PubMedGoogle Scholar
- Lee J, Fukumoto H, Orne J, Klucken J, Raju S, Vanderburg CR, Irizarry MC, Hyman BT, Ingelsson M: Decreased levels of BDNF protein in Alzheimer temporal cortex are independent of BDNF polymorphisms. Exp Neurol. 2005, 194: 91-96. 10.1016/j.expneurol.2005.01.026.View ArticlePubMedGoogle Scholar
- Hempstead BL, Martin-Zanca D, Kaplan DR, Parada LF, Chao MV: High-affinity NGF binding requires coexpression of the trk proto-oncogene and the low-affinity NGF receptor. Nature. 1991, 350: 678-683. 10.1038/350678a0.View ArticlePubMedGoogle Scholar
- Segal RA, Greenberg ME: Intracellular signaling pathways activated by neurotrophic factors. Annu Rev Neurosci. 1996, 19: 463-489.View ArticlePubMedGoogle Scholar
- Barbin G, Manthorpe M, Varon S: Purification of the chick eye ciliary neuronotrophic factor. J Neurochem. 1984, 43: 1468-1478. 10.1111/j.1471-4159.1984.tb05410.x.View ArticlePubMedGoogle Scholar
- Petersen TE, Thøgersen HC, Skorstengaard K, Vibe-Pedersen K, Sahl P, Sottrup-Jensen L, Magnusson S: Partial primary structure of bovine plasma fibronectin: three types of internal homology. Proc Natl Acad Sci USA. 1983, 80: 137-141. 10.1073/pnas.80.1.137.PubMed CentralView ArticlePubMedGoogle Scholar
- Little E, Bork P, Doolittle RF: Tracing the spread of fibronectin type III domains in bacterial glycohydrolases. J Mol Evol. 1994, 39: 631-643. 10.1007/BF00160409.View ArticlePubMedGoogle Scholar
- Huber AH, Wang YM, Bieber AJ, Bjorkman PJ: Crystal structure of tandem type III fibronectin domains from Drosophila neuroglian at 2.0 A. Neuron. 1994, 12: 717-731. 10.1016/0896-6273(94)90326-3.View ArticlePubMedGoogle Scholar
- Main AL, Harvey TS, Baron M, Boyd J, Campbell ID: The three-dimensional structure of the tenth type III module of fibronectin: an insight into RGD-mediated interactions. Cell. 1992, 71: 671-678. 10.1016/0092-8674(92)90600-H.View ArticlePubMedGoogle Scholar
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