應(yīng)用cDNA微陣列技術(shù)篩選大鼠脊髓損傷修復(fù)相關(guān)基因-

1、Research PapercDNA microarray analysis of spinal cord injury and regeneration related genes in ratXIAO Lin, MA Zhen-Lian, LI Xin, LIN Qiu-Xia, QUE Hai-Ping, LIU Shao-Jun *Department of Neurobiology, Institute of Basic Medical Sciences, Academy of Military Medical Sciences, Beijing 100850, China Abst

2、ract: The acute traumatic spinal cord injury (SCI is a commonly seen and severe case in clinic. However, the repair and regeneration of injured spinal cord is limited. This is likely due to that different kinds of factors are involved in regeneration after SCI.In the present study, we used complemen

3、tary DNA microarray consisting of 4 041 specific probes from rat to identify genes that were differentially expressed after SCI. The animals were subjected to complete transection injury of the thoracic spinal cord (T8-T9. Sham operated animals received only a laminectomy. Four and a half days later

4、, rat spinal cord was dissected out for total RNA isolation. The fluorescent (Cy3 and Cy5 labeled probes were prepared and hybridized to the microarray. Genes that showed 2-fold difference in SCI tissue were identified. Sixty-five up-regulated genes consisted of 21 known genes, 30 known expressed se

5、quence tags (ESTs and 14unknown genes. Seventy-nine down-regulated genes comprised 20 known genes, 42 known ESTs and 17 unknown genes. In 41differentially expressed known genes, 5 up-regulated genes, i.e., tissue inhibitor of metalloproteinase 1 (Timp1, transgelin (Tagln,vimentin (Vim, Fc gamma rece

6、ptor, cathepsin S (Ctss, and 3 down-regulated genes, i.e., stearyl-CoA desaturase, coagulation factor II (F2, endosulfin alpha (Ensa, were further confirmed by reverse transcription polymerase chain reaction (RT-PCR. These genes may play a role in the response to tissue damage or repair following SC

7、I and characterization of them might be helpful to elucidate the molecular mechanisms of spinal cord injury and regeneration.Key words: spinal cord; gene expression; cDNA microarray; RT-PCR應(yīng)用cDNA 微陣列技術(shù)篩選大鼠脊髓損傷修復(fù)相關(guān)基因肖 林,馬振蓮,李 欣,林秋霞,闕海萍,劉少君*軍事醫(yī)學(xué)科學(xué)院基礎(chǔ)醫(yī)學(xué)研究所神經(jīng)生物學(xué)研究室,北京100850摘 要:脊髓損傷是一類常見的、高致殘率的中樞神經(jīng)系統(tǒng)疾病,由

8、于多種復(fù)雜因素影響其損傷后的修復(fù)過程,損傷脊髓的再生能力非常有限。本研究采用cDNA 微陣列技術(shù)篩選大鼠脊髓損傷后出現(xiàn)的差異表達(dá)基因。實(shí)驗(yàn)組動(dòng)物在T8-T9進(jìn)行脊髓全橫斷手術(shù),對(duì)照組動(dòng)物只打開椎板;4.5 d 后取脊髓進(jìn)行RNA 提取并在反轉(zhuǎn)錄過程中進(jìn)行Cy3/Cy5標(biāo)記,然后與預(yù)制的、帶有4 041條特異性探針的芯片進(jìn)行雜交。Cy5/Cy3信號(hào)比值2.0視為脊髓損傷后出現(xiàn)差異表達(dá)的基因。通過篩選,我們得到了65個(gè)上調(diào)表達(dá)基因(21個(gè)已知基因,30個(gè)已知EST 和14個(gè)未知基因和79個(gè)下調(diào)基因(20個(gè)已知基因,42個(gè)已知EST 和17個(gè)未知基因。進(jìn)一步通過半定量RT-PCR 對(duì)其中的5個(gè)上調(diào)已

9、知基因(Timp1, Tagln, Vim, Fc gamma receptor, Ctss和三個(gè)下調(diào)已知基因(stearyl-CoA desaturase, F2, Ensa的表達(dá)情況進(jìn)行了驗(yàn)證,結(jié)果顯示與芯片結(jié)果一致。這些基因可能在脊髓損傷后的修復(fù)過程中起一定的作用,對(duì)其深入研究將有助于揭示脊髓損傷修復(fù)的分子機(jī)制。關(guān)鍵詞:脊髓;基因表達(dá);c D N A 微陣列;反轉(zhuǎn)錄P C R 中圖分類號(hào):Q 42Received 2005-05-31 Accepted 2005-09-29This work was supported by the National Natural Science Fo

10、undation of China (No. 30200094, National Basic Research Priorities Programme of China (No.001CB510206, and National Key Project of Chinese Sanitation Miministries (No. WKZ-2001-1-18. *Corresponding author. Tel : +86-10-66931304; Fax: +86-10-68213039 ; E-mail: LiusjAcute traumatic spinal cord injury

11、 (SCI is an unexpected,devastating event, the consequences of which often per-sist for the life of the patients and influence in diverse ways not only the patients, but also family members and societyat large. In most countries, acute SCI occurs at an annual rate of 2040 persons per million1. Althou

12、gh prevention programs have been initiated, there is no evidence that the incidence is declining. The initial costs of hospitalization are high, and subsequent medical care is expensive. Thus, the development of effective treatments for SCI will have great benefits. The trauma to the spinal cord can

13、 result in the destruction of neurons, nerve fibers passing through the spinal cord, supporting glial cells and blood vessels, at the site of injury. At the site of mechanical insult, approxi-mately 30% of the neurofilament proteins were degraded within 1 h, and 70% of them were lost within 4 h afte

14、r injury. At the same time, the trauma to the spinal cord gives rise to changes of many genes expression level. These altered genes may lead to damage to the injured spinal cord or lack of regeneration in the injured spinal cord and per-manent functional impairment. SCI induced by trauma is a conseq

15、uence of an initial physical insult and a subsequent progressive injury process that involves various pathochemical events leading to tissue destruction. The response to SCI is known to occur in two phases. The first phase, the primary injury, is the mechanical trauma initially sustained. The second

16、 phase, termed secondary injury, is posttraumatic tissue damage. The neurological deficits caused by secondary injury occur within minutes of the injury and continue for days, weeks or longer2. The second phase is an autodestructive process that in-cludes physiological, biological and metabolic chan

17、ges. These changes result in axonal damage and cell loss. So, the second phase should be a target of pharmacological treatment. But despite intensive treatment efforts, the prog-nosis in acute SCI remains a pessimistic one. The injured spinal cord fails to regenerate due to two reasons, lack of rege

18、neration promoters and production of regeneration inhibitors. The injured mammalian neurons can success-fully regenerate in the peripheral nervous system (PNS. This regenerative capacity has been attributed to produc-tion of a variety of secreted polypeptides known as neu-rotrophic factors during th

19、e regeneration process3. In 2000, scientists found that Nogo protein may inhibit axon regeneration4. In addition, it has become increasingly rec-ognized that the nervous system also initiates reactive pro-cess in response to trauma that are neuroprotective and regenerative5. All these responses to S

20、CI are, in part, due to changes at the gene expression level.To further understand the molecular regulation of com-plex process of injury and regeneration after SCI, many genes have been isolated and extensively studied with con-ventional methods. Previous studies identified several SCI-related gene

21、 expression and protein changes using in situ hybridization, RT-PCR, Western blotting and immunohis-tochemistry6-11. However, these techniques are slow and laborious thereby enabling only a few genes to be investi-gated at a time. In order to identify more genes at the same time, many new technologi

22、es have been developed in re-cent years. GeneChip is one of the newest technologies. It provides insights into changes of global gene expression at a time. GeneChip or microarrays are constructed ei-ther with thousands of immobilized cDNAs or with photo-chemically synthesized oligonucleotides within

23、 1 cm2 on a glass or a plastic slide12. The development of GeneChipand related techniques has enabled researchers to profile the expression of thousands of genes simultaneously, providing an effective tool for large-scale gene expression studies.Song et al.analyzed changes in the mRNA abundance at 3

24、 and 24 h after SCI in adult rats using GeneChip13. Fan et al.identified and compared the genes that were differentially expressed in the periphery nervous systems and central nervous systems following injury by microarray techniques14. So microarray analysis is a pow-erful tool to quickly examine e

25、xpression of thousands of genes at a time.In the present study, we tried to analyze the changes in mRNA abundance at 4.5 d after traumatic injury to rat spinal cord by microarray techniques. Our results demon-strate that SCI causes a significant change in the expres-sion of genes, the products of wh

26、ich are involved in signal transduction, inflammation, apoptosis, lipid metabolism, acute phase reaction, remodeling injured tissue. Changes observed by microarray analysis for representative genes were also confirmed by RT-PCR.1 MATERIALS AND METHODS1.1 AnimalsSix adult littermate male Wistar rats,

27、 bought from the Ex-periment Animal Center of Academy of Military Medical Sciences, were used in this investigation. The animals, weighing 200300 g, were divided randomly into two groups, injured and control. All rats were anesthetized with intraperitoneal injections of sodium pentobarbital (40 mg/

28、kg. The skin was surgically scrubbed with ethanol and the hair at the surgical field was removed. The rats in in-jured group were subjected to a complete transection in-jury of the thoracic spinal cord (T8-T9. The control group received only a laminectomy. The animals, survived for another 4.5 d, we

29、re killed by decapitation. The whole spi-nal cord of each rat was dissected out for total RNA707 XIAO Lin et al: cDNA Microarray Analysis of Spinal Cord Injury and Regeneration Related Genes in Ratextraction.1.2 Total RNA extractionWe used RNeasy Mini Kit (Qiagen, Germany to extract total RNA. The s

30、pinal cords were homogenized using a conventional rotor-stator homogenizer. Then total RNA was extracted according to the protocol described by the manufacturer. The purity of the isolated total RNA was analyzed by absorption at 260 nm and 280 nm with ultra-violet spectrophotometry Unicam 330. The i

31、ntegrity of the total RNA was assessed with TAE agarose gel electro-phoresis.1.3 Preparation of probesTotal RNA (30 g of each group was converted to cDNA probes by reverse transcription with oligodT as primer. The cDNA probes were labeled with Cy3-dCTP for con-trol group and Cy5-dCTP for injured gro

32、up, respectively. Two kinds of cDNA probes were mixed up and dissolved in the hybridization solution.1.4 Hybridization and washingThe cDNA microarray including 4 041 spots was obtained from the BioStar Genechip, Inc., Shanghai. The 4 041 rat specific probes on the cDNA microarray were obtained by su

33、btraction hybridization between rat tissues. The probes were denatured at 95C for 2 min and chilled on the ice quickly. The cDNA microarray (prehybridization processed were denatured in 95C water for 30 s and then put into water-free ethanol. The denatured probes were added to region of chip and the

34、n sealed with a cover glass. Hybridization reaction lasted for 18 h at 42C. Then the cDNA microarray were washed with 0.5% washing solu-tion 1, following with the solution containing 0.5% wash-ing solution 1 and 2% washing solution 2 for 10 min at 60C and then with 5% washing solution 3 for 10 min a

35、t 60C. The chip was washed with 0.5% washing solution 1 again and then dried at room temperature. All hybridization solutions and washing solutions were provided by BioStar Genechip.1.5 Data analysisThe cDNA micrparray used contained several probes spe-cific for rat housekeepers (-actin, -actin, GAP

36、DH, 5 S rRNA, and so on, which served as positive controls. Sev-eral rice probes on the chip severed as negative controls and several probes severed as blank controls for back-ground subtraction. The specific probes on the chip are products of PCR from subtraction hybridization of rat tissues, that

37、is, these probes are specific for each tissue. The cDNA microarray was scanned with ScanArray4000 and the images were processed by GenePix 3.0 software.At first, the values of Cy3 or Cy5 were obtained after back-ground subtraction. The values of Cy5 under 200 were replaced with 200. The number of ef

38、fective genes was counted. The effective genes, valued according to both values of Cy3 and Cy5, are beyond 200 or either beyond 800 and Ri (Cy5/Cy3 is between 0.1 and 10. The average of the natural logarithm of Ri was computed, i.e. R. The normalization index (ND equals EXP(R. Second, the adjusted v

39、alue of Cy3, which multiply ND by Cy3, is Cy3*. The values of Cy3* under 200 were replaced with 200. At last, the value of Cy5/Cy3* of all genes were computed. The genes that ratio (Cy5/Cy3* is beyond 2 or under 0.5 are differentially expressed in injured group and control group.1.6 Confirmation of

40、differential expression by semi-quantitative RT-PCRThe semi-quantitative PCR protocols were employed to further confirm the cDNA microarray results. We chose five up-regulated known genes and three down-regulated known genes, they were, cathepsin S (Ctss, Fc gamma receptor, vimentin (Vim, Transgelin

41、 (Tagln, tissue inhibi-tor of metalloproteinase 1 (Timp1 and stearyl-CoA desaturase, coagulation factor II (F2, endosulfine alpha (Ensa respectively. At the same time, glyceraldehyde 3-phosphate dehydrogenase (GAPDH was amplified as an internal control. Total RNA (2 g from each group sample was reve

42、rsely transcribed with oligo(dT15primers using Superscipt II reverse transcriptase (Gibco-BRL. RT-PCR was performed in the Gene Amp PCR System 9700 (Applied Biosystems, USA. Briefly, 2 l cDNA and gene specific primers (Table 1 were added to TaKaRa PCR Mix (TaKaRa T aq DNA polymerase, dNTPs, optimal

43、buffer components; TaKaRa and subjected to PCR amplification. PCR prod-ucts were analyzed by electrophoresis on 1.5% agarose gels. Images of ethidium-bromide-stained bands were scaned with ImageMaster VDS (Amersham Pharmacia Biotech.2 RESUL TS2.1 Results of extraction of total RNAThe total RNA isola

44、ted from spinal cords was evaluated with ultraviolet analysis and agarose gel electrophoresis.The values of OD260/OD280of the total RNA from injury group and control group were 1.905 and 2.087 with ultra-violet analysis, respectively. The electrophoresis result showed that the ratio of 18 S/28 S was

45、 approximately 1/2 and the bands from low to high molecular weight appeared smear (Fig. 1. The data indicated that the total RNA iso-Acta Physiologica Sinica , December 25, 2005, 57 (6: 705-713708lated bears higher purity and integrity.2.2 Differentially expressed genes between the in-jured and the

46、control groupsThe hybridized cDNA microarray were scaned with ScanArray4000. The obtained images were analyzed with GenePix Pro 3.0. 3 913 spots were effective genes. Our experiment revealed that the expression of 144 genes changed significantly at 4.5 d after SCI as compared with control spinal cor

47、d tissue, including up-regulation of 65genes and down-regulation of 79 genes. The 144 differen-tially expressed genes included 41 known genes (Table 2,72 known ESTs and 31 unknown genes. A scatter diagram (Fig. 2 was made and the spots near the 45 straight line represented the genes without change i

48、n expression level,while those genes far away from the 45 straight line rep-resented the genes with differential expression. Fig. 1. Total RNA electrophoresis figure of control group and injuredgroup. The left is the control group and the right is the injured group.Fig. 2. A scatter diagram with X a

49、xis reflecting the intensity of hybridization signal of Cy3 and Y axis reflecting that of Cy5. Each spot stands for hybridized signal of a gene. The red spots indicate that value Y/value X are between 0.5 and 2.0 and belong to undifferentially expressed genes. The yellow spots indicate that theratio

50、 of value Y to value X is beyond 2.0 or under 0.5 and likely to be differentially expressed genes.Table 1. Sequences of primer pairs used for semi-quantitative RT-PCRGene (GenBank accession # Primer pairs Product Bases Sequence (5-3 size (bpTimp 1(NM_053819 135 - 163GCTTTCTGCAACTCGGACCTGGTTA 488 - 5

51、13AAGGGATGGCTGAACAGGGAAACAC 378Tagln (NM_031549 529 - 554ATGGCAGCAGTGCAGAGGACTGTAA 833 - 858TACCTCAAAGCTGTCCGGGCTAAGA 329Ctss (NM_017320 860 - 880GTGTTCTCGTGGTTGGCTAT 1 179 - 1 199GCGTCCTTGCTTACAGACTT 339Vim (NM_031140715 - 740ATGCTTCTCTGGCACGTCTTGACCT 1 028 - 1 053ACTGCACCTGTCTCCGGTATTCGTT 338Fc ga

52、mma receptor (X73371 388 - 413GTTTAAGGCCACAGTCAATGATAGT 807 - 832GACCAAGGATACCAGGATAATAACA 444F2 (NM_022924 1 137 - 1 162GATTCTTACATAGATGGGCGCATCG 1 464 - 1 489AAGGGCACTGGCTTCTTTAGCTTGA 352Ensa (NM_02184248 - 73GGAGAAGCAGGATACACAGGAGAAA 224 - 249CGGTAGCTGCTTGTTCTTCATCTTG 201Stearyl-CoA desaturase (J

53、02585 1 624 - 1 644AGGCAACCTTTCTGCTTTCT 2 001 - 2 021TTTCCCA TTCCCTTCACTCT 397GAPDH(NM_017008451 - 470TCCCTCAAGATTGTCAGCAA 739 - 758AGATCCACAACGGATACATT308709 XIAO Lin et al: cDNA Microarray Analysis of Spinal Cord Injury and Regeneration Related Genes in RatTable 2. Known genes differentially expre

54、ssed at 4.5 d after SCINo.GenBank Gene name Fold Function number changeUp-regulated1NM_019358Glycoprotein 38 (Gp38 2.011Membrane transport2V01222Preproalbumin 2.059Albumin precursor3Z49761RT1.Ma 2.123Unknown4NM_031083Phosphatidylinositol 4-kinase( Pik4cb 2.124Signal transduction5NM_012679Clusterin (

55、Clu 2.181Antiapoptotic protein6NM_019289Actin-related protein complex 1b (Arpc1b 2.197Cytoplasm transport7AF154572ERG2 protein 2.207Control of cellular excitability 8Y09111tMDC IV protein 2.274Unknown9NM_053538Lysosomal-associated protein transmembrane 5 (Laptm5 2.382Protein degradation10AJ223184DOR

56、A protein 2.425Cell surface receptor11X82669RT1.Au 2.471MHC class molecule12AF065438Mama 2.525Unknown13NM_012771Lysozyme (Lyz 2.549Metabolism14AF370882TORID 2.660Membrane component15NM_022597Cathepsin B (Ctsb 2.739Inflammation factor16AB023781Cathepsin Y 2.786Inflammation factor17NM_017320Cathepsin

57、S (Ctss 2.973Inflammation factor18X73371Fc gamma receptor 3.161Receptor19NM_031140Vimentin (Vim 3.306Cytoskeletal elements20NM_031549Transgelin(Smooth muscle 22 protein (Tagln 3.403Actin cross-linking protein21NM_053819Tissue inhibitor of metalloproteinase1 (Timp1 4.575Tissue reconstructionDown-regu

58、lated1J02585Stearyl-CoA desaturase0.197Lipid metabolism2NM_053389Survival of motor neuron protein interacting protein10.358Splicing pre-mRNA3NM_022924Coagulation factor II (F20.390Apoptosis4NM_021842Endosulfine alpha (Ensa0.411Inhibitor of voltage-gatedCa2+ channels5NM_012681Transthyretin (prealbumin,amyloidosis type I (Ttr0.425Acute-phase response6NM_053917Inositol polyphosphate-4-phosphatase type II0.447Signal transduction7NM_012598Lipoprotein lipase (Lpl0.456Lipid metabolism8NM_022629Gamma-butyrobetaine hydroxylase (Bbox0.458Lipid metabolism9U94856Paraoxonase0.465Antioxid