Identification of biomarkers for metastatic osteosarcoma based on DNA microarray data

Neoplasma

Volumn 62, Issue 3, 2015, Pages 365-371

  Wang, Q ^a  

^a THE SECOND AFFILIATED HOSPITAL OF HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

Differential coexpression network; Differentially expressed genes; Gene ontology; Osteosarcoma

Indexed keywords

BRAIN SPECIFIC ANGIOGENESIS INHIBITOR 2; C120RF35; CBP 80 DEPENDENT TRANSLATION INITIATION FACTOR; DUAL SPECIFICITY PHOSPHATASE 7; FORMIN LIKE 1; INITIATION FACTOR; PROTEIN; RHO GUANINE NUCLEOTIDE BINDING PROTEIN; TRANSIENT RECEPTOR POTENTIAL CHANNEL M3; TUMOR MARKER; UNCLASSIFIED DRUG;

ACTIN FILAMENT; ANGIOGENESIS; ARTICLE; CLUSTER ANALYSIS; DIFFERENTIALLY EXPRESSED GENE; FALSE POSITIVE RESULT; GENE; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE ONTOLOGY; GENE PRODUCT; GENETIC DATABASE; HUMAN; LUNG METASTASIS; METASTASIS; MICROARRAY ANALYSIS; MOLECULAR GENETICS; OSTEOSARCOMA;

EID: 84969705833     PISSN: 00282685     EISSN: 13384317     Source Type: Journal    
DOI: 10.4149/neo_2015_044     Document Type: Article

References (52)

1. OTTAVIANI G, JAFFE N. The epidemiology of osteosarcoma. Cancer Treat Res. 2009; 152: 3-13. http: //dx. doi. org/10. 1007/978-1-4419-0284-9 1
2. KASTE SC PC, CAIN AM ET AL. Metastases detected at the time of diagnosis of primary pediatric extremity oste-osarcomaat diagnosis: imaging features. Cancer. 1999; 86: 1602-1608. http: //dx. doi. org/10. 1002/(SICI)1097-0142-(19991015)86: 8<1602:: AID-CNCR31>3. 0. CQ: 2-R
3. SALINAS-SOUZA C, DE OLIVEIRA R, ALVES MT, GARCIA FILHO RJ, PETRILLI AS et al. The metastatic behavior of osteosarcoma by gene expression and cytogenetic analyses. Hum Pathol. 2013; 44: 2188-2198. http: //dx. doi. org/10. 1016/j. humpath. 2013. 04. 013
4. MARINA N, GEBHARDT M, TEOT L, GORLICK R. Biology and therapeutic advances for pediatric osteosarcoma, oncologist. 2004; 9: 422-441. http: //dx. doi. org/10. 1634/ theoncologist. 9-4-422
5. BACCI G, PICCI P, RUGGIERI P, MERCURI M, AVELLA M et al. Primary chemotherapy and delayed surgery (neoadjuvant chemotherapy) for osteosarcoma of the extremities. The Isti-tuto Rizzoli Experience in 127 patients treated preoperatively with intravenous methotrexate (high versus moderate doses) andintraarterial cisplatin. Cancer. 1990; 65: 2539-2553. http: // dx. doi. org/10. 1002/1097-0142(19900601)65: 11<2539:: AID-CNCR2820651125>3. 0. CQ; 2-M
6. CLARK JC, THOMAS DM, CHOONG PF, DASS CR. RECK--a newly discovered inhibitor of metastasis with prognostic significance in multiple forms of cancer. Cancer Metastasis Rev. 2007; 26: 675-683. http: //dx. doi. org/10. 1007/slQ555-007-9093-8
7. FUCHS B, PRITCHARD DJ. Etiology of osteosarcoma. Clin Orthop Relat Res. 2002: 40-52. http: //dx. doi. org/10. 1097/00003086-200204000-00007
8. DENSMORE CL, KLEINERMAN ES, GAUTAM A, JIA SF, XU B et al. Growth suppression of established human osteosarcoma lung metastases in mice by aerosol gene therapy with PEI-p53 complexes. Cancer Gene Ther. 2001; 8: 619-627. http: //dx. doi. org/10. 1038/sj. cgt. 7700343
9. LADANYI M, CHA C, LEWIS R, JHANWAR SC, HUVOS AG et al. MDM2 gene amplification in metastatic osteosarcoma. Cancer Res. 1993; 53: 16-18.
10. KHANNA C, WAN X, BOSE S, CASSADAY R, OLOMU O et al. The membrane-cytoskeleton linker ezrin is necessary for osteosarcoma metastasis. Nat Med. 2004; 10: 182-186. http: // dx. doi. org/10. 1038/nm982
11. STAMENKOVIC I. Matrix metalloproteinases in tumor invasion and metastasis. Semin Cancer Biol. 2000; 10: 415-433. http: //dx. doi. org/10. 1006/scbi. 2000. 0379
12. TANIMURA S, KADOMOTO R, TANAKA T, ZHANG YJ, KOUNO I et al. Suppression of tumor cell invasiveness by hydrolyzable tannins (plant polyphenols) via the inhibition of matrix metalloproteinase-2/-9 activity. Biochem Biophys Res Commun. 2005; 330: 1306-1313. http: //dx. doi. Org/10. 1016/j. bbrc. 2005. 03. 116
13. KAYAGA J, SOUBERBIELLE BE, SHEIKH N, MORROW WJ, SCOTT-TAYLOR T et al. Anti-tumour activity against B16-F10 melanoma with a GM-CSF secreting allogeneic tumour cell vaccine. Gene Ther. 1999; 6: 1475-1481. http: //dx. doi. org/10. 1038/si. gt. 3300961
14. WOLF M, EL-RIFAI W, TARKKANEN M, KONONEN J, SERRA M et al. Novel findings in gene expression detected in human osteosarcoma by cDNA microarray. Cancer Genet Cytogenet. 2000; 123: 128-132. http: //dx. doi. org/10. 1016/ SO165-4608(00)00319-8
15. FRITSCHE-GUENTHER R, NOSKE A, UNGETH MU, KUBAN RJ, SCHLAG PM et al. De novo expression of EphA2 in osteosarcoma modulates activation ofthe mitogenic signalling pathway. Histopathology. 2010; 57: 836-850. http: //dx. doi. org/10. 1111/j. 1365-2559. 2010. 03713. x
16. LUO Y, DENG Z, CHEN J. Pivotal regulatory network and genes in osteosarcoma. Archives of medical science: AMS. 2013; 9: 569-575. http: //dx. doi. org/10. 5114/aoms. 2012. 30956
17. GAUTIER L, COPE L, BOLSTAD BM, IRIZARRY RA. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004; 20: 307-315. http: //dx. doi. org/10. 1093/ bioinformatics/btg405
18. IRIZARRY RA, HOBBS B, COLLIN F, BEAZER-BARCLAY YD, ANTONELLIS KJ et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003; 4: 249-264. http: //dx. doi. org/10. 1093/biostatistics/4. 2. 249
19. SMYTH GK. Limma: linear models for microarray data. Bioinformatics and computational biology solutions using R and Bioconductor. Springer; 2005. p. 397-420.
20. BENJAMINI Y, DRAI D, ELMER G, KAFKAFI N, GOLANI I. Controlling the false discovery rate in behavior genetics research. Behav Brain Res. 2001; 125: 279-284. http: //dx. doi. org/10. 1016/SO 166-4328(01)00297-2
21. WARNES GR, BOLKER B, BONEBAKKER L, GENTLEMAN R, HUBER W et al. gplots: Various R programming tools for plotting data. R package version. 2009; 2(4).
22. ASHBURNER M, BALL CA, BLAKE JA, BOTSTEIN D, BUTLER H et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25: 25-29. http: //dx. doi. org/10. 1038/75556
23. HUANG DA W, SHERMAN BT, LEMPICKI RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4: 44-57. http: //dx. doi. org/10. 1038/nprot. 2008. 211
24. FANG G, KUANG R, PANDEY G, STEINBACH M, MYERS CL et al. Subspace differential coexpression analysis: problem definition and a general approach. Pac Symp Biocomput. 2010: 145-156.
25. SMOOT ME, ONO K, RUSCHEINSKI J, WANG PL, IDEKER T. Cytoscape 2. 8: new features for data integration and network visualization. Bioinformatics. 2011; 27: 431-432. http: // dx. doi. org/10. 1093/bioinformatics/btq675
26. VASILIEV JM. Cytoskeletal mechanisms responsible for invasive migration of neoplastic cells. The International journal of developmental biology. 2004; 48: 425-439. http: //dx. doi. org/10. 1387/ijdb. 041806iv
27. WODARZ A, NATHKE I. Cell polarity in development and cancer. Nat Cell Biol. 2007; 9: 1016-1024. http: //dx. doi. org/10. 1038/ncb433
28. HIGGS HN. Formin proteins: a domain-based approach. Trends Biochem Sci. 2005; 30: 342-353. http: //dx. doi. org/10. 1016/j. tibs. 2005. 04. 014
29. YOUNG KG, COPELAND JW. Formins in cell signaling. Biochim Biophys Acta. 2010; 1803: 183-190. http: //dx. doi. org/10. 1016/j. bbamcr. 2008. 09. 017
30. KOVAR DR. Cell polarity: formin on the move. Curr Biol. 2006; 16: R535-538. http: //dx. doi. Org/10. 1016/j. cub. 2006. 06. 039
31. COLON-FRANCO JM, GOMEZ TS, BILLADEAU DD. Dynamic remodeling ofthe actin cytoskeleton by FMNLlgamma is required for structural maintenance of the Golgi complex. J Cell Sci. 2011; 124: 3118-3126. http: //dx. doi. org/10. 1242/ jcs. 083725
32. FAVARO P, TRAINA F, MACHADO-NETO JA, LAZARINI M, LOPES MR et al. FMNL1 promotes proliferation and migration of leukemia cells. J Leukoc Biol. 2013; 94: 503-512. http: //dx. doi. org/10. 1189/jlb. 0113057
33. YAYOSHI-YAMAMOTO S, TANIUCHI I, WATANABE T. FRL, a novel formin-related protein, binds to Rac and regulates cell motility and survival of macrophages. Mol Cell Biol. 2000; 20: 6872-6881. http: //dx. doi. org/10. 1128/MCB. 20. 18. 6872-6881. 2000
34. FOLKMAN J. Angiogenesis in cancer, vascular, rheumatoid and other disease. Nat Med. 1995; 1: 27-31. http: //dx. doi. org/10. 1038/nm0195-27
35. LEUNG DW, CACHIANES G, KUANG WJ, GOEDDEL DV, FERRARA N. Vascular endothelial growth factor is a secreted angiogenic mitogen. Science. 1989; 246: 1306-1309. http: // dx. doi. org/10. 1126/science. 2479986
36. COOMBER BL, DENTON J, SYLVESTRE A, KRUTH S. Bloodvessel density in canine osteosarcoma. Canadian journal of veterinary research = Revue canadienne de recherche veterinaire. 1998; 62: 199-204.
37. KREUTER M, BIEKER R, BIELACK SS, AURAS T, BUERGER H et al. Prognostic relevance of increased angiogenesis in osteosarcoma. Clin Cancer Res. 2004; 10: 8531-8537. http: // dx. doi. org/10. 1158/1078-0432. CCR-04-0969
38. CHARITY RM FA, DESHMUKH NS, GRIMER RJ. Vascular endothelial growth factor expression in osteosarcoma. Clin Orthop Relat Res. 2006; 448: 193-198. http: //dx. doi. org/10. 1097/0 l. blo. 0000205877. 05093. c9
39. JEONG BC, KIM MY, LEE JH, KEE HJ, KHO DH et al. Brain-specific angiogenesis inhibitor 2 regulates VEGF through GABP that acts as a transcriptional repressor. FEBS letters. 2006; 580: 669-676. http: //dx. doi. Org/10. 1016/j. febslet. 2005. 12. 086
40. OWENS DM, KEYSE SM. Differential regulation of MAP kinase signalling by dual-specificity protein phosphatases. Oncogene. 2007; 26: 3203-3213. http: //dx. doi. org/10. 1038/ sj. one. 1210412
41. LI GD CZ, ZHANG YQ, GONG HY, TANG H, ZHANG QL. Gene profiling of MAPK pathway in human osteosarcoma. Chinese Joural of Oncology. 2009; 31: 340-345.
42. NA KY KY, PARK YK. Mitogen-activated protein kinase pathway in osteosarcoma. Pathology. 2012; 44: 540-546. http: //dx. doi. org/10. 1097/PAT. 0b013e32835803bc
43. SPALLAROSSA P, ALTIERI P, GARIBALDI S, GHIGLI-OTTI G, BARISIONE C et al. Matrix metalloproteinase-2 and-9 are induced differently by doxorubicin in H9c2 cells: The role of MAP kinases and NAD(P)H oxidase. Car-diovasc Res. 2006; 69: 736-745. http: //dx. doi. Org/10. 1016/j. cardiores. 2005. 08. 009
44. LORENZ HM, HERRMANN M, WINKLER T, GAIPL U, KA-LDEN JR. Role of apoptosis in autoimmunity. Apoptosis. 2000; 5: 443-449. http: //dx. doi. Org/10. 1023/A: 1009692902805
45. SCHULZE-BERGKAMEN H, KRAMMER PH. Apoptosis in cancer-implications for therapy. Semin Oncol. 2004; 31: 90-119. http: //dx. doi. Org/10. 1053/j. seminoncol. 2003. ll. 006
46. WYLLIE AH. Apoptosis and the regulation of cell numbers in normal and neoplastic tissues: an overview. Cancer Metastasis Rev. 1992; 11: 95-103. http: //dx. doi. org/10. 1007/ BF00048057
47. FERRARI S, BERTONI F, ZANELLA L, SETOLA E, BAC-CHINI P et al. Evaluation of P-glycoprotein, HER-2/ErbB-2, p53, and Bcl-2 in primary tumor and metachronous lung metastases in patients with high-grade osteosarcoma. Cancer. 2004; 100: 1936-1942. http: //dx. doi. org/10. 1002/cncr. 2Q151
48. WU X, CAI ZD, LOU LM, ZHU YB. Expressions of p53, c-MYC, BCL-2 and apoptotic index in human osteosarcoma and their correlations with prognosis of patients. Cancer Epidemiol. 2012; 36: 212-216. http: //dx. doi. Org/10. 1016/j. canep. 2011. 08. 002
49. ZHANG W, HIRSCHLER-LASZKIEWICZ I, TONG Q, CONRAD K, SUN SC et al. TRPM2 is an ion channel that modulates hematopoietic cell death through activation of caspases and PARP cleavage. Am J Physiol Cell Physiol. 2006; 290: Cl 146-1159. http: //dx. doi. org/10. 1152/ aipcell. 00205. 2005
50. ZENG X, SIKKA SC, HUANG L, SUN C, XU C et al. Novel role for the transient receptor potential channel TRPM2 in prostate cancer cell proliferation. Prostate Cancer Prostatic Dis. 2010; 13: 195-201. http: //dx. doi. org/10. 1038/ pcan. 2009. 55
51. RENNIE PS, MAWJI NR, COLDMAN AJ, GODOLPHIN W, JONES EC et al. Relationship between variant forms of estrogen receptor RNA and an apoptosis-related RNA, TRPM-2, with survival in patients with breast cancer. Cancer. 1993; 72: 3648-3654. http: //dx. doi. org/10. 1002/1097-Q142-(19931215)72: 12<3648:: AID-CNCR2820721216>3. 0. CQ: 2-L
52. ORFANELLI U, WENKE AK, DOGLIONI C, RUSSO V, BOSSERHOFF AK et al. Identification of novel sense and antisense transcription at the TRPM2 locus in cancer. Cell Res. 2008; 18: 1128-1140. http: //dx. doi. org/10. 1038/ cr. 2008. 296