Gene expression profiling for the investigation of soft tissue sarcoma pathogenesis and the identification of diagnostic, prognostic, and predictive biomarkers

Virchows Archiv

Volumn 456, Issue 2, 2010, Pages 141-151

  Beck, Andrew H ^a   West, Robert B ^a,b   Van De Rijn, Matt ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VA PALO ALTO HEALTH CARE SYSTEM   (United States)

Author keywords

Bioinformatics; Biomarkers; Gene expression profiling; Genomics; Microarrays; Molecular pathology; Sarcomas; Soft tissue tumors; Surgical pathology; Tumor biology

Indexed keywords

BIOLOGICAL MARKER; DNA; GEFITINIB; RNA; TUMOR MARKER;

CANCER GRADING; CARCINOGENESIS; CLINICAL TRIAL; DNA DETERMINATION; FLUORESCENCE IN SITU HYBRIDIZATION; GASTROINTESTINAL STROMAL TUMOR; GENE EXPRESSION PROFILING; GENETIC IDENTIFICATION; GENETIC MARKER; GIANT CELL TUMOR; HISTIOCYTIC SARCOMA; HUMAN; IMMUNOHISTOCHEMISTRY; LEIOMYOSARCOMA; LIPOSARCOMA; PIGMENTED VILLONODULAR SYNOVITIS; PLEOMORPHIC ADENOMA; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; PROGNOSIS; REVIEW; RNA ANALYSIS; RNA TRANSLATION; SMALL CELL SARCOMA; SOFT TISSUE SARCOMA; SYNOVIAL SARCOMA; TISSUE MICROARRAY; TREATMENT OUTCOME; TUMOR CLASSIFICATION; GENETICS; METABOLISM; PREDICTION AND FORECASTING; SARCOMA;

GENE EXPRESSION PROFILING; HUMANS; PREDICTIVE VALUE OF TESTS; PROGNOSIS; SARCOMA; TUMOR MARKERS, BIOLOGICAL;

EID: 77950365765     PISSN: 09456317     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00428-009-0774-2     Document Type: Review

References (97)

1. Weiss SW, Goldblum JR (2008) Enzinger and Weiss's soft tissue tumors, 5th edn. Mosby/Elsevier, Philadelphia
2. Fletcher CDM, Unni KK, Mertens F et al (2002) Pathology and genetics of tumours of soft tissue and bone. IARC Press, Lyon
3. Wendtner CM, Abdel-Rahman S, Krych M et al (2002) Response to neoadjuvant chemotherapy combined with regional hyperthermia predicts long-term survival for adult patients with retroperitoneal and visceral high-risk soft tissue sarcomas. J Clin Oncol 20:3156-3164
4. O'Sullivan B, Davis AM, Turcotte R et al (2002) Preoperative versus postoperative radiotherapy in soft-tissue sarcoma of the limbs: a randomised trial. Lancet 359:2235-2241
5. Borden EC, Baker LH, Bell RS et al (2003) Soft tissue sarcomas of adults: state of the translational science. Clin Cancer Res 9:1941-1956
6. Judson I (2008) State-of-the-art approach in selective curable tumours: soft tissue sarcoma. Ann Oncol 19(Suppl 7):vii166- vii169
7. Schena M, Shalon D, Davis RW et al (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
8. Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21:33-37
9. Lockhart DJ, Winzeler EA (2000) Genomics, gene expression and DNA arrays. Nature 405:827-836
10. Fodor SP, Rava RP, Huang XC et al (1993) Multiplexed biochemical assays with biological chips. Nature 364:555-556
11. Allison DB, Cui X, Page GP et al (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7:55-65
12. Butte A (2002) The use and analysis of microarray data. Nat Rev Drug Discov 1:951-960
13. Rhodes DR, Chinnaiyan AM (2004) Bioinformatics strategies for translating genome-wide expression analyses into clinically useful cancer markers. Ann N Y Acad Sci 1020:32-40
14. Rhodes DR, Kalyana-Sundaram S, Tomlins SA et al (2007) Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. Neoplasia 9:443-454
15. Segal E, Friedman N, Kaminski N et al (2005) From signatures to models: understanding cancer using microarrays. Nat Genet 37 (Suppl):S38-S45
16. Potti A, Dressman HK, Bild A et al (2006) Genomic signatures to guide the use of chemotherapeutics. Nat Med 12:1294-1300
17. Tschoep K, Kohlmann A, Schlemmer M et al (2007) Gene expression profiling in sarcomas. Crit Rev Oncol Hematol 63:111-124
18. Eilber FC, Dry SM (2008) Diagnosis and management of synovial sarcoma. J Surg Oncol 97:314-320
19. Clark J, Rocques PJ, Crew AJ et al (1994) Identification of novel genes, SYT and SSX, involved in the t(X;18)(p11.2;q11.2) translocation found in human synovial sarcoma. Nat Genet 7:502-508
20. Kawai A, Woodruff J, Healey JH et al (1998) SYT-SSX gene fusion as a determinant of morphology and prognosis in synovial sarcoma. N Engl J Med 338:153-160 (Pubitemid 28041862)
21. Haldar M, Randall RL, Capecchi MR (2008) Synovial sarcoma: from genetics to genetic-based animal modeling. Clin Orthop Relat Res 466:2156-2167
22. Nielsen TO, West RB, Linn SC et al (2002) Molecular characterisation of soft tissue tumours: a gene expression study. Lancet 359:1301-1307
23. Nakayama R, Nemoto T, Takahashi H et al (2007) Gene expression analysis of soft tissue sarcomas: characterization and reclassification of malignant fibrous histiocytoma. Mod Pathol 20:749-759
24. Baird K, Davis S, Antonescu CR et al (2005) Gene expression profiling of human sarcomas: insights into sarcoma biology. Cancer Res 65:9226-9235
25. Segal NH, Pavlidis P, Antonescu CR et al (2003) Classification and subtype prediction of adult soft tissue sarcoma by functional genomics. Am J Pathol 163:691-700
26. Allander SV, Illei PB, Chen Y et al (2002) Expression profiling of synovial sarcoma by cDNA microarrays: association of ERBB2, IGFBP2, and ELF3 with epithelial differentiation. Am J Pathol 161:1587-1595
27. Francis P, Namlos HM, Muller C et al (2007) Diagnostic and prognostic gene expression signatures in 177 soft tissue sarcomas: hypoxia-induced transcription profile signifies metastatic potential. BMC Genomics 8:73
28. Nagayama S, Katagiri T, Tsunoda T et al (2002) Genome-wide analysis of gene expression in synovial sarcomas using a cDNA microarray. Cancer Res 62:5859-5866 (Pubitemid 35204746)
29. Henderson SR, Guiliano D, Presneau N et al (2005) A molecular map of mesenchymal tumors. Genome Biol 6:R76
30. Nielsen TO, Hsu FD, O'Connell JX et al (2003) Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology. Am J Pathol 163:1449-1456
31. Terry J, Saito T, Subramanian S et al (2007) TLE1 as a diagnostic immunohistochemical marker for synovial sarcoma emerging from gene expression profiling studies. Am J Surg Pathol 31:240-246
32. Barco R, Hunt LB, Frump AL et al (2007) The synovial sarcoma SYT-SSX2 oncogene remodels the cytoskeleton through activation of the ephrin pathway. Mol Biol Cell 18:4003-4012
33. Lee YF, John M, Edwards S et al (2003) Molecular classification of synovial sarcomas, leiomyosarcomas and malignant fibrous histiocytomas by gene expression profiling. Br J Cancer 88:510-515
34. Fernebro J, Francis P, Eden P et al (2006) Gene expression profiles relate to SS18/SSX fusion type in synovial sarcoma. Int J Cancer 118:1165-1172
35. Ladanyi M, Antonescu CR, Leung DH et al (2002) Impact of SYT-SSX fusion type on the clinical behavior of synovial sarcoma: a multi-institutional retrospective study of 243 patients. Cancer Res 62:135-140
36. Guillou L, Benhattar J, Bonichon F et al (2004) Histologic grade, but not SYT-SSX fusion type, is an important prognostic factor in patients with synovial sarcoma: a multicenter, retrospective analysis. J Clin Oncol 22:4040-4050
37. Takenaka S, Ueda T, Naka N et al (2008) Prognostic implication of SYT-SSX fusion type in synovial sarcoma: a multi-institutional retrospective analysis in Japan. Oncol Rep 19:467-476 (Pubitemid 351176109)
38. Ray-Coquard I, Le Cesne A, Whelan JS et al (2008) A phase II study of gefitinib for patients with advanced HER-1 expressing synovial sarcoma refractory to doxorubicin-containing regimens. Oncologist 13:467-473 (Pubitemid 351679928)
39. Lubieniecka JM, de Bruijn DR, Su L et al (2008) Histone deacetylase inhibitors reverse SS18-SSX-mediated polycomb silencing of the tumor suppressor early growth response 1 in synovial sarcoma. Cancer Res 68:4303-4310
40. Lee YF, John M, Falconer A et al (2004) A gene expression signature associated with metastatic outcome in human leiomyosarcomas. Cancer Res 64:7201-7204 (Pubitemid 39372051)
41. Lee CH, Espinosa I, Vrijaldenhoven S et al (2008) Prognostic significance of macrophage infiltration in leiomyosarcomas. Clin Cancer Res 14:1423-1430 (Pubitemid 351413925)
42. Dei Tos AP (2000) Liposarcoma: new entities and evolving concepts. Ann Diagn Pathol 4:252-266
43. Singer S, Socci ND, Ambrosini G et al (2007) Gene expression profiling of liposarcoma identifies distinct biological types/ subtypes and potential therapeutic targets in well-differentiated and dedifferentiated liposarcoma. Cancer Res 67:6626-6636 (Pubitemid 47105508)
44. Sirvent N, Coindre JM, Maire G et al (2007) Detection of MDM2- CDK4 amplification by fluorescence in situ hybridization in 200 paraffin-embedded tumor samples: utility in diagnosing adipocytic lesions and comparison with immunohistochemistry and real-time PCR. Am J Surg Pathol 31:1476-1489 (Pubitemid 47482460)
45. Matushansky I, Hernando E, Socci ND et al (2008) A developmental model of sarcomagenesis defines a differentiation-based classification for liposarcomas. Am J Pathol 172:1069-1080 (Pubitemid 351520003)
46. Tos AP (2006) Classification of pleomorphic sarcomas: where are we now? Histopathology 48:51-62
47. Ozzello L, Stout AP, Murray MR (1963) Cultural characteristics of malignant histiocytomas and fibrous xanthomas. Cancer 16:331-344
48. Fletcher CD (1992) Pleomorphic malignant fibrous histiocytoma: fact or fiction? A critical reappraisal based on 159 tumors diagnosed as pleomorphic sarcoma. Am J Surg Pathol 16:213-228
49. Fletcher CD, Gustafson P, Rydholm A et al (2001) Clinicopathologic re-evaluation of 100 malignant fibrous histiocytomas: prognostic relevance of subclassification. J Clin Oncol 19:3045-3050 (Pubitemid 32565442)
50. Fletcher CD (2006) The evolving classification of soft tissue tumours: an update based on the new WHO classification. Histopathology 48:3-12
51. Matushansky I, Hernando E, Socci ND et al (2007) Derivation of sarcomas from mesenchymal stem cells via inactivation of the Wnt pathway. J Clin Invest 117:3248-3257 (Pubitemid 350096982)
52. Miettinen M, Lasota J (2006) Gastrointestinal stromal tumors: review on morphology, molecular pathology, prognosis, and differential diagnosis. Arch Pathol Lab Med 130:1466-1478 (Pubitemid 44520713)
53. Joensuu H, Roberts PJ, Sarlomo-Rikala M et al (2001) Effect of the tyrosine kinase inhibitor STI571 in a patient with a metastatic gastrointestinal stromal tumor. N Engl J Med 344:1052-1056 (Pubitemid 32267975)
54. Heinrich MC, Corless CL, Demetri GD et al (2003) Kinase mutations and imatinib response in patients with metastatic gastrointestinal stromal tumor. J Clin Oncol 21:4342-4349 (Pubitemid 46621810)
55. Sciot R, Debiec-Rychter M, Daugaard S et al (2008) Distribution and prognostic value of histopathologic data and immunohistochemical markers in gastrointestinal stromal tumours (GISTs): an analysis of the EORTC phase III trial of treatment of metastatic GISTs with imatinib mesylate. Eur J Cancer 44:1855-1860
56. Subramanian S, West RB, Corless CL et al (2004) Gastrointestinal stromal tumors (GISTs) with KIT and PDGFRA mutations have distinct gene expression profiles. Oncogene 23:7780-7790 (Pubitemid 39457028)
57. West RB, Corless CL, Chen X et al (2004) The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status. Am J Pathol 165:107-113 (Pubitemid 38821818)
58. Espinosa I, Lee CH, Kim MK et al (2008) A novel monoclonal antibody against DOG1 is a sensitive and specific marker for gastrointestinal stromal tumors. Am J Surg Pathol 32:210-218 (Pubitemid 351172135)
59. Yang YD, Cho H, Koo JY et al (2008) TMEM16A confers receptor-activated calcium-dependent chloride conductance. Nature 455:1210-1215
60. Price ND, Trent J, El-Naggar AK et al (2007) Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci U S A 104:3414-3419 (Pubitemid 46364173)
61. Khan J, Wei JS, Ringner M et al (2001) Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 7:673-679 (Pubitemid 32588022)
62. Ohali A, Avigad S, Zaizov R et al (2004) Prediction of high risk Ewing's sarcoma by gene expression profiling. Oncogene 23:8997-9006 (Pubitemid 39657791)
63. Cheung IY, Feng Y, Danis K et al (2007) Novel markers of subclinical disease for Ewing family tumors from gene expression profiling. Clin Cancer Res 13:6978-6983 (Pubitemid 350276878)
64. Ferreira BI, Alonso J, Carrillo J et al (2008) Array CGH and geneexpression profiling reveals distinct genomic instability patterns associated with DNA repair and cell-cycle checkpoint pathways in Ewing's sarcoma. Oncogene 27:2084-2090 (Pubitemid 351442743)
65. Hancock JD, Lessnick SL (2008) A transcriptional profiling metaanalysis reveals a core EWS-FLI gene expression signature. Cell Cycle 7:250-256
66. Davicioni E, Finckenstein FG, Shahbazian V et al (2006) Identification of a PAX-FKHR gene expression signature that defines molecular classes and determines the prognosis of alveolar rhabdomyosarcomas. Cancer Res 66:6936-6946 (Pubitemid 44197668)
67. Ebauer M, Wachtel M, Niggli FK et al (2007) Comparative expression profiling identifies an in vivo target gene signature with TFAP2B as a mediator of the survival function of PAX3/ FKHR. Oncogene 26:7267-7281 (Pubitemid 350085317)
68. Lae M, Ahn EH, Mercado GE et al (2007) Global gene expression profiling of PAX-FKHR fusion-positive alveolar and PAX-FKHR fusion-negative embryonal rhabdomyosarcomas. J Pathol 212:143-151 (Pubitemid 46852092)
69. Wachtel M, Dettling M, Koscielniak E et al (2004) Gene expression signatures identify rhabdomyosarcoma subtypes and detect a novel t(2;2)(q35;p23) translocation fusing PAX3 to NCOA1. Cancer Res 64:5539-5545 (Pubitemid 39095545)
70. Ren YX, Finckenstein FG, Abdueva DA et al (2008) Mouse mesenchymal stem cells expressing PAX-FKHR form alveolar rhabdomyosarcomas by cooperating with secondary mutations. Cancer Res 68:6587-6597
71. Schaefer KL, Eisenacher M, Braun Y et al (2008) Microarray analysis of Ewing's sarcoma family of tumours reveals characteristic gene expression signatures associated with metastasis and resistance to chemotherapy. Eur J Cancer 44:699-709
72. Linn SC, West RB, Pollack JR et al (2003) Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. Am J Pathol 163:2383-2395 (Pubitemid 37466479)
73. West RB, Harvell J, Linn SC et al (2004) Apo D in soft tissue tumors: a novel marker for dermatofibrosarcoma protuberans. Am J Surg Pathol 28:1063-1069 (Pubitemid 38971432)
74. Lazar AJ, Tuvin D, Hajibashi S et al (2008) Specific mutations in the {beta}-catenin gene (CTNNB1) correlate with local recurrence in sporadic desmoid tumors. Am J Pathol 173:1518-1527
75. Beck AH, Espinosa I, Gilks CB et al (2008) The fibromatosis signature defines a robust stromal response in breast carcinoma. Lab Invest 88:591-601 (Pubitemid 351733278)
76. West RB, Nuyten DS, Subramanian S et al (2005) Determination of stromal signatures in breast carcinoma. PLoS Biol 3:e187
77. Bacac M, Migliavacca E, Stehle JC et al (2006) A gene expression signature that distinguishes desmoid tumours from nodular fasciitis. J Pathol 208:543-553 (Pubitemid 43329341)
78. Heinrich MC, McArthur GA, Demetri GD et al (2006) Clinical and molecular studies of the effect of imatinib on advanced aggressive fibromatosis (desmoid tumor). J Clin Oncol 24:1195-1203 (Pubitemid 46638818)
79. Kotiligam D, Lazar AJ, Pollock RE et al (2008) Desmoid tumor: a disease opportune for molecular insights. Histol Histopathol 23:117-126
80. West RB, Rubin BP, Miller MA et al (2006) A landscape effect in tenosynovial giant-cell tumor from activation of CSF1 expression by a translocation in a minority of tumor cells. Proc Natl Acad Sci U S A 103:690-695
81. Murray LJ, Abrams TJ, Long KR et al (2003) SU11248 inhibits tumor growth and CSF-1R-dependent osteolysis in an experimental breast cancer bone metastasis model. Clin Exp Metastasis 20:757-766 (Pubitemid 38019277)
82. Beck AH, Espinosa I, Edris B et al (2009) The macrophage colony-stimulating factor 1 response signature in breast carcinoma. Clin Cancer Res 15:778-787
83. Edgar R, Domrachev M, Lash AE (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210 (Pubitemid 34679544)
84. Parkinson H, Sarkans U, ShojatalabMet al (2005) ArrayExpress- a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 33:D553-D555
85. Bild AH, Potti A, Nevins JR (2006) Linking oncogenic pathways with therapeutic opportunities. Nat Rev Cancer 6:735-741 (Pubitemid 44304232)
86. Hu P, Bader G, Wigle DA et al (2007) Computational prediction of cancer-gene function. Nat Rev Cancer 7:23-34 (Pubitemid 46023413)
87. Lamb J, Crawford ED, Peck D et al (2006) The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313:1929-1935
88. Lamb J (2007) The connectivity map: a new tool for biomedical research. Nat Rev Cancer 7:54-60
89. Dennis G Jr, Sherman BT, Hosack DA et al (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4:P3
90. von Mering C, Jensen LJ, Kuhn M et al (2007) STRING 7- recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35:D358-D362
91. Subramanian A, Tamayo P, Mootha VK et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102:15545-15550
92. Segal E, Friedman N, Koller D et al (2004) A module map showing conditional activity of expression modules in cancer. Nat Genet 36:1090-1098
93. Rhodes DR, Yu J, Shanker K et al (2004) Large-scale metaanalysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A 101:9309-9314
94. Bonnefoi H, Potti A, Delorenzi M et al (2007) Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00- 01 clinical trial. Lancet Oncol 8:1071-1078
95. Dressman HK, Berchuck A, Chan G et al (2007) An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer. J Clin Oncol 25:517-525
96. Subramanian S, Lui WO, Lee CH et al (2008) MicroRNA expression signature of human sarcomas. Oncogene 27:2015-2026
97. Camp RL, Neumeister V, Rimm DL (2008) A decade of tissue microarrays: progress in the discovery and validation of cancer biomarkers. J Clin Oncol 26:5630-5637