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Review

TRARESA: a tissue microarray-based hospital system for biomarker validation and discovery

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Pages 441-449 | Received 11 Feb 2008, Accepted 20 Feb 2008, Published online: 06 Jul 2009

References

  • Crawford J M, Tykocinski M L. Pathology as the enabler of human research. Lab Invest 2005; 85: 1058–1064
  • Kajdacsy-Balla A, Geynisman J M, Macias V, et al. Cooperative Prostate Cancer Tissue Resource. Practical aspects of planning, building, and interpreting tissue microarrays: the Cooperative Prostate Cancer Tissue Resource experience. J Mol Histol 2007; 38: 113–121
  • Sinard J H, Morrow J S. Informatics and anatomic pathology: meeting the challenges and charting the future. Hum Pathol 2001; 32: 143–148
  • Drake T A, Braun J, Marchevsky A, et al. A system for sharing routine surgical pathology specimens across institutions: the Shared Pathology Informatics Network. Hum Pathol 2007; 38: 1212–1225
  • Mohanty S K, Parwani A V, Crowley R S, et al. The importance of pathology informatics in translational research. Adv Anat Pathol 2007; 14: 320–322
  • Zhang D H, Salto-Tellez M, Chiu L L, et al. Tissue microarray study for classification of breast tumors. Life Sciences 2003; 73: 3189–3199
  • Battifora H. The multitumor (sausage) tissue block: novel method for immuno-histochemical antibody testing. Lab Invest 1986; 55: 244–248
  • Kononen J, Bubendorf L, Kallioniemi A, et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med 1998; 4: 844–847
  • Eguiluz C, Viguera E, Millan L, et al. Multitissue array review: a chronological description of tissue array techniques, applications and procedures. Pathol Res Pract 2006; 202: 561–568
  • Hoos A, Cordon-Cardo C. Tissue microarray profiling of cancer specimens and cell lines: opportunities and limitations. Lab Invest 2001; 81: 1331–1338
  • Manley S, Mucci N R, De Marzo A M, et al. Rubin relational database structure to manage high-density tissue microarray data and images for pathology studies focusing on clinical outcome. Am J Pathol 2001; 159: 837–843
  • Takikita C, Chung J Y, Hewitt S M. Tissue microarrays enabling high-throughput molecular pathology. Curr Opin Biotech 2007; 18: 318–325
  • Hans C P, Weisenburger D D, Greiner T C, et al. Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray. Blood 2004; 103: 275–282
  • Mousses S, Bubendorf L, Wagner U, et al. Clinical validation of candidate genes associated with prostate cancer progression in the CWR22 model system using tissue microarrays. Cancer Res 2002; 62: 1256–1260
  • Ito K, Liu Q, Salto-Tellez M, et al. Frequent cytoplasmic retention of RUNX3 in gastric cancer cells: A novel mechanism of inactivation. Cancer Res 2005; 65: 7743–7750
  • Huang B H, Laban M, Leung C HW, et al. Inhibition of histone deacetylase 2 increases apoptosis and p21Cip1/WAF1 expression, independent of histone deacetylase 1. Cell Death Differ 2005; 12: 395–404
  • Makretsov N A, Huntsman D G, Nielsen T O, et al. Hierarchical clustering analysis of tissue microarray immunostaining data identifies prognostically significant groups of breast carcinoma. Clin Cancer Res 2004; 10: 6143–6151
  • Jacquemier J, Ginestier C, Rougemont J, et al. Protein expression profiling identifies subclasses of breast cancer and predicts prognosis. Cancer Res 2005; 65: 767–779
  • Sauter G, Simon R, Hillan K. Tissue microarrays in drug discovery. Nat Rev Drug Discov 2003; 2: 962–972
  • Horvath L, Henshall S. Timely Topic: The application of tissue microarrays to cancer research. Pathology 2001; 33: 125–129
  • Zhang D H, Salto-Tellez M, Putti T C, et al. Reliability of tissue microarrays in detecting protein expression and gene amplification in breast cancer. Mod Pathol 2003; 16: 79–84
  • Shibata D, Martin W J, Arnheim N. Analysis of DNA sequences in forty-year old paraffin-embedded thin-tissue sections: a bridge between molecular biology and classical histology. Cancer Res 1988; 48: 4564–4566
  • Zhuang Z, Bertheau P, Emmert-Buck M R, et al. A microdissection technique for archival DNA analysis if specific cell populations in lesions <1 mm in size. Am J Pathol 1995; 146: 620–625
  • Emmert-Buck M R, Bonner R F, Smith P D, et al. Laser capture microdissection. Science 1996; 274: 998–1001
  • Rubin M A. Tech.Sight. Understanding disease cell by cell. Science 2002; 296: 1329–1330
  • Prince M E, Ubell M L, Castro J, et al. Tissue preserving approach to extracting DNA from paraffin-embedding specimens using tissue microarray technology. Head Neck 2007; 29: 465–471
  • Coombs N J, Gough A C, Primrose J N. Optimisation of DNA and RNA extraction from archival formalin-fixed tissue. Nucleic Acids Res 1999; 27: e12–e17
  • Shi S R, Cote R J, Wu L, et al. DNA extraction from archival formalin-fixed, paraffin-embedded tissue sections based on the antigen retrieval principle: heating under the influence of pH. J Histochem Cytochem 2002; 50: 1005–1011
  • Tos-Gillo A, Marco L D, Fiano V, et al. Efficient DNA extraction from 25 year old paraffin-embedded tissues: studies of 365 samples. Pathology 2007; 39: 345–348
  • Sjoholm M IL, Hoffmann G, Lindgren S, et al. Comparison of archival plasma and formalin-fixed paraffin-embedded tissue for genotyping in hepatocellular carcinoma. Cancer Epidemiol Biomarkers Prev 2005; 14: 251–255
  • Mc Sherry E A, McGoldrick A, Kay E W, et al. Formalin fixed paraffin embedded clinical tissues show spurious copy number changes in array-CGH profiles. Clin Genet 2007; 72: 441–447
  • Rupp G M, Locker J. Purification and analysis of RNA from paraffin-embedded tissues. Biotechniques 1988; 6: 56–60
  • Finke J, Fritzen R, Temes P, et al. An improved strategy and a useful housekeeping gene for RNA analysis from formalin-fixed, paraffin-embedded tissues by PCR. Biotechniques 1993; 14: 448–453
  • Stanta G, Bonin S. RNA quantitative analysis from fixed and paraffin-embedded tissues: membrane hybridization and capillary electrophoresis. Biotechniques 1998; 24: 271–276
  • Godfrey T E, Kim S H, Chavira M, et al. Quantitative mRNA expression analysis from formalin-fixed paraffin-embedded tissues using 5’ nuclease quantitative reverse transcription-polymerase chain reaction. J Mol Diagn 2000; 2: 84–91
  • Specht K, Richter T, Muller U, et al. Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumour tissue. Am J Pathol 2001; 158: 419–429
  • Coudry R A, Meireles S I, Stoyanova R, et al. Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue. J Mol Diagn 2007; 9: 70–79
  • Tsuji S, Hisaoka M, Morimitsu Y, et al. Detection of SYT-SSX fusion transcripts in synovial sarcoma by reverse transcription-polymerase chain reaction using archival paraffin-embedded tissues. Am J Pathol 1998; 153: 1807–1812
  • Tvrdik D, Povysil C, Svatosova J, et al. Molecular diagnosis of synovial sarcoma: RT-PCR detection of SYT-SSX1/2 fusion transcripts in paraffin-embedded tissue. Med Sci Monit 2005; 11: MT1–7
  • Aziz M H, Manoharan H T, Church D R, et al. Protein kinase C[euro] interacts with signal transducers and activators of transcription 3 (Stat3), phosphorylates Stat3ser727 and regulates its constitutive activation in prostate cancer. Cancer Res 2007; 67: 8828–8838
  • Mansilla F, Birkenkamp-Demtroder K, Kruhoffer M, et al. Differential expression of DHHC9 in microsatellite stable and instable human colorectal cancer subgroups. Br J Cancer 2007; 96: 1896–1903
  • Prasad M L, Pellegata N S, Kloos R T, Barbacioru C, Huang Y, Chapelle de la A. CITED1 protein expression suggests papillary thyroid carcinoma in high throughput tissue microarray based study. Thyroid 2004; 14: 169–175
  • Ito Y, Miyazono K. RUNX transcription factors as key targets of TGF-beta superfamily signaling. Curr Opin Genet Dev 2003; 132: 43–47
  • Blyth K, Cameron E R, Neil J C. The RUNX Genes: gain or loss of function in cancer. Nat Rev Cancer 2005; 5: 76–87
  • Li Q L, Ito K, Sakakura C, et al. Causal relationship between the loss of RUNX3 expression and gastric cancer. Cell 2002; 109: 113–124
  • Lau Q C, Raja E, Salto-Tellez M, et al. RUNX3 is frequently inactivated by dual mechanisms of protein mislocalization and promoter hypermethylation in breast cancer. Cancer Res 2006; 66: 6512–6520
  • Chen W, Salto-Tellez M, Palanisamy N, et al. Targets of genome copy number reduction in primary breast cancers identified by integrative genomics. Genes Chromosomes Cancer 2007; 46: 288–301
  • Gurrieri C, Capodieci P, Bernardi R, et al. Loss of tumor suppressor PML in human cancers of multiple histologic origins. J Natl Cancer Inst 2004; 96: 269–279
  • Shi T, Seligson D, Belldegrun A S, et al. Tumor classification by tissue microarray profiling: random forest clustering applied to renal cell carcinoma. Mod Pathol 2005; 18: 547–557
  • Duxbury M S, Matros E, Clancy T, et al. CEACAM6 is a novel biomarker in pancreatic adenocarcinoma and panIN lesions. Ann Surg 2005; 241: 491–496
  • Salto-Tellez M, Peh B K, Ito K, et al. Runx3 protein is overexpressed in human basal cell carcinomas. Oncogene 2006; 25: 7646–7649
  • Salto-Tellez M, Nga M E, Han H C, et al. Tissue microarrays characterize the clinical significance of a VEGF-A protein expression signature in gastro-intestinal stromal tumors. Br J Cancer 2007; 96: 776–782
  • Ferrara N, Kerbel R S. Angiogenesis as a therapeutic target. Nature 2005; 438: 967–974
  • Marx J. Medicine: Cancer-suppressing enzyme adds a link to type 2 diabetes. Science 2005; 310: 1259
  • Waltz E. Informed consent issues hobble cancer genome scheme. Nat Med 2006; 12: 719
  • Waltz E. Pricey cancer genome project struggles with sample shortage. Nat Med 2007; 13: 391
  • Salto-Tellez M. A case for integrated morphomolecular pathologists. Clin Chem 2007; 53: 1188–1190

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