Development of novel real-time PCR methodology for quantification of COL11A1 mRNA variants and evaluation in breast cancer tissue specimens

BMC Cancer

Volumn 15, Issue 1, 2015, Pages

  Karaglani, Makrina ^a   Toumpoulis, Ioannis ^b   Goutas, Nikolaos ^a   Poumpouridou, Nikoleta ^a   Vlachodimitropoulos, Dimitrios ^a   Vasilaros, Spyridon ^c   Rizos, Ioannis ^b   Kroupis, Christos ^a  

^a UNIVERSITY OF ATHENS MEDICAL SCHOOL   (Greece)

^b NATIONAL AND KAPODISTRIAN UNIVERSITY OF ATHENS   (Greece)

^c Prolipsis Breast Cancer Clinic   (Greece)

Author keywords

Breast cancer; COL11A1; Real time qPCR; Variants

Indexed keywords

BIOLOGICAL MARKER; COLLAGEN TYPE 11; COLLAGEN TYPE 11 A1; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; MESSENGER RNA; PROGESTERONE RECEPTOR; UNCLASSIFIED DRUG; COL11A1 PROTEIN, HUMAN; TUMOR MARKER;

ADULT; AGE; AMPLICON; ARTICLE; BREAST CANCER; CANCER GRADING; CANCER PROGNOSIS; CANCER TISSUE; COL11A1 GENE; CONTROLLED STUDY; DISEASE ASSOCIATION; DISEASE FREE INTERVAL; DNA SEQUENCE; GENE; GENE DOSAGE; GENE EXPRESSION; GENETIC VARIABILITY; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; LYMPH NODE METASTASIS; MAJOR CLINICAL STUDY; MIDDLE AGED; MOUSE; NONHUMAN; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REAL TIME QUANTITATIVE POLYMERASE CHAIN REACTION; REPRODUCIBILITY; RNA ANALYSIS; SENSITIVITY AND SPECIFICITY; TUMOR VOLUME; AGED; ALTERNATIVE RNA SPLICING; BREAST NEOPLASMS; CANCER STAGING; FEMALE; GENETIC VARIATION; GENETICS; KAPLAN MEIER METHOD; METASTASIS; MORTALITY;

ADULT; AGED; ALTERNATIVE SPLICING; BIOMARKERS, TUMOR; BREAST NEOPLASMS; COLLAGEN TYPE XI; FEMALE; GENE EXPRESSION; GENETIC VARIATION; HUMANS; KAPLAN-MEIER ESTIMATE; MIDDLE AGED; NEOPLASM GRADING; NEOPLASM METASTASIS; NEOPLASM STAGING; REAL-TIME POLYMERASE CHAIN REACTION; RNA, MESSENGER; TUMOR BURDEN;

EID: 84944410036     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/s12885-015-1725-8     Document Type: Article

References (41)

1. Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M, et al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer. 2015;136(5):359-86.
2. Mendler M, Eich-Bender SG, Vaughan L, Winterhalter KH, Bruckner P. Cartilage contains mixed fibrils of collagen types II, IX, and XI. J Cell Biol. 1989;108(1):191-7.
3. Bernard M, Yoshioka H, Rodriguez E, Van der Rest M, Kimura T, Ninomiya Y, et al. Cloning and sequencing of pro-alpha 1 (XI) collagen cDNA demonstrates that type XI belongs to the fibrillar class of collagens and reveals that the expression of the gene is not restricted to cartilagenous tissue. J Biol Chem. 1988;263(32):17159-66.
4. Morris NP, Bachinger HP. Type XI collagen is a heterotrimer with the composition (1 alpha, 2 alpha, 3 alpha) retaining non-triple-helical domains. J Biol Chem. 1987;262(23):11345-50.
5. Burgeson RE, Hollister DW. Collagen heterogeneity in human cartilage: identification of several new collagen chains. Biochem Biophys Res Commun. 1979;87(4):1124-31.
6. Thom JR, Morris NP. Biosynthesis and proteolytic processing of type XI collagen in embryonic chick sterna. J Biol Chem. 1991;266(11):7262-9.
7. Fallahi A, Kroll B, Warner LR, Oxford RJ, Irwin KM, Mercer LM, et al. Structural model of the amino propeptide of collagen XI alpha1 chain with similarity to the LNS domains. Protein Sci. 2005;14(6):1526-37.
8. Oxford JT, DeScala J, Morris N, Gregory K, Medeck R, Irwin K, et al. Interaction between amino propeptides of type XI procollagen alpha1 chains. J Biol Chem. 2004;279(12):10939-45.
9. Toumpoulis IK, Oxford JT, Cowan DB, Anagnostopoulos CE, Rokkas CK, Chamogeorgakis TP, et al. Differential expression of collagen type V and XI alpha-1 in human ascending thoracic aortic aneurysms. Ann Thorac Surg. 2009;88(2):506-13.
10. Fischer H, Stenling R, Rubio C, Lindblom A. Colorectal carcinogenesis is associated with stromal expression of COL11A1 and COL5A2. Carcinogenesis. 2001;22(6):875-8.
11. Banyard J, Bao L, Hofer MD, Zurakowski D, Spivey KA, Feldman AS, et al. Collagen XXIII expression is associated with prostate cancer recurrence and distant metastases. Clin Cancer Res. 2007;13(9):2634-42.
12. Misawa K, Kanazawa T, Imai A, Endo S, Mochizuki D, Fukushima H, et al. Prognostic value of type XXII and XXIV collagen mRNA expression in head and neck cancer patients. Mol Clin Oncol. 2014;2(2):285-91.
13. Zhao Y, Zhou T, Li A, Yao H, He F, Wang L, et al. A potential role of collagens expression in distinguishing between premalignant and malignant lesions in stomach. Anat Rec. 2009;292(5):692-700.
14. Wang KK, Liu N, Radulovich N, Wigle DA, Johnston MR, Shepherd FA, et al. Novel candidate tumor marker genes for lung adenocarcinoma. Oncogene. 2002;21(49):7598-604.
15. Chong IW, Chang MY, Chang HC, Yu YP, Sheu CC, Tsai JR, et al. Great potential of a panel of multiple hMTH1, SPD, ITGA11 and COL11A1 markers for diagnosis of patients with non-small cell lung cancer. Oncol Rep. 2006;16(5):981-8.
16. Garcia-Pravia C, Galvan JA, Gutierrez-Corral N, Solar-Garcia L, Garcia-Perez E, Garcia-Ocana M, et al. Overexpression of COL11A1 by cancer-associated fibroblasts: clinical relevance of a stromal marker in pancreatic cancer. PLoS One. 2013;8(10):e78327.
17. Schmalbach CE, Chepeha DB, Giordano TJ, Rubin MA, Teknos TN, Bradford CR, et al. Molecular profiling and the identification of genes associated with metastatic oral cavity/pharynx squamous cell carcinoma. Arch Otolaryngol Head Neck Surg. 2004;130(3):295-302.
18. Wu YH, Chang TH, Huang YF, Huang HD, Chou CY. COL11A1 promotes tumor progression and predicts poor clinical outcome in ovarian cancer. Oncogene. 2013;33(26):3432-40.
19. Kim H, Watkinson J, Varadan V, Anastassiou D. Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1. BMC Med Genet. 2010;3:51.
20. Vargas AC, McCart Reed AE, Waddell N, Lane A, Reid LE, Smart CE, et al. Gene expression profiling of tumour epithelial and stromal compartments during breast cancer progression. Breast Cancer Res Treat. 2012;135(1):153-65.
21. Halsted KC, Bowen KB, Bond L, Luman SE, Jorcyk CL, Fyffe WE, et al. Collagen alpha1(XI) in normal and malignant breast tissue. Mod Pathol. 2008;21(10):1246-54.
22. Feng Y, Sun B, Li X, Zhang L, Niu Y, Xiao C, et al. Differentially expressed genes between primary cancer and paired lymph node metastases predict clinical outcome of node-positive breast cancer patients. Breast Cancer Res Treat. 2007;103(3):319-29.
23. Ellsworth RE, Seebach J, Field LA, Heckman C, Kane J, Hooke JA, et al. A gene expression signature that defines breast cancer metastases. Clin Exp Metastasis. 2009;26(3):205-13.
24. Yoshioka H, Inoguchi K, Khaleduzzaman M, Ninomiya Y, Andrikopoulos K, Ramirez F. Coding sequence and alternative splicing of the mouse alpha 1(XI) collagen gene (Col11a1). Genomics. 1995;28(2):337-40.
25. Zhidkova NI, Justice SK, Mayne R. Alternative mRNA processing occurs in the variable region of the pro-alpha 1(XI) and pro-alpha 2(XI) collagen chains. J Biol Chem. 1995;270(16):9486-93.
26. Oxford JT, Doege KJ, Morris NP. Alternative exon splicing within the amino-terminal nontriple-helical domain of the rat pro-alpha 1(XI) collagen chain generates multiple forms of the mRNA transcript which exhibit tissue-dependent variation. J Biol Chem. 1995;270(16):9478-85.
27. Medeck RJ, Sosa S, Morris N, Oxford JT. BMP-1-mediated proteolytic processing of alternatively spliced isoforms of collagen type XI. Biochem J. 2003;376(Pt 2):361-8.
28. Sinn P, Aulmann S, Wirtz R, Schott S, Marme F, Varga Z, et al. Multigene Assays for Classification, Prognosis, and Prediction in Breast Cancer: a Critical Review on the Background and Clinical Utility. Geburtshilfe Frauenheilkd. 2013;73(9):932-40.
29. Habel LA, Sakoda LC, Achacoso N, Ma XJ, Erlander MG, Sgroi DC, et al. HOXB13:IL17BR and molecular grade index and risk of breast cancer death among patients with lymph node-negative invasive disease. Breast Cancer Res. 2013;15(2):R24.
30. Caan BJ, Sweeney C, Habel LA, Kwan ML, Kroenke CH, Weltzien EK, et al. Intrinsic subtypes from the PAM50 gene expression assay in a population-based breast cancer survivor cohort: prognostication of short- and long-term outcomes. Cancer Epidemiol Biomarkers Prev. 2014;23(5):725-34.
31. Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med. 2004;351(27):2817-26.
32. Poumpouridou N, Kroupis C. Hereditary breast cancer: beyond BRCA genetic analysis; PALB2 emerges. Clin Chem Lab Med. 2012;50(3):423-34.
33. Pavlidou A, Kroupis C, Goutas N, Dalamaga M, Dimas K. Validation of a Real-Time Quantitative Polymerase Chain Reaction Method for the Quantification of 3 Survivin Transcripts and Evaluation in Breast Cancer Tissues. Clin Breast Cancer. 2014;14(2):122-31.
34. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55(4):611-22.
35. Kroupis C, Stathopoulou A, Zygalaki E, Ferekidou L, Talieri M, Lianidou ES. Development and applications of a real-time quantitative RT-PCR method (QRT-PCR) for BRCA1 mRNA. Clin Biochem. 2005;38(1):50-7.
36. Nolan T, Hands RE, Bustin SA. Quantification of mRNA using real-time RT-PCR. Nat Protoc. 2006;1(3):1559-82.
37. Tricarico C, Pinzani P, Bianchi S, Paglierani M, Distante V, Pazzagli M, et al. Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal Biochem. 2002;309(2):293-300.
38. Zygalaki E, Tsaroucha EG, Kaklamanis L, Lianidou ES. Quantitative real-time reverse transcription PCR study of the expression of vascular endothelial growth factor (VEGF) splice variants and VEGF receptors (VEGFR-1 and VEGFR-2) in non small cell lung cancer. Clin Chem. 2007;53(8):1433-9.
39. Warner LR, Brown RJ, Yingst SMC, Oxford JT. Isoform-specific Heparan Sulfate Binding within the Amino-terminal Noncollagenous Domain of Collagen aα1(XI). J Biol Chem. 2006;281(51):39507-16.
40. Nolan T, Hands RE, Ogunkolade W, Bustin SA. SPUD: a quantitative PCR assay for the detection of inhibitors in nucleic acid preparations. Anal Biochem. 2006;351(2):308-10.
41. Bowen KB, Reimers AP, Luman S, Kronz JD, Fyffe WE, Oxford JT. Immunohistochemical localization of collagen type XI alpha1 and alpha2 chains in human colon tissue. J Histochem Cytochem. 2008;56(3):275-83.