Defining suitable reference genes for RT-qPCR analysis on intestinal epithelial cells

Molecular Biotechnology

Volumn 54, Issue 3, 2013, Pages 930-938

  Sirakov, Maria ^a   Borra, Marco ^b   Cambuli, Francesca Maria ^c   Plateroti, Michelina ^c  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

^c CENTRE DE GÉNÉTIQUE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

IEC6; Intestinal crypt; Intestinal epithelium; Reference gene; RT qPCR

Indexed keywords

IEC6; INTESTINAL CRYPT; INTESTINAL EPITHELIUM; REFERENCE GENES; RT-QPCR;

CELL CULTURE; CELL PROLIFERATION; CELLS; GENES; MAMMALS; MOLECULAR BIOLOGY; POLYMERASE CHAIN REACTION;

TRANSCRIPTION;

FATTY ACID BINDING PROTEIN 2; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; HYPOXANTHINE GUANINE PHOSPHOTIBOSYL TRANSFERASE; MESSENGER RNA; PEPTIDYL PROLYL ISOMERASE A; PEPTIDYLPROLYL ISOMERASE B; PROTEIN; RIBOSOMAL PROTEIN P0; UNCLASSIFIED DRUG; VILLIN 1;

ANIMAL CELL; ARTICLE; CELL DIFFERENTIATION; CELL PROLIFERATION; COMPUTER PROGRAM; CONTROLLED STUDY; EPITHELIUM CELL; GAPDH GENE; GENE; GENE EXPRESSION; HPRT1 GENE; INTESTINE EPITHELIUM CELL; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOPHYSIOLOGY; PPIA GENE; PPIB GENE; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RPLP0 GENE; VIL1 GENE;

ANIMALS; CELL LINE; EPITHELIAL CELLS; GENE EXPRESSION; GENES; GENETIC MARKERS; INTESTINAL MUCOSA; MICE; RATS; REFERENCE VALUES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

MAMMALIA;

EID: 84882815773     PISSN: 10736085     EISSN: 15590305     Source Type: Journal    
DOI: 10.1007/s12033-012-9643-3     Document Type: Article

References (42)

1. Stappenbeck, T. S.; Wong, M. H.; Saam, J. R.; Mysorekar, I. U.; Gordon, J. I. (1998). Notes from some crypt watchers: Regulation of renewal in the mouse intestinal epithelium. Current Opinion in Cell Biology, 10(6), 702-709.
2. Huang, E. H.; Wicha, M. S. (2008). Colon cancer stem cells: Implications for prevention and therapy. Trends in Molecular Medicine, 14(11), 503-509.
3. Stadtfeld, M.; Maherali, N.; Borkent, M.; Hochedlinger, K. (2010). A reprogrammable mouse strain from gene-targeted embryonic stem cells. Nature Methods, 7(1), 53-55.
4. Yu, J.; Vodyanik, M. A.; Smuga-Otto, K.; Antosiewicz-Bourget, J.; Frane, J. L.; Tian, S.; et al. (2007). Induced pluripotent stem cell lines derived from human somatic cells. Science, 318(5858), 1917-1920.
5. Wu, W. K.; Cho, C. H.; Lee, C. W.; Fan, D.; Wu, K.; Yu, J.; et al. (2010). Dysregulation of cellular signaling in gastric cancer. Cancer Letters, 295(2), 144-153.
6. Dheda, K.; Huggett, J. F.; Chang, J. S.; Kim, L. U.; Bustin, S. A.; Johnson, M. A.; et al. (2005). The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Analytical Biochemistry, 344(1), 141-143.
7. Bustin, S. A. (2010). Why the need for qPCR publication guidelines?-The case for MIQE. Methods, 50(4), 217-226.
8. Huggett, J.; Dheda, K.; Bustin, S.; Zumla, A. (2005). Real-time RT-PCR normalisation; strategies and considerations. Genes and Immunity, 6(4), 279-284.
9. Bustin, S. A.; Beaulieu, J. F.; Huggett, J.; Jaggi, R.; Kibenge, F. S.; Olsvik, P. A.; et al. (2010). MIQE precis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments. BMC Molecular Biology, 11, 74.
10. Vandesompele, J.; De Preter, K.; Pattyn, F.; Poppe, B.; Van Roy, N.; De Paepe, A.; et al. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology, 3(7), RESEARCH0034.
11. Andersen, C. L.; Jensen, J. L.; Orntoft, T. F. (2004). Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Research, 64(15), 5245-5250.
12. Quaroni, A.; Beaulieu, J. F. (1997). Cell dynamics and differentiation of conditionally immortalized human intestinal epithelial cells. Gastroenterology, 113(4), 1198-1213.
13. Quaroni, A.; May, R. J. (1980). Establishment and characterizaton of intestinal epithelial cell cultures. Methods in Cell Biology, 21B, 403-427.
14. Green, R. P.; Cohn, S. M.; Sacchettini, J. C.; Jackson, K. E.; Gordon, J. I. (1992). The mouse intestinal fatty acid binding protein gene: nucleotide sequence, pattern of developmental and regional expression, and proposed structure of its protein product. DNA and Cell Biology, 11(1), 31-41.
15. Levy, E.; Menard, D.; Delvin, E.; Montoudis, A.; Beaulieu, J. F.; Mailhot, G.; et al. (2009). Localization, function and regulation of the two intestinal fatty acid-binding protein types. Histochemistry and Cell Biology, 132(3), 351-367.
16. Dydensborg, A. B.; Herring, E.; Auclair, J.; Tremblay, E.; Beaulieu, J. F. (2006). Normalizing genes for quantitative RT-PCR in differentiating human intestinal epithelial cells and adenocarcinomas of the colon. American Journal of Physiology. Gastrointestinal and Liver Physiology, 290(5), G1067-G1074.
17. Wang, F.; Wang, J.; Liu, D.; Su, Y. (2010). Normalizing genes for real-time polymerase chain reaction in epithelial and nonepithelial cells of mouse small intestine. Analytical Biochemistry, 399(2), 211-217.
18. Strube, C.; Buschbaum, S.; Wolken, S.; Schnieder, T. (2008). Evaluation of reference genes for quantitative real-time PCR to investigate protein disulfide isomerase transcription pattern in the bovine lungworm Dictyocaulus viviparus. Gene, 425(1-2), 36-43.
19. Van Hiel, M. B.; Van Wielendaele, P.; Temmerman, L.; Van Soest, S.; Vuerinckx, K.; Huybrechts, R.; et al. (2009). Identification and validation of housekeeping genes in brains of the desert locust Schistocerca gregaria under different developmental conditions. BMC Molecular Biology, 10, 56.
20. Drago, S.; El Asmar, R.; Di Pierro, M.; Grazia Clemente, M.; Tripathi, A.; Sapone, A.; et al. (2006). Gliadin, zonulin and gut permeability: Effects on celiac and non-celiac intestinal mucosa and intestinal cell lines. Scandinavian Journal of Gastroenterology, 41(4), 408-419.
21. Trompette, A.; Blanchard, C.; Zoghbi, S.; Bara, J.; Claustre, J.; Jourdan, G.; et al. (2004). The DHE cell line as a model for studying rat gastro-intestinal mucin expression: Effects of dexamethasone. European Journal of Cell Biology, 83(7), 347-358.
22. Bavaria, M. N.; Ray, R. M.; Johnson, L. R. (2011). The phosphorylation state of MRLC is polyamine dependent in intestinal epithelial cells. American Journal of Physiology. Cell Physiology, 300(1), C164-C175.
23. Balakrishnan, A.; Stearns, A. T.; Park, P. J.; Dreyfuss, J. M.; Ashley, S. W.; Rhoads, D. B.; et al. (2010). MicroRNA mir-16 is anti-proliferative in enterocytes and exhibits diurnal rhythmicity in intestinal crypts. Experimental Cell Research, 316(20), 3512-3521.
24. Samuels, H. H.; Stanley, F.; Casanova, J. (1979). Depletion of l-3,5,3′-triiodothyronine and l-thyroxine in euthyroid calf serum for use in cell culture studies of the action of thyroid hormone. Endocrinology, 105(1), 80-85.
25. Weiser, M. M. (1973). Intestinal epithelial cell surface membrane glycoprotein synthesis. I. An indicator of cellular differentiation. Journal of Biological Chemistry, 248(7), 2536-2541.
26. Kress, E.; Rezza, A.; Nadjar, J.; Samarut, J.; Plateroti, M. (2009). The frizzled-related sFRP2 gene is a target of thyroid hormone receptor alpha1 and activates beta-catenin signaling in mouse intestine. Journal of Biological Chemistry, 284(2), 1234-1241.
27. Resuehr, D.; Spiess, A. N. (2003). A real-time polymerase chain reaction-based evaluation of cDNA synthesis priming methods. Analytical Biochemistry, 322(2), 287-291.
28. Rozen, S.; Skaletsky, H. (2000). Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology, 132, 365-386.
29. Fu, L. Y.; Jia, H. L.; Dong, Q. Z.; Wu, J. C.; Zhao, Y.; Zhou, H. J.; et al. (2009). Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses. BMC Cancer, 9, 49.
30. Shen, Y.; Li, Y.; Ye, F.; Wang, F.; Lu, W.; Xie, X. (2010). Identification of suitable reference genes for measurement of gene expression in human cervical tissues. Analytical Biochemistry, 405(2), 224-229.
31. Baba, T.; Kobayashi, H.; Kawasaki, H.; Mineki, R.; Naito, H.; Ohmori, D. (2010). Glyceraldehyde-3-phosphate dehydrogenase interacts with phosphorylated Akt resulting from increased blood glucose in rat cardiac muscle. FEBS Letters, 584(13), 2796-2800.
32. Wang, G. P.; Xu, C. S. (2010). Reference gene selection for real-time RT-PCR in eight kinds of rat regenerating hepatic cells. Molecular Biotechnology, 46(1), 49-57.
33. Akamine, R.; Yamamoto, T.; Watanabe, M.; Yamazaki, N.; Kataoka, M.; Ishikawa, M.; et al. (2007). Usefulness of the 5′ region of the cDNA encoding acidic ribosomal phosphoprotein P0 conserved among rats, mice, and humans as a standard probe for gene expression analysis in different tissues and animal species. Journal of Biochemical and Biophysical Methods, 70(3), 481-486.
34. Laborda, J. (1991). 36B4 cDNA used as an estradiol-independent mRNA control is the cDNA for human acidic ribosomal phosphoprotein PO. Nucleic Acids Research, 19(14), 3998.
35. Iwai, N.; Inagami, T. (1990). Molecular cloning of a complementary DNA to rat cyclophilin-like protein mRNA. Kidney International, 37(6), 1460-1465.
36. Arber, S.; Krause, K. H.; Caroni, P. (1992). s-cyclophilin is retained intracellularly via a unique COOH-terminal sequence and colocalizes with the calcium storage protein calreticulin. Journal of Cell Biology, 116(1), 113-125.
37. Kainer, D. B.; Doris, P. A. (2000). Cyclophilin B expression in renal proximal tubules of hypertensive rats. Hypertension, 35(4), 958-964.
38. Rycyzyn, M. A.; Reilly, S. C.; O'Malley, K.; Clevenger, C. V. (2000). Role of cyclophilin B in prolactin signal transduction and nuclear retrotranslocation. Molecular Endocrinology, 14(8), 1175-1186.
39. Pinto, D.; Robine, S.; Jaisser, F.; El Marjou, F. E.; Louvard, D. (1999). Regulatory sequences of the mouse villin gene that efficiently drive transgenic expression in immature and differentiated epithelial cells of small and large intestines. Journal of Biological Chemistry, 274(10), 6476-6482.
40. Robine, S.; Huet, C.; Moll, R.; Sahuquillo-Merino, C.; Coudrier, E.; Zweibaum, A.; et al. (1985). Can villin be used to identify malignant and undifferentiated normal digestive epithelial cells? Proceedings of the National Academy of Sciences of the United States of America, 82(24), 8488-8492.
41. Sirakov, M.; Zarrella, I.; Borra, M.; Rizzo, F.; Biffali, E.; Arnone, M. I.; et al. (2009). Selection and validation of a set of reliable reference genes for quantitative RT-PCR studies in the brain of the cephalopod mollusc Octopus vulgaris. BMC Molecular Biology, 10, 70.
42. Pfaffl, M. W.; Tichopad, A.; Prgomet, C.; Neuvians, T. P. (2004). Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-excel-based tool using pair-wise correlations. Biotechnology Letters, 26(6), 509-515.