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Gene expression analysis by transcript profiling coupled to a gene database query

Nature Biotechnology volume 17, pages 798–803 (1999)Cite this article

Abstract

We describe an mRNA profiling technique for determining differential gene expression that utilizes, but does not require, prior knowledge of gene sequences. This method permits high-throughput reproducible detection of most expressed sequences with a sensitivity of greater than 1 part in 100,000. Gene identification by database query of a restriction endonuclease fingerprint, confirmed by competitive PCR using gene-specific oligonucleotides, facilitates gene discovery by minimizing isolation procedures. This process, called GeneCalling, was validated by analysis of the gene expression profiles of normal and hypertrophic rat hearts following in vivo pressure overload.

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Figure 1: Generation of GeneCalling profiles.
Figure 2: GeneCalling coverage.
Figure 3: Correlation study comparing reproducibility of fluorescence intensity of peaks produced from independent reactions or samples.
Figure 4: (A) Dilutions of 1:5,000, 1:25,000, and 1:125,000 of plasmid DNA were added to rat liver cDNA before performing GeneCalling reactions and compared to undoped profiles (B).
Figure 5: (A) Hematoxylin and eosin staining of coronary artery branch from a sham-treated (panel 1) or POL rat heart (panel 2).

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References

  1. Lee, N.H. et al. Comparative expressed-sequence-tag analysis of differential gene expression profiles in PC-12 cells before and after nerve growth factor treatment. Proc. Natl. Acad. Sci. USA 92, 8303– 8307 (1995).

    Article  CAS  Google Scholar 

  2. Velculescu, V., Zhang, L., Vogelstein, B. & Kinzler, K. Serial analysis of gene expression. Science 270, 484–487 (1995).

    Article  CAS  Google Scholar 

  3. Lee, S., Tomasetto, C. & Sager, R. Positive selection of candidate tumor-suppressor genes by subtractive hybridization. Proc. Natl. Acad. Sci. USA 88, 2825–2829 (1991).

    Article  CAS  Google Scholar 

  4. Liang, P. & Pardee, A.B. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257, 967–970 ( 1992).

    Article  CAS  Google Scholar 

  5. Ivanova, N.B. & Belyavsky, A.V. Identification of differentially expressed genes by restriction endonuclease-based gene expression fingerprinting. Nucleic Acids Res. 23, 2954– 2958 (1995).

    Article  CAS  Google Scholar 

  6. Kato, K. Description of the entire mRNA population by a 3´ end cDNA fragment generated by class IIS restriction enzymes. Nucleic Acids Res. 23 , 3685–3690 (1995).

    Article  CAS  Google Scholar 

  7. Hubank, M. & Schatz, D.G. Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucleic Acids Res. 22, 5640–5648 (1994).

    Article  CAS  Google Scholar 

  8. Bachem, C.W.B., van der Hoeven, R.S., de Bruijin, S.M., Vreugdenhil, D., Zabeau, M. & Visser, R.G.F. Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: Analysis of gene expression during potato tuber development. Plant J. 9, 745– 753 (1996).

    Article  CAS  Google Scholar 

  9. Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 ( 1995).

    Article  CAS  Google Scholar 

  10. Lockhart, D.J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14, 1675– 1680 (1996).

    Article  CAS  Google Scholar 

  11. Shalon, D., Smith, S.J. & Brown, P.O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639–645 ( 1996).

    Article  CAS  Google Scholar 

  12. Wodicka, L., Dong, H., Mittmann, M., Ho, M.H. & Lockhart, D.J. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15, 1359 –1367 (1997).

    Article  CAS  Google Scholar 

  13. DeRisi, J.L., Iyer, V.R. & Brown, P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680– 686 (1997).

    Article  CAS  Google Scholar 

  14. Milosavljevic, A. et al. DNA sequence recognition by hybridization to short oligomers: experimental verification of the method on the E. coli genome. Genomics 37, 77–86 ( 1996).

    Article  CAS  Google Scholar 

  15. Milosavljevic, A., Strezoska, Z., Zeremski, M., Grujic, D., Paunesku, T. & Crkvenjakov, R. Clone clustering by hybridization. Genomics 27, 83–89 ( 1995).

    Article  CAS  Google Scholar 

  16. Milosavljevic, A. et al. Discovering distinct genes represented in 29,570 clones from infant brain cDNA libraries by applying sequencing by hybridization methodology. Genome Res. 6, 132–141 (1996).

    Article  CAS  Google Scholar 

  17. Drmanac, S. et al. Gene-representing cDNA clusters defined by hybridization of 57,419 clones from infant brain libraries with short oligonucleotide probes. Genomics 37, 29–40 ( 1996).

    Article  CAS  Google Scholar 

  18. Chien, K.R., Knowlton, K.U., Zhu, H. & Chien, S. Regulation of cardiac gene expression during myocardial growth and hypertrophy: molecular studies of an adaptive physiologic response. FASEB J. 5, 3037–3046 (1991).

    Article  CAS  Google Scholar 

  19. Boheler, K.R. & Schwartz, K. Gene expression in cardiac hypertrophy. Trends Cardiovasc. Med. 2, 176– 182 (1992).

    Article  CAS  Google Scholar 

  20. Cooper, G. IV. Cardiocyte adaptation to chronically altered load. Ann. Rev. Physiol. 49, 501–518 ( 1987).

    Article  CAS  Google Scholar 

  21. Weber, K.T. & Brilla, C.G. Pathological hypertrophy and cardiac interstitium: fibrosis and renin–angiotensin–aldosterone system. Circulation 83, 1849–1865 (1991).

    Article  CAS  Google Scholar 

  22. Day, M. et al. Ventricular atriopeptin. Unmasking of messenger RNA and peptide synthesis by hypertrophy or dexamethasone. Hypertension 9, 485–491 (1987).

    Article  CAS  Google Scholar 

  23. Izumo, S., Nadal-Ginard, B. & Mahdavi, V. Protooncogene induction and reprogramming of the cardiac gene expression produced by pressure overload. Proc. Natl. Acad. Sci. USA 85, 339–343 ( 1988).

    Article  CAS  Google Scholar 

  24. Schiaffino, S. et al. Nonsynchronous accumulation of α-skeletal actin and β-myosin heavy chain mRNAs during early stages of pressure-overload-induced cardiac hypertrophy demonstrated by in situ hybridization. Circ. Res. 64, 937–948 (1989).

    Article  CAS  Google Scholar 

  25. Schwartz, K., de la Bastie, D., Bouvaret, P., Oliviéro, P., Alonso, S. & Buckingham, M. α-Skeletal muscle actin mRNA's accumulate in hypertrophied adult rat hearts. Circ. Res. 59, 551– 555 (1986).

    Article  CAS  Google Scholar 

  26. Samuel, J.L. et al. Accumulation of fetal fibronectin mRNAs during the development of rat cardiac hypertrophy induced by pressure overload. J. Clin. Invest. 88, 1737–1746 ( 1991).

    Article  CAS  Google Scholar 

  27. Chapman, D., Weber, K.T. & Eghbali, M. Regulation of fibrillar collagen types I and III and basement membrane type IV collagen gene expression in pressure overloaded rat myocardium. Circ. Res. 67, 787– 794 (1990).

    Article  CAS  Google Scholar 

  28. Schönherr, E., Witsch-Prehm, P., Harrach, B., Robenek, H., Rauterberg, J. & Kresse, H. Interaction of biglycan with type 1 collagen. J. Biol. Chem. 270, 2776–2783 (1995).

    Article  Google Scholar 

  29. Bhalerao, J., Tylzanowksi, P., Filie, J.D., Kozak, C.A. & Merregaert, J. Molecular cloning, characterization, and genetic mapping of the cDNA coding for a novel secretory protein of mouse. J. Biol. Chem. 270, 16385– 16394 (1995).

    Article  CAS  Google Scholar 

  30. Vanden Heuvel, G.B., Leardkamolkarn, V., St. John, P.L. & Abrahamson, D.R. Carboxy terminal sequence and synthesis of rat kidney laminin γ1 chain. Kidney Int. 49, 752–760 (1996).

    Article  CAS  Google Scholar 

  31. Pepe, G. et al. A major involvement of the cardiovascular system in patients affected by Marfan syndrome: novel mutations in fibrillin 1 gene. J. Mol. Cell. Cardiol. 29, 1877–1884 ( 1997).

    Article  CAS  Google Scholar 

  32. Engelmann, G., Campbell, S. & Rakusan, K. Immediate postnatal rat heart development modifed by abdominal aortic banding: analysis of gene expression. Mol. Cell. Biochem. 163–164, 47–56 (1996).

    Article  Google Scholar 

  33. Sage, E.H. Terms of attachment: SPARC and tumorigenesis. Nat. Med. 3, 144–146 (1997).

    Article  CAS  Google Scholar 

  34. Springhorn, J.P. & Claycomb, W.C. Preproenkephalin mRNA expression in developing rat heart and in cultured ventricular cardiac muscle cells. Biochem. J. 258, 73– 78 (1989).

    Article  CAS  Google Scholar 

  35. Paradis, P., Dumont, M., Belichard, P., Rouleau, J.L., Lemaire, S. & Brakier-Gingras, L. Increased preproenkephalin A gene expression in the rat heart after induction of a myocardial infarction. Biochem. Cell Biol. 70, 593–598 ( 1992).

    Article  CAS  Google Scholar 

  36. Anversa, P., Olivetti, G., Melissari, M. & Loud, A.V. Stereological measurement of cellular and subcellular hypertrophy and hyperplasia in the papillary muscle of adult rat. J. Mol. Cell. Cardiol. 12, 781–795 (1980).

    Article  CAS  Google Scholar 

  37. Korecky, B. & Rakusan, K. Normal and hypertrophic growth of the rat heart: changes in cell dimensions and number. Am. J. Physiol. 234, H123–H128 ( 1978).

    CAS  PubMed  Google Scholar 

  38. Boluyt, M.O. et al. Alterations in cardiac gene expression during the transition from stable hypertrophy to heart failure. Circ. Res. 75, 23–32 (1994).

    Article  CAS  Google Scholar 

  39. Kimura, S., Bassett, A.L., Saida, K., Shimizu, M. & Myerburg, R.J. Sarcoplasmic reticulum function in skinned fibers of hypertrophied rat ventricle. Heart Circ. Physiol. 25, H1006–H1011 (1989).

    Article  Google Scholar 

  40. Batra, S. & Rakusan, K. Capillarization of the hypertrophic heart: Discrepancy of the results obtained by the triangulation and domain methods. J. Cardiovasc. Pharmacol. 17 (Suppl 2), S151–S153 (1991).

    Article  Google Scholar 

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Acknowledgements

The authors thank Dr. Richard Lifton for helpful comments on this manuscript, the Genentech in situ hybridization laboratories for technical assistance with anatomical pathology and Dr. Anne Ryan for interpretation of histopathology.

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Author notes

  1. Julie Tsu-Ning Tai & Patricia Sehl

    Present address: CVTherapeutics, 3172 Porter Dr., Palo Alto, CA, 94304

  2. Richard A. Shimkets and David G. Lowe: Both authors contributed equally to this work.

Authors and Affiliations

  1. CuraGen Corporation, 555 Long Wharf Drive , New Haven, 06511, CT

    Richard A. Shimkets, Paul F. Predki, Bonnie E. G. Rothberg, Michael T. Murtha, Matthew E. Roth, Suresh G. Shenoy, Andreas Windemuth, John W. Simpson, Jan F. Simons, Michael P. Daley, Steven A. Gold, Michael P. McKenna, Gregory T. Went & Jonathan M. Rothberg

  2. Departments of Cardiovascular Research and Pathology Genentech, Inc., 1 DNA Way, South, San Francisco , 94080, CA

    David G. Lowe, Julie Tsu-Ning Tai, Hongkui Jin, Renhui Yang & Kenneth Hillan

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Correspondence to Richard A. Shimkets.

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Shimkets, R., Lowe, D., Tai, JN. et al. Gene expression analysis by transcript profiling coupled to a gene database query. Nat Biotechnol 17, 798–803 (1999). https://doi.org/10.1038/11743

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