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Microarrays: new tools to unravel parasite transcriptomes

Published online by Cambridge University Press:  01 June 2005

G. N. GOBERT ,
L. P. MOERTEL  and
D. P. McMANUS
G. N. GOBERT
Affiliation:
Molecular Parasitology Laboratory, Australian Centre for International and Tropical Health and Nutrition, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4029 Australia
L. P. MOERTEL
Affiliation:
Molecular Parasitology Laboratory, Australian Centre for International and Tropical Health and Nutrition, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4029 Australia The School of Chemical and Biomedical Sciences, Central Queensland University, Bruce Hwy, North Rockhampton, QLD 4702 Australia
D. P. McMANUS
Affiliation:
Molecular Parasitology Laboratory, Australian Centre for International and Tropical Health and Nutrition, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4029 Australia
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Abstract

The ability to monitor the expression levels of thousands of genes in a single microarray experiment is a huge progression from conventional Northern blot analysis or PCR-based techniques. Microarrays can play a pivotal role in the mass screening of genes in a wide range of fields including parasitology. The relatively few parasites that can be readily cultured or isolated from a host, as compared with cell lines or tissue sources, makes microarray technology ideal for maximizing experimental results from a limiting source of starting material. Khan et al. (1999a) commented in an early review of microarray technology “With this system in place, one can anticipate a time when data from thousands of gene expression experiments will be available for meta-analysis…..… leading to more robust results and subtle conclusions”. Now in 2005, microarrays represent a very powerful resource that can play an important role in the characterization and annotation of the transcriptomes of many parasites of medical and veterinary importance.

Keywords

microarraygene expressiongenomic sequencingtranscriptome
Type
Review Article
Information
Parasitology , Volume 131 , Issue 4 , October 2005 , pp. 439 - 448
Copyright
© 2005 Cambridge University Press

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References

REFERENCES

Bahl, A., Brunk, B., Crabtree, J., Fraunholz, M. J., Gajria, B., Grant, G. R., Ginsburg, H., Gupta, D., Kissinger, J. C., Labo, P., Li, L., Mailman, M. D., Milgram, A. J., Pearson, D. S., Roos, D. S., Schug, J., Stoeckert, C. J. Jr and Whetzel, P. ( 2003). PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Research 31, 212–215.Google Scholar
Baptista, C. S., Vencio, R. Z., Abdala, S., Valadares, M. P., Martins, C., De Braganca-Pereira, C. A. and Zingales, B. ( 2004). DNA microarrays for comparative genomics and analysis of gene expression in Trypanosoma cruzi. Molecular and Biochemical Parasitology 138, 183–194.CrossRefGoogle Scholar
Blaxter, M., Daub, J., Guiliano, D., Parkinson, J. and Whitton, C. ( 2002). Filarial Genome Project. The Brugia malayi genome project: expressed sequence tags and gene discovery. Transactions of the Royal Society of Tropical Medicine and Hygiene 96, 7–17.Google Scholar
Bozdech, Z., Zhu, J., Joachimiak, M. P., Cohen, F. E., Pulliam, B. and Derisi, J. L. ( 2003). Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biology 4, R9.CrossRefGoogle Scholar
Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C. J., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., Gaasterland, T., Glenisson, P., Holstege, F. C., Kim, I. F., Markowitz, V., Matese, J. C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R. and Vingron, M. ( 2001). Minimum information about a microarray experiment (MIAME) – toward standards for microarray data. Nature Genetics 29, 365–371.CrossRefGoogle Scholar
Carlton, J., Silva, J. and Hall, N. ( 2005). The genome of model malaria parasites, and comparative genomics. Current Issues in Molecular Biology 7, 23–37.Google Scholar
Carucci, D. J., Gardner, M. J., Tettelin, H., Cummings, L. M., Smith, H. O., Adams, M. D., Hoffman, S. L. and Venter, J. C. ( 1998). The malaria genome sequencing project. Expert Reviews in Molecular Medicine 1, 1–9.CrossRefGoogle Scholar
Chen, H., Wang, J., Liang, P., Karsay-Klein, M., James, A. A., Brazeau, D. and Yan, G. ( 2004 b). Microarray analysis for identification of Plasmodium-refractoriness candidate genes in mosquitoes. Genome 47, 1061–1070.Google Scholar
Chen, Y. A., McKillen, D. J., Wu, S., Jenny, M. J., Chapman, R., Gross, P. S., Warr, G. W. and Almeida, J. S. ( 2004 a). Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. BMC Bioinformatics 5, 191.Google Scholar
Clontech Laboratories ( 2001). Creator SMART cDNA library construction kit user manual, [>available at http://www.bdbiosciences.com/clontech/techinfo/manuals/PDF/ PT3577-1.pdf]. BD Biosciences.
Diez-Tascon, C., Keane, O. M., Wilson, T., Zadissa, A., Hyndman, D. L., Baird, D. B., McEwan, J. C. and Crawford, A. M. ( 2005). Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep. Physiological Genomics 21, 59–69.CrossRefGoogle Scholar
Dugas, M., Merk, S., Breit, S. and Dirschedl, P. ( 2004). MDCLUST – exploratory microarray analysis by multidimensional clustering. Bioinformatics 20, 931–936.CrossRefGoogle Scholar
Fitzpatrick, J. M., Johansen, M. V., Johnston, D. A., Dunne, D. W. and Hoffmann, K. F. ( 2004). Gender-associated gene expression in two related strains of Schistosoma japonicum. Molecular and Biochemical Parasitology 136, 191–209.CrossRefGoogle Scholar
Fitzpatrick, J. M., Johnston, D. A., Williams, G. W., Williams, D. J., Freeman, T. C., Dunne, D. W. and Hoffmann, K. F. ( 2005). An oligonucleotide microarray for transcriptome analysis of Schistosoma mansoni and its application/use to investigate gender-associated gene expression. Molecular and Biochemical Parasitology 141, 1–13.CrossRefGoogle Scholar
Foster, J. M., Kumar, S., Ganatra, M. B., Kamal, I. H., Ware, J., Ingram, J., Pope-Chappell, J., Guiliano, D., Whitton, C., Daub, J., Blaxter, M. L. and Slatko, B. E. ( 2004). Construction of bacterial artificial chromosome libraries from the parasitic nematode Brugia malayi and physical mapping of the genome of its Wolbachia endosymbiont. International Journal for Parasitology 34, 733–746.CrossRefGoogle Scholar
Gissot, M., Refour, P., Briquet, S., Boschet, C., Coupe, S., Mazier, D. and Vaquero, C. ( 2004). Transcriptome of 3D7 and its gametocyte-less derivative F12 Plasmodium falciparum clones during erythrocytic development using a gene-specific microarray assigned to gene regulation, cell cycle and transcription factors. Gene 341, 267–277.CrossRefGoogle Scholar
Gu, Z., Rifkin, S. A., White, K. P. and Li, W. H. ( 2004). Duplicate genes increase gene expression diversity within and between species. Nature Genetics 36, 577–579.CrossRefGoogle Scholar
Hoffmann, K. F., Johnston, D. A. and Dunne, D. W. ( 2002). Identification of Schistosoma mansoni gender-associated gene transcripts by cDNA microarray profiling. Genome Biology 3, 0041.1–0041.11.Google Scholar
Hoffmann, K. F., McCarty, T. C., Segal, D. H., Chiaramonte, M., Hesse, M., Davis, E. M., Cheever, A. W., Meltzer, P. S., Morse, Hc 3rd and Wynn, Ta. ( 2001). Disease fingerprinting with cDNA microarrays reveals distinct gene expression profiles in lethal type 1 and type 2 cytokine-mediated inflammatory reactions. FASEB Journal 15, 2545–2547.CrossRefGoogle Scholar
Hu, W., Yan, Q., Shen, D. K., Liu, F., Zhu, Z. D., Song, H. D., Xu, X. R., Wang, Z. J., Rong, Y. P., Zeng, L. C., Wu, J., Zhang, X., Wang, J. J., Xu, X. N., Wang, S. Y., Fu, G., Zhang, X. L., Wang, Z. Q., Brindley, P. J., McManus, D. P., Xue, C. L., Feng, Z., Chen, L. and Han, Z. G. ( 2003). Evolutionary and biomedical implications of a Schistosoma japonicum complimentary DNA resource. Nature Genetics 35, 139–147.CrossRefGoogle Scholar
Hughes, T. R., Mao, M., Jones, A. R., Burchard, J., Marton, M. J., Shannon, K. W., Lefkowitz, S. M., Ziman, M., Schelter, J. M., Meyer, M. R., Kobayashi, S., Davis, C., Dai, H., He, Y. D., Stephaniants, S. B., Cavet, G., Walker, W. L., West, A., Coffey, E., Shoemaker, D. D., Stoughton, R., Blanchard, A. P., Friend, S. and Linsley, P. S. ( 2001). Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nature Biotechnology 19, 342–347.CrossRefGoogle Scholar
Johnston, D. A., Blaxter, M. L., Degrave, W. M., Foster, J., Ivens, A. C. and Melville, S. E. ( 1999). Genomics and the biology of parasites. Bioessays 21, 131–147.3.0.CO;2-I>CrossRefGoogle Scholar
Khan, J., Bittner, M. L., Chen, Y., Meltzer, P. S. and Trent, J. M. ( 1999 a). DNA microarray technology: the anticipated impact on the study of human disease. Biochimica et Biophysica Acta 1423, M17–28.Google Scholar
Khan, J., Saal, L., Bittner, M., Chen, Y., Trent, J. and Meltzer, P. S. ( 1999 b). Expression profiling in cancer using cDNA microarray. Electrophoresis 20, 223–229.Google Scholar
Kissinger, J. C., Gajria, B., Li, L., Paulsen, I. T. and Roos, D. S. ( 2003). ToxoDB: accessing the Toxoplasma gondii genome. Nucleic Acids Research 31, 234–236.CrossRefGoogle Scholar
Knox, D. P. ( 2004). Technological advances and genomics in metazoan parasites. International Journal for Parasitology 34, 139–152.CrossRefGoogle Scholar
Kurella, M., Hsiao, L. L., Yoshida, T., Randall, J. D., Chow, G., Sarang, S. S., Jensen, R. V. and Gullans, S. R. ( 2001). DNA microarray analysis of complex biologic processes. Journal of the American Society of Nephrology 12, 1072–1078.Google Scholar
Le Roch, K. G., Zhou, Y., Blair, P. L., Grainger, M., Moch, J. K., Haynes, J. D., De La Vega, P., Holder, A. A., Batalov, S., Carucci, D. J. and Winzeler, E. A. ( 2003). Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 301, 1503–1508.CrossRefGoogle Scholar
Min, W., Lillehoj, H. S., Kim, S., Zhu, J. J., Beard, H., Alkharouf, N. and Matthews, B. F. ( 2003). Profiling local gene expression changes associated with Eimeria maxima and Eimeria acervulina using cDNA microarray. Applied Microbiology and Biotechnology 62, 392–399.CrossRefGoogle Scholar
Minning, T. A., Bua, J., Garcia, G. A., McGraw, R. A. and Tarleton, R. L. ( 2003). Microarray profiling of gene expression during trypomastigote to amastigote transition in Trypanosoma cruzi. Molecular and Biochemical Parasitology 131, 55–64.CrossRefGoogle Scholar
Nielsen, H. B., Wernersson, R. and Knudsen, S. ( 2003). Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Research 31, 3491–3496.CrossRefGoogle Scholar
Randall, R. L., Wade, M., Albritton, K. H., Coffin, C. M. and Joyner, D. E. ( 2003). Validation of cDNA microarray analysis to distinguish tumor type ex vivo Clinical Orthopaedics and Related Research 415S, S110–S119.Google Scholar
Renn, S. C., Aubin-Horth, N. and Hofmann, H. A. ( 2004). Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics 5, 42.CrossRefGoogle Scholar
Rise, M. L., Von Schalburg, K. R., Brown, G. D., Mawer, M. A., Devlin, R. H., Kuipers, N., Busby, M., Beetz-Sargent, M., Alberto, R., Gibbs, A. R., Hunt, P., Shukin, R., Zeznik, J. A., Nelson, C., Jones, S. R., Smailus, D. E., Jones, S. J., Schein, J. E., Marra, M. A., Butterfield, Y. S., Stott, J. M., Ng, S. H., Davidson, W. S. and Koop, B. F. ( 2004). Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Research 14, 478–490.CrossRefGoogle Scholar
Schena, M., Shalon, D., Davis, R. W. and Brown, P. O. ( 1995). Quantitative monitoring of gene expression patterns with a complimentary DNA microarray. Science 270, 467–470.CrossRefGoogle Scholar
Sexton, A. C., Good, R. T., Hansen, D. S., D'Ombrain, M. C., Buckingham, L., Simpson, K. and Schofield, L. ( 2004). Transcriptional profiling reveals suppressed erythropoiesis, up-regulated glycolysis, and interferon-associated responses in murine malaria. Journal of Infectious Diseases 189, 1245–1256.CrossRefGoogle Scholar
Street, M. ( 2002). DNA microarrays: manufacture and applications. Australasian Biotechnology 12, 38–39.Google Scholar
Summan, M., McKinstry, M., Warren, G. L., Hulderman, T., Mishra, D., Brumbaugh, K., Luster, M. I. and Simeonova, P. P. ( 2003). Inflammatory mediators and skeletal muscle injury: a DNA microarray analysis. Journal of Interferon and Cytokine Research 23, 237–245.CrossRefGoogle Scholar
Tolstrup, N., Nielsen, P. S., Kolberg, J. G., Frankel, A. M., Vissing, H. and Kauppinen, S. ( 2003). OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Research 31, 3758–3762.CrossRefGoogle Scholar
Verjovski-Almeida, S., Demarco, R., Martins, E. A., Guimaraes, P. E., Ojopi, E. P., Paquola, A.C, Piazza, J. P., Nishiyamamy, J. R., Kitajima, J. P., Adamson, R. E., Ashton, P. D., Bonaldo, M. F., Coulson, P. S., Dillon, G. P., Farias, L. P., Gregorio, S. P., Ho, P. L., Leite, R. A., Malaquias, L. C., Marques, R. C., Miyasato, P. A., Nascimento, A. L., Ohlweiler, F. P., Reis, E. M., Ribeiro, M. A., Sa, R. G., Stukart, G. C., Soares, M. B., Gargioni, C., Kawano, T., Rodrigues, V., Madeira, A. M., Wilson, R. A., Menck, C. F., Setubal, J. C., Leite, L. C. and Dias-Neto, E. ( 2003). Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nature Genetics 35, 148–157.CrossRefGoogle Scholar
Verma, P. and Sharma, Y. D. ( 2003). Malaria genome project and its impact on the disease. Journal of Vector Borne Diseases 40, 9–15.Google Scholar
Watanabe, T., Murata, Y., Oka, S., Iwahashi, H. ( 2004). A new approach to species determination for yeast strains: DNA microarray-based comparative genomic hybridization using a yeast DNA microarray with 6000 genes. Yeast 21, 351–365.CrossRefGoogle Scholar
Williams, S. A., Lizotte-Waniewski, M. R., Foster, J., Guiliano, D., Daub, J., Scott, A. L., Slatko, B. and Blaxter, M. L. ( 2000). The filarial genome project: analysis of the nuclear, mitochondrial and endosymbiont genomes of Brugia malayi. International Journal for Parasitology 30, 411–409.CrossRefGoogle Scholar
Wilson, R. J. ( 2004). The transcriptome: malariologists ride the wave. Bioessays 26, 339–42.CrossRefGoogle Scholar
Xu, P., Widmer, G., Wang, Y., Ozaki, L. S., Alves, J. M., Serrano, M. G., Puiu, D., Manque, P., Akiyoshi, D., Mackey, A. J., Pearson, W. R., Dear, P. H., Bankier, A. T., Peterson, D. L., Abrahamsen, M. S., Kapur, V., Tzipori, S. and Buck, G. A. ( 2004). The genome of Cryptosporidium hominis. Nature 431, 1107–1112.CrossRefGoogle Scholar
Ylostalo, J., Randall, A. C., Myers, T. A., Metzger, M., Krogstad, D. J. and Cogswell, F. B. ( 2005). Transcriptome profiles of host gene expression in a monkey model of human malaria. The Journal of Infectious Diseases 191, 400–409.CrossRefGoogle Scholar