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Development of the first oligonucleotide microarray for global gene expression profiling in guinea pigs: defining the transcription signature of infectious diseases.

Jain R, Dey B, Tyagi AK - BMC Genomics (2012)

Bottom Line: To validate and demonstrate the merit of this microarray, we have studied, as an example, the expression profile of guinea pig lungs during the advanced phase of M. tuberculosis infection.A significant upregulation of 1344 genes and a marked down regulation of 1856 genes in the lungs identified a disease signature of pulmonary tuberculosis infection.An important gap in the area of infectious diseases has been addressed and a valuable molecular tool is provided to optimally harness the potential of guinea pig model to develop better vaccines and therapies against human diseases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.

ABSTRACT

Background: The Guinea pig (Cavia porcellus) is one of the most extensively used animal models to study infectious diseases. However, despite its tremendous contribution towards understanding the establishment, progression and control of a number of diseases in general and tuberculosis in particular, the lack of fully annotated guinea pig genome sequence as well as appropriate molecular reagents has severely hampered detailed genetic and immunological analysis in this animal model.

Results: By employing the cross-species hybridization technique, we have developed an oligonucleotide microarray with 44,000 features assembled from different mammalian species, which to the best of our knowledge is the first attempt to employ microarray to study the global gene expression profile in guinea pigs. To validate and demonstrate the merit of this microarray, we have studied, as an example, the expression profile of guinea pig lungs during the advanced phase of M. tuberculosis infection. A significant upregulation of 1344 genes and a marked down regulation of 1856 genes in the lungs identified a disease signature of pulmonary tuberculosis infection.

Conclusion: We report the development of first comprehensive microarray for studying the global gene expression profile in guinea pigs and validation of its usefulness with tuberculosis as a case study. An important gap in the area of infectious diseases has been addressed and a valuable molecular tool is provided to optimally harness the potential of guinea pig model to develop better vaccines and therapies against human diseases.

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Comparison of transcriptional response of guinea pig, human, non-human primate and mouse to M. tuberculosis infection. The Venn diagrams depict the degree of overlap between up regulated genes of (A) Guinea pig, human and non-human primates and (B) Guinea pig, human and mouse. The analysis included comparison of the list of differentials obtained from our study with that obtained from various microarray data available in the public database for TB infection in case of; human [GEO Accession no. GSE20050], mouse [GEO Accession no. GSE15335] and non-human primate [GEO Accession no. GPL10183]. Down regulated genes did not show any considerable overlap across the species, hence not depicted in the figure.
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Figure 4: Comparison of transcriptional response of guinea pig, human, non-human primate and mouse to M. tuberculosis infection. The Venn diagrams depict the degree of overlap between up regulated genes of (A) Guinea pig, human and non-human primates and (B) Guinea pig, human and mouse. The analysis included comparison of the list of differentials obtained from our study with that obtained from various microarray data available in the public database for TB infection in case of; human [GEO Accession no. GSE20050], mouse [GEO Accession no. GSE15335] and non-human primate [GEO Accession no. GPL10183]. Down regulated genes did not show any considerable overlap across the species, hence not depicted in the figure.

Mentions: In our study, the pulmonary transcriptional profiling of M. tuberculosis infected guinea pigs revealed a significant regulation of 3200 unique targets. While, 1344 unique genes exhibited a marked up regulation, 1856 genes were significantly down regulated. Differentially regulated genes were further classified into different categories based on their direct or indirect involvement in various biological processes or pathways. A massive re-alignment of metabolic pathways, mostly associated with catabolism, emerged as one of the interesting themes from this analysis. Although, altered metabolic functions of the host have earlier been reported in human subjects and in laboratory animals in response to febrile infections involving wasting of body tissues[12], most studies have been restricted to biochemical and in silico analysis and have not looked beyond immune mechanisms in order to probe the underlying cause of pathology and active disease in case of TB[13,14]. Only recently, Mi-Jeong and colleagues reported a correlation between caseation of human TB granulomas with elevated host lipid metabolism in these infected tissues by microarray[15]. Extensive necrosis observed in the pulmonary granulomas in our study as well as a marked up regulation of several of these lipid homeostasis related genes, such as, ABHD2, ABHD8, ACSL1, ACSL5, CYP27A1, CYP2B18A, CYP26B1, CYP2F1, CYP2A13, CYP1A2, CYP11A1, CYP2D40, CYP2F1, FDPS, HADHA and LPL correspond well with the observations associated with human caseous granulomas[15]. On comparing the entire list of up and down regulated genes from our guinea pig study with that obtained from human TB granuloma study [GEO Accession no. GSE20050][15], we observed that 38% of the up regulated genes of guinea pig [512 out of 1344 genes] exhibited an overlap with the genes up regulated in humans (Figure4). Further, on comparing the microarray data available in the public database for TB infection in case of humans [GEO Accession no. GSE20050][15], mouse [GEO Accession no. GSE15335][16] and non-human primates [GEO Accession no. GPL10183][17], while, the non-human primates and humans exhibited a 19% overlap between up regulated genes, the overlap between mouse and humans was 18% (Figure4 and Additional file5). The guinea pig model is known for its close similarity to humans in terms of pathological response to M. tuberculosis infection[2]. Our observations indicate that guinea pigs also exhibit higher resemblance to humans in terms of transcriptional response to M. tuberculosis infection, which further validates it as an excellent animal model to study TB. Hence, findings of this study would have a direct implication towards the development of novel therapeutic interventions. Besides, it would also permit the development and validation of biomarkers for effective vaccines and drugs in guinea pig model.


Development of the first oligonucleotide microarray for global gene expression profiling in guinea pigs: defining the transcription signature of infectious diseases.

Jain R, Dey B, Tyagi AK - BMC Genomics (2012)

Comparison of transcriptional response of guinea pig, human, non-human primate and mouse to M. tuberculosis infection. The Venn diagrams depict the degree of overlap between up regulated genes of (A) Guinea pig, human and non-human primates and (B) Guinea pig, human and mouse. The analysis included comparison of the list of differentials obtained from our study with that obtained from various microarray data available in the public database for TB infection in case of; human [GEO Accession no. GSE20050], mouse [GEO Accession no. GSE15335] and non-human primate [GEO Accession no. GPL10183]. Down regulated genes did not show any considerable overlap across the species, hence not depicted in the figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3475082&req=5

Figure 4: Comparison of transcriptional response of guinea pig, human, non-human primate and mouse to M. tuberculosis infection. The Venn diagrams depict the degree of overlap between up regulated genes of (A) Guinea pig, human and non-human primates and (B) Guinea pig, human and mouse. The analysis included comparison of the list of differentials obtained from our study with that obtained from various microarray data available in the public database for TB infection in case of; human [GEO Accession no. GSE20050], mouse [GEO Accession no. GSE15335] and non-human primate [GEO Accession no. GPL10183]. Down regulated genes did not show any considerable overlap across the species, hence not depicted in the figure.
Mentions: In our study, the pulmonary transcriptional profiling of M. tuberculosis infected guinea pigs revealed a significant regulation of 3200 unique targets. While, 1344 unique genes exhibited a marked up regulation, 1856 genes were significantly down regulated. Differentially regulated genes were further classified into different categories based on their direct or indirect involvement in various biological processes or pathways. A massive re-alignment of metabolic pathways, mostly associated with catabolism, emerged as one of the interesting themes from this analysis. Although, altered metabolic functions of the host have earlier been reported in human subjects and in laboratory animals in response to febrile infections involving wasting of body tissues[12], most studies have been restricted to biochemical and in silico analysis and have not looked beyond immune mechanisms in order to probe the underlying cause of pathology and active disease in case of TB[13,14]. Only recently, Mi-Jeong and colleagues reported a correlation between caseation of human TB granulomas with elevated host lipid metabolism in these infected tissues by microarray[15]. Extensive necrosis observed in the pulmonary granulomas in our study as well as a marked up regulation of several of these lipid homeostasis related genes, such as, ABHD2, ABHD8, ACSL1, ACSL5, CYP27A1, CYP2B18A, CYP26B1, CYP2F1, CYP2A13, CYP1A2, CYP11A1, CYP2D40, CYP2F1, FDPS, HADHA and LPL correspond well with the observations associated with human caseous granulomas[15]. On comparing the entire list of up and down regulated genes from our guinea pig study with that obtained from human TB granuloma study [GEO Accession no. GSE20050][15], we observed that 38% of the up regulated genes of guinea pig [512 out of 1344 genes] exhibited an overlap with the genes up regulated in humans (Figure4). Further, on comparing the microarray data available in the public database for TB infection in case of humans [GEO Accession no. GSE20050][15], mouse [GEO Accession no. GSE15335][16] and non-human primates [GEO Accession no. GPL10183][17], while, the non-human primates and humans exhibited a 19% overlap between up regulated genes, the overlap between mouse and humans was 18% (Figure4 and Additional file5). The guinea pig model is known for its close similarity to humans in terms of pathological response to M. tuberculosis infection[2]. Our observations indicate that guinea pigs also exhibit higher resemblance to humans in terms of transcriptional response to M. tuberculosis infection, which further validates it as an excellent animal model to study TB. Hence, findings of this study would have a direct implication towards the development of novel therapeutic interventions. Besides, it would also permit the development and validation of biomarkers for effective vaccines and drugs in guinea pig model.

Bottom Line: To validate and demonstrate the merit of this microarray, we have studied, as an example, the expression profile of guinea pig lungs during the advanced phase of M. tuberculosis infection.A significant upregulation of 1344 genes and a marked down regulation of 1856 genes in the lungs identified a disease signature of pulmonary tuberculosis infection.An important gap in the area of infectious diseases has been addressed and a valuable molecular tool is provided to optimally harness the potential of guinea pig model to develop better vaccines and therapies against human diseases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.

ABSTRACT

Background: The Guinea pig (Cavia porcellus) is one of the most extensively used animal models to study infectious diseases. However, despite its tremendous contribution towards understanding the establishment, progression and control of a number of diseases in general and tuberculosis in particular, the lack of fully annotated guinea pig genome sequence as well as appropriate molecular reagents has severely hampered detailed genetic and immunological analysis in this animal model.

Results: By employing the cross-species hybridization technique, we have developed an oligonucleotide microarray with 44,000 features assembled from different mammalian species, which to the best of our knowledge is the first attempt to employ microarray to study the global gene expression profile in guinea pigs. To validate and demonstrate the merit of this microarray, we have studied, as an example, the expression profile of guinea pig lungs during the advanced phase of M. tuberculosis infection. A significant upregulation of 1344 genes and a marked down regulation of 1856 genes in the lungs identified a disease signature of pulmonary tuberculosis infection.

Conclusion: We report the development of first comprehensive microarray for studying the global gene expression profile in guinea pigs and validation of its usefulness with tuberculosis as a case study. An important gap in the area of infectious diseases has been addressed and a valuable molecular tool is provided to optimally harness the potential of guinea pig model to develop better vaccines and therapies against human diseases.

Show MeSH
Related in: MedlinePlus