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RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection.

Wilk E, Pandey AK, Leist SR, Hatesuer B, Preusse M, Pommerenke C, Wang J, Schughart K - BMC Genomics (2015)

Bottom Line: Expression levels of influenza segments correlated well with the viral load and may thus be used as surrogates for conventional viral load measurements.Using RNAseq analysis we identified novel genes important for viral replication or the host defense.This study adds further important knowledge to host-pathogen-interactions and suggests additional candidates that are crucial for host susceptibility or survival during influenza A infections.

View Article: PubMed Central - PubMed

Affiliation: Department of Infection Genetics, Helmholtz Centre for Infection Research and University of Veterinary Medicine Hannover, Inhoffenstr. 7, 38124, Braunschweig, Germany.

ABSTRACT

Background: The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suited to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilized a dual RNAseq approach that allowed us to investigate both viral and host gene expression in the same individual mouse after H1N1 infection.

Results: We performed a detailed expression analysis to identify (i) correlations between changes in expression of host and virus genes, (ii) host genes involved in viral replication, and (iii) genes showing differential expression between two mouse strains that strongly differ in resistance to influenza infections. These genes may be key players involved in regulating the differences in pathogenesis and host defense mechanisms after influenza A infections. Expression levels of influenza segments correlated well with the viral load and may thus be used as surrogates for conventional viral load measurements. Furthermore, we investigated the functional role of two genes, Reg3g and Irf7, in knock-out mice and found that deletion of the Irf7 gene renders the host highly susceptible to H1N1 infection.

Conclusions: Using RNAseq analysis we identified novel genes important for viral replication or the host defense. This study adds further important knowledge to host-pathogen-interactions and suggests additional candidates that are crucial for host susceptibility or survival during influenza A infections.

No MeSH data available.


Related in: MedlinePlus

PCA analysis of normalized host gene counts for all samples. Principle component analysis reveals separate grouping of non-infected mice and infected mice for both mouse strains. Replicates for a given day p.i. grouped together well. For C57BL/6J mice, groups from different days p.i. were well separated. For DBA/2J a much stronger infection response was observed compared to C57BL/6J mice and individual mice at days 3 and 5 p.i. were not well separated. Note that for day 14 p.i., two of three samples were not separated and only two spots are visible. B6md1, D2md1 and B6md3, D2md3: C57BL/6J and DBA/2J mice mock-treated and analyzed at days 1 or 3 post treatment, respectively. Sample labels: C57BL/6J at days 1, 3, 5, 8 and 14 p.i.: B6d1, B6d3, B6d5, B6d8, B6d14, respectively; and DBA/2J mice at days 1, 3, 5 p.i.: D2d1, D2d3, D2d5, respectively
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Fig1: PCA analysis of normalized host gene counts for all samples. Principle component analysis reveals separate grouping of non-infected mice and infected mice for both mouse strains. Replicates for a given day p.i. grouped together well. For C57BL/6J mice, groups from different days p.i. were well separated. For DBA/2J a much stronger infection response was observed compared to C57BL/6J mice and individual mice at days 3 and 5 p.i. were not well separated. Note that for day 14 p.i., two of three samples were not separated and only two spots are visible. B6md1, D2md1 and B6md3, D2md3: C57BL/6J and DBA/2J mice mock-treated and analyzed at days 1 or 3 post treatment, respectively. Sample labels: C57BL/6J at days 1, 3, 5, 8 and 14 p.i.: B6d1, B6d3, B6d5, B6d8, B6d14, respectively; and DBA/2J mice at days 1, 3, 5 p.i.: D2d1, D2d3, D2d5, respectively

Mentions: RNA was extracted from the lungs of C57BL/6J and DBA/2J mice infected with PR8M (a variant of A/Puerto Rico/8/1934 H1N1) as described in [14], and gene expression was quantified using RNA sequencing (RNAseq) technology. Principal component analysis (PCA) of normalized counts for host genes confirmed separate groupings of non-infected (controls) and infected lungs (Fig. 1). The transcriptome profiles of C57BL/6J mice and DBA/2J mice were distinct as shown by the second principle component, whereas the host response to the infection is mostly represented by the first principle component which explains 59 % of the expression variation. PC2 reveals distinct expression profiles for the two strains due to their different genetic backgrounds explaining 18 % of the expression variation. C57BL/6J mice exhibited a change in transcriptome profiles that was distinct for days 3, 5, 8, and 14 after infection. However, infected DBA/2J mice showed an early and stronger change in transcriptome profiles at day 3 post infection (p.i.) compared to C57BL/6J. Their expression profile did not show any major changes until day 5 when DBA/2J mice were moribund.Fig. 1


RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection.

Wilk E, Pandey AK, Leist SR, Hatesuer B, Preusse M, Pommerenke C, Wang J, Schughart K - BMC Genomics (2015)

PCA analysis of normalized host gene counts for all samples. Principle component analysis reveals separate grouping of non-infected mice and infected mice for both mouse strains. Replicates for a given day p.i. grouped together well. For C57BL/6J mice, groups from different days p.i. were well separated. For DBA/2J a much stronger infection response was observed compared to C57BL/6J mice and individual mice at days 3 and 5 p.i. were not well separated. Note that for day 14 p.i., two of three samples were not separated and only two spots are visible. B6md1, D2md1 and B6md3, D2md3: C57BL/6J and DBA/2J mice mock-treated and analyzed at days 1 or 3 post treatment, respectively. Sample labels: C57BL/6J at days 1, 3, 5, 8 and 14 p.i.: B6d1, B6d3, B6d5, B6d8, B6d14, respectively; and DBA/2J mice at days 1, 3, 5 p.i.: D2d1, D2d3, D2d5, respectively
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Fig1: PCA analysis of normalized host gene counts for all samples. Principle component analysis reveals separate grouping of non-infected mice and infected mice for both mouse strains. Replicates for a given day p.i. grouped together well. For C57BL/6J mice, groups from different days p.i. were well separated. For DBA/2J a much stronger infection response was observed compared to C57BL/6J mice and individual mice at days 3 and 5 p.i. were not well separated. Note that for day 14 p.i., two of three samples were not separated and only two spots are visible. B6md1, D2md1 and B6md3, D2md3: C57BL/6J and DBA/2J mice mock-treated and analyzed at days 1 or 3 post treatment, respectively. Sample labels: C57BL/6J at days 1, 3, 5, 8 and 14 p.i.: B6d1, B6d3, B6d5, B6d8, B6d14, respectively; and DBA/2J mice at days 1, 3, 5 p.i.: D2d1, D2d3, D2d5, respectively
Mentions: RNA was extracted from the lungs of C57BL/6J and DBA/2J mice infected with PR8M (a variant of A/Puerto Rico/8/1934 H1N1) as described in [14], and gene expression was quantified using RNA sequencing (RNAseq) technology. Principal component analysis (PCA) of normalized counts for host genes confirmed separate groupings of non-infected (controls) and infected lungs (Fig. 1). The transcriptome profiles of C57BL/6J mice and DBA/2J mice were distinct as shown by the second principle component, whereas the host response to the infection is mostly represented by the first principle component which explains 59 % of the expression variation. PC2 reveals distinct expression profiles for the two strains due to their different genetic backgrounds explaining 18 % of the expression variation. C57BL/6J mice exhibited a change in transcriptome profiles that was distinct for days 3, 5, 8, and 14 after infection. However, infected DBA/2J mice showed an early and stronger change in transcriptome profiles at day 3 post infection (p.i.) compared to C57BL/6J. Their expression profile did not show any major changes until day 5 when DBA/2J mice were moribund.Fig. 1

Bottom Line: Expression levels of influenza segments correlated well with the viral load and may thus be used as surrogates for conventional viral load measurements.Using RNAseq analysis we identified novel genes important for viral replication or the host defense.This study adds further important knowledge to host-pathogen-interactions and suggests additional candidates that are crucial for host susceptibility or survival during influenza A infections.

View Article: PubMed Central - PubMed

Affiliation: Department of Infection Genetics, Helmholtz Centre for Infection Research and University of Veterinary Medicine Hannover, Inhoffenstr. 7, 38124, Braunschweig, Germany.

ABSTRACT

Background: The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suited to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilized a dual RNAseq approach that allowed us to investigate both viral and host gene expression in the same individual mouse after H1N1 infection.

Results: We performed a detailed expression analysis to identify (i) correlations between changes in expression of host and virus genes, (ii) host genes involved in viral replication, and (iii) genes showing differential expression between two mouse strains that strongly differ in resistance to influenza infections. These genes may be key players involved in regulating the differences in pathogenesis and host defense mechanisms after influenza A infections. Expression levels of influenza segments correlated well with the viral load and may thus be used as surrogates for conventional viral load measurements. Furthermore, we investigated the functional role of two genes, Reg3g and Irf7, in knock-out mice and found that deletion of the Irf7 gene renders the host highly susceptible to H1N1 infection.

Conclusions: Using RNAseq analysis we identified novel genes important for viral replication or the host defense. This study adds further important knowledge to host-pathogen-interactions and suggests additional candidates that are crucial for host susceptibility or survival during influenza A infections.

No MeSH data available.


Related in: MedlinePlus