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The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.

Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG - Nat. Biotechnol. (2014)

Bottom Line: Here we describe the 2.41 Gb draft genome assembly of the domestic ferret, constituting 2.28 Gb of sequence plus gaps.We annotated 19,910 protein-coding genes on this assembly using RNA-seq data from 21 ferret tissues.Using microarray data from 16 ferret samples reflecting cystic fibrosis disease progression, we showed that transcriptional changes in the CFTR-knockout ferret lung reflect pathways of early disease that cannot be readily studied in human infants with cystic fibrosis disease.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.

ABSTRACT
The domestic ferret (Mustela putorius furo) is an important animal model for multiple human respiratory diseases. It is considered the 'gold standard' for modeling human influenza virus infection and transmission. Here we describe the 2.41 Gb draft genome assembly of the domestic ferret, constituting 2.28 Gb of sequence plus gaps. We annotated 19,910 protein-coding genes on this assembly using RNA-seq data from 21 ferret tissues. We characterized the ferret host response to two influenza virus infections by RNA-seq analysis of 42 ferret samples from influenza time-course data and showed distinct signatures in ferret trachea and lung tissues specific to 1918 or 2009 human pandemic influenza virus infections. Using microarray data from 16 ferret samples reflecting cystic fibrosis disease progression, we showed that transcriptional changes in the CFTR-knockout ferret lung reflect pathways of early disease that cannot be readily studied in human infants with cystic fibrosis disease.

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Transcriptomic analyses of the host response to influenza virus infection and CF disease progression in ferrets. a. Heat map visualization shows distinct gene expression changes in lung and trachea samples from ferrets infected with either the 2009 pandemic H1N1 influenza A/CA/04/2009 virus (CA04) or the 1918 pandemic H1N1 influenza A/Brevig Mission/1/1918 virus (1918). Each row shows the log2 (fold-change) for three infected animals relative to corresponding tissue from three mock-infected ferrets. The heat map is organized by the specificity of the changes with respect to tissue or virus. From left to right black bars at the top of the panel indicate four groups of genes: specific to trachea; distinct profiles in trachea and lung; similar profiles in trachea and lung; specific to lung (for additional details see Supplementary Fig. 18); within each group orange subsections differ between the virus strains, green subsections do not. b. Multidimensional scaling (MDS) representation of the distances among samples based on the indicated cluster of 2,592 genes from a that distinguish viruses in trachea but not in lung. Points show individual animals as indicated on the far right. The x- and y-axes represent a conceptual 2-dimensional space to which the MDS algorithm projected individual lung and trachea samples of high-dimensionality; i.e., the number of genes in the block associated with each sample, while preserving the distances/dissimilarities between samples as closely as possible. Double arrow illustrates that the gene signature distinguishes the two virus infections in trachea at 1 dpi, while lung samples show no separation (dotted rectangle). c. As in b, for the indicated cluster of 152 genes that is differentially regulated in lung but not trachea tissues and separates the two virus strains on 1 dpi. d and e. Differential transcriptional responses in an experiment comparing lung samples from 15-day-old CF ferrets (n=3) vs. non-CF ferrets (n=5). d. Similar pathways enriched in genes differentially expressed in 15-day-old CF ferret lung samples and CF human bronchial brushings, derived from Ingenuity Pathway Analysis. The values in parenthesis are the enrichment p-values for the corresponding pathways in the genes differentially expressed in CF human bronchial brushing19. In brackets are genes which were differentially expressed in both ferret and human CF/non-CF comparisons. e. Network illustration of 32 genes of the function ‘inflammatory response’, which were differentially expressed in the same direction in ferret and human CF datasets (for additional details see Supplementary Fig. 20). Red and blue shading reflects the extent of increased or decreased expression, respectively, in CF relative to non-CF individuals. A solid line between two genes indicates direct interaction(s) among them and a dotted line for indirect interaction(s), as documented in the literature.
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Figure 2: Transcriptomic analyses of the host response to influenza virus infection and CF disease progression in ferrets. a. Heat map visualization shows distinct gene expression changes in lung and trachea samples from ferrets infected with either the 2009 pandemic H1N1 influenza A/CA/04/2009 virus (CA04) or the 1918 pandemic H1N1 influenza A/Brevig Mission/1/1918 virus (1918). Each row shows the log2 (fold-change) for three infected animals relative to corresponding tissue from three mock-infected ferrets. The heat map is organized by the specificity of the changes with respect to tissue or virus. From left to right black bars at the top of the panel indicate four groups of genes: specific to trachea; distinct profiles in trachea and lung; similar profiles in trachea and lung; specific to lung (for additional details see Supplementary Fig. 18); within each group orange subsections differ between the virus strains, green subsections do not. b. Multidimensional scaling (MDS) representation of the distances among samples based on the indicated cluster of 2,592 genes from a that distinguish viruses in trachea but not in lung. Points show individual animals as indicated on the far right. The x- and y-axes represent a conceptual 2-dimensional space to which the MDS algorithm projected individual lung and trachea samples of high-dimensionality; i.e., the number of genes in the block associated with each sample, while preserving the distances/dissimilarities between samples as closely as possible. Double arrow illustrates that the gene signature distinguishes the two virus infections in trachea at 1 dpi, while lung samples show no separation (dotted rectangle). c. As in b, for the indicated cluster of 152 genes that is differentially regulated in lung but not trachea tissues and separates the two virus strains on 1 dpi. d and e. Differential transcriptional responses in an experiment comparing lung samples from 15-day-old CF ferrets (n=3) vs. non-CF ferrets (n=5). d. Similar pathways enriched in genes differentially expressed in 15-day-old CF ferret lung samples and CF human bronchial brushings, derived from Ingenuity Pathway Analysis. The values in parenthesis are the enrichment p-values for the corresponding pathways in the genes differentially expressed in CF human bronchial brushing19. In brackets are genes which were differentially expressed in both ferret and human CF/non-CF comparisons. e. Network illustration of 32 genes of the function ‘inflammatory response’, which were differentially expressed in the same direction in ferret and human CF datasets (for additional details see Supplementary Fig. 20). Red and blue shading reflects the extent of increased or decreased expression, respectively, in CF relative to non-CF individuals. A solid line between two genes indicates direct interaction(s) among them and a dotted line for indirect interaction(s), as documented in the literature.

Mentions: As quantified by RNA-seq, host transcriptional changes were much more extensive in infected trachea (9,869 differentially expressed (DE) genes, adjusted p-value < 0.01) than in infected lung (4,646 DE genes), and the kinetics of the response differed by virus and compartment (Supplementary Fig. 17). In the trachea, the 1918 virus induced a pronounced transcriptional response, both in the number of DE genes and in the magnitude of their changes, that commenced at 1 dpi and was largely sustained through day 8; in contrast, infection with the CA04 virus resulted in a gradual escalation of overall transcriptional changes in these same genes, resulting in peak expression by 8 dpi. Different kinetics occurred in the lung, where both viruses induced a similar number of DE genes at 1 dpi, followed by a decline to far fewer DE genes by day 8. A detailed tissue-by-virus comparison revealed distinct transcriptional signatures that differentiated the response to the 1918 and CA04 viruses in the two respiratory tissues (Figure 2a, Supplementary Fig. 18, Supplementary Table 15). Within the trachea-specific host response, a subset of 2,592 ferret genes distinguished the two viruses, with extensive perturbation at 1 dpi in response to the 1918 virus and minimal alteration in response to CA04 (Figure 2b). This gene set has an over-representation of diverse biological processes such as Apoptosis Signaling, NGF Signaling, and Ceramide Signaling (one-sided Fisher exact test p-values of 4.28×10−7, 1.61×10−6, 3.76×10−6, respectively, Supplementary Table 16). Related lipid-receptor signaling systems, such as sphingosine-1-phosphate (S1P) receptor signaling, can protect the host from influenza virus-induced “cytokine storm” by inhibiting pro-inflammatory responses12, 13. Similarly, some DE transcripts were exclusively observed within the lung compartment, with a subset of 152 ferret genes that differentiated the two virus infections (Figure 2c). Within this subset, we observed enrichment of Prothrombin Activation Pathway and differential expression of Il13 and Il20, associated with Role of Cytokines in Mediating Communication between Immune Cells (p-value of 1.53×10−2), that are produced by pulmonary innate lymphoid cells14 and maturing dendritic cells15, respectively. In summary, the ferret genomic resources described here enabled a side-by-side comparison of ferret transcriptional responses to two human pandemic influenza viruses. The results revealed that the host response to the two pandemic viruses differs in a tissue compartment–dependent manner.


The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.

Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG - Nat. Biotechnol. (2014)

Transcriptomic analyses of the host response to influenza virus infection and CF disease progression in ferrets. a. Heat map visualization shows distinct gene expression changes in lung and trachea samples from ferrets infected with either the 2009 pandemic H1N1 influenza A/CA/04/2009 virus (CA04) or the 1918 pandemic H1N1 influenza A/Brevig Mission/1/1918 virus (1918). Each row shows the log2 (fold-change) for three infected animals relative to corresponding tissue from three mock-infected ferrets. The heat map is organized by the specificity of the changes with respect to tissue or virus. From left to right black bars at the top of the panel indicate four groups of genes: specific to trachea; distinct profiles in trachea and lung; similar profiles in trachea and lung; specific to lung (for additional details see Supplementary Fig. 18); within each group orange subsections differ between the virus strains, green subsections do not. b. Multidimensional scaling (MDS) representation of the distances among samples based on the indicated cluster of 2,592 genes from a that distinguish viruses in trachea but not in lung. Points show individual animals as indicated on the far right. The x- and y-axes represent a conceptual 2-dimensional space to which the MDS algorithm projected individual lung and trachea samples of high-dimensionality; i.e., the number of genes in the block associated with each sample, while preserving the distances/dissimilarities between samples as closely as possible. Double arrow illustrates that the gene signature distinguishes the two virus infections in trachea at 1 dpi, while lung samples show no separation (dotted rectangle). c. As in b, for the indicated cluster of 152 genes that is differentially regulated in lung but not trachea tissues and separates the two virus strains on 1 dpi. d and e. Differential transcriptional responses in an experiment comparing lung samples from 15-day-old CF ferrets (n=3) vs. non-CF ferrets (n=5). d. Similar pathways enriched in genes differentially expressed in 15-day-old CF ferret lung samples and CF human bronchial brushings, derived from Ingenuity Pathway Analysis. The values in parenthesis are the enrichment p-values for the corresponding pathways in the genes differentially expressed in CF human bronchial brushing19. In brackets are genes which were differentially expressed in both ferret and human CF/non-CF comparisons. e. Network illustration of 32 genes of the function ‘inflammatory response’, which were differentially expressed in the same direction in ferret and human CF datasets (for additional details see Supplementary Fig. 20). Red and blue shading reflects the extent of increased or decreased expression, respectively, in CF relative to non-CF individuals. A solid line between two genes indicates direct interaction(s) among them and a dotted line for indirect interaction(s), as documented in the literature.
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Related In: Results  -  Collection

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Figure 2: Transcriptomic analyses of the host response to influenza virus infection and CF disease progression in ferrets. a. Heat map visualization shows distinct gene expression changes in lung and trachea samples from ferrets infected with either the 2009 pandemic H1N1 influenza A/CA/04/2009 virus (CA04) or the 1918 pandemic H1N1 influenza A/Brevig Mission/1/1918 virus (1918). Each row shows the log2 (fold-change) for three infected animals relative to corresponding tissue from three mock-infected ferrets. The heat map is organized by the specificity of the changes with respect to tissue or virus. From left to right black bars at the top of the panel indicate four groups of genes: specific to trachea; distinct profiles in trachea and lung; similar profiles in trachea and lung; specific to lung (for additional details see Supplementary Fig. 18); within each group orange subsections differ between the virus strains, green subsections do not. b. Multidimensional scaling (MDS) representation of the distances among samples based on the indicated cluster of 2,592 genes from a that distinguish viruses in trachea but not in lung. Points show individual animals as indicated on the far right. The x- and y-axes represent a conceptual 2-dimensional space to which the MDS algorithm projected individual lung and trachea samples of high-dimensionality; i.e., the number of genes in the block associated with each sample, while preserving the distances/dissimilarities between samples as closely as possible. Double arrow illustrates that the gene signature distinguishes the two virus infections in trachea at 1 dpi, while lung samples show no separation (dotted rectangle). c. As in b, for the indicated cluster of 152 genes that is differentially regulated in lung but not trachea tissues and separates the two virus strains on 1 dpi. d and e. Differential transcriptional responses in an experiment comparing lung samples from 15-day-old CF ferrets (n=3) vs. non-CF ferrets (n=5). d. Similar pathways enriched in genes differentially expressed in 15-day-old CF ferret lung samples and CF human bronchial brushings, derived from Ingenuity Pathway Analysis. The values in parenthesis are the enrichment p-values for the corresponding pathways in the genes differentially expressed in CF human bronchial brushing19. In brackets are genes which were differentially expressed in both ferret and human CF/non-CF comparisons. e. Network illustration of 32 genes of the function ‘inflammatory response’, which were differentially expressed in the same direction in ferret and human CF datasets (for additional details see Supplementary Fig. 20). Red and blue shading reflects the extent of increased or decreased expression, respectively, in CF relative to non-CF individuals. A solid line between two genes indicates direct interaction(s) among them and a dotted line for indirect interaction(s), as documented in the literature.
Mentions: As quantified by RNA-seq, host transcriptional changes were much more extensive in infected trachea (9,869 differentially expressed (DE) genes, adjusted p-value < 0.01) than in infected lung (4,646 DE genes), and the kinetics of the response differed by virus and compartment (Supplementary Fig. 17). In the trachea, the 1918 virus induced a pronounced transcriptional response, both in the number of DE genes and in the magnitude of their changes, that commenced at 1 dpi and was largely sustained through day 8; in contrast, infection with the CA04 virus resulted in a gradual escalation of overall transcriptional changes in these same genes, resulting in peak expression by 8 dpi. Different kinetics occurred in the lung, where both viruses induced a similar number of DE genes at 1 dpi, followed by a decline to far fewer DE genes by day 8. A detailed tissue-by-virus comparison revealed distinct transcriptional signatures that differentiated the response to the 1918 and CA04 viruses in the two respiratory tissues (Figure 2a, Supplementary Fig. 18, Supplementary Table 15). Within the trachea-specific host response, a subset of 2,592 ferret genes distinguished the two viruses, with extensive perturbation at 1 dpi in response to the 1918 virus and minimal alteration in response to CA04 (Figure 2b). This gene set has an over-representation of diverse biological processes such as Apoptosis Signaling, NGF Signaling, and Ceramide Signaling (one-sided Fisher exact test p-values of 4.28×10−7, 1.61×10−6, 3.76×10−6, respectively, Supplementary Table 16). Related lipid-receptor signaling systems, such as sphingosine-1-phosphate (S1P) receptor signaling, can protect the host from influenza virus-induced “cytokine storm” by inhibiting pro-inflammatory responses12, 13. Similarly, some DE transcripts were exclusively observed within the lung compartment, with a subset of 152 ferret genes that differentiated the two virus infections (Figure 2c). Within this subset, we observed enrichment of Prothrombin Activation Pathway and differential expression of Il13 and Il20, associated with Role of Cytokines in Mediating Communication between Immune Cells (p-value of 1.53×10−2), that are produced by pulmonary innate lymphoid cells14 and maturing dendritic cells15, respectively. In summary, the ferret genomic resources described here enabled a side-by-side comparison of ferret transcriptional responses to two human pandemic influenza viruses. The results revealed that the host response to the two pandemic viruses differs in a tissue compartment–dependent manner.

Bottom Line: Here we describe the 2.41 Gb draft genome assembly of the domestic ferret, constituting 2.28 Gb of sequence plus gaps.We annotated 19,910 protein-coding genes on this assembly using RNA-seq data from 21 ferret tissues.Using microarray data from 16 ferret samples reflecting cystic fibrosis disease progression, we showed that transcriptional changes in the CFTR-knockout ferret lung reflect pathways of early disease that cannot be readily studied in human infants with cystic fibrosis disease.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, Washington, USA.

ABSTRACT
The domestic ferret (Mustela putorius furo) is an important animal model for multiple human respiratory diseases. It is considered the 'gold standard' for modeling human influenza virus infection and transmission. Here we describe the 2.41 Gb draft genome assembly of the domestic ferret, constituting 2.28 Gb of sequence plus gaps. We annotated 19,910 protein-coding genes on this assembly using RNA-seq data from 21 ferret tissues. We characterized the ferret host response to two influenza virus infections by RNA-seq analysis of 42 ferret samples from influenza time-course data and showed distinct signatures in ferret trachea and lung tissues specific to 1918 or 2009 human pandemic influenza virus infections. Using microarray data from 16 ferret samples reflecting cystic fibrosis disease progression, we showed that transcriptional changes in the CFTR-knockout ferret lung reflect pathways of early disease that cannot be readily studied in human infants with cystic fibrosis disease.

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Related in: MedlinePlus