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Human TRIM gene expression in response to interferons.

Carthagena L, Bergamaschi A, Luna JM, David A, Uchil PD, Margottin-Goguet F, Mothes W, Hazan U, Transy C, Pancino G, Nisole S - PLoS ONE (2009)

Bottom Line: We found that 27 of the 72 human TRIM genes are sensitive to IFN.Our analysis identifies 9 additional TRIM genes that are up-regulated by IFNs, among which only 3 have previously been found to display an antiviral activity.Our results present the first comprehensive TRIM gene expression analysis in primary human immune cells, and suggest the involvement of additional TRIM proteins in regulating host antiviral activities.

View Article: PubMed Central - PubMed

Affiliation: Département des Maladies Infectieuses, Institut Cochin, Université Paris Descartes, CNRS, UMR 8104, Paris, France.

ABSTRACT

Background: Tripartite motif (TRIM) proteins constitute a family of proteins that share a conserved tripartite architecture. The recent discovery of the anti-HIV activity of TRIM5alpha in primate cells has stimulated much interest in the potential role of TRIM proteins in antiviral activities and innate immunity.

Principal findings: To test if TRIM genes are up-regulated during antiviral immune responses, we performed a systematic analysis of TRIM gene expression in human primary lymphocytes and monocyte-derived macrophages in response to interferons (IFNs, type I and II) or following FcgammaR-mediated activation of macrophages. We found that 27 of the 72 human TRIM genes are sensitive to IFN. Our analysis identifies 9 additional TRIM genes that are up-regulated by IFNs, among which only 3 have previously been found to display an antiviral activity. Also, we found 2 TRIM proteins, TRIM9 and 54, to be specifically up-regulated in FcgammaR-activated macrophages.

Conclusions: Our results present the first comprehensive TRIM gene expression analysis in primary human immune cells, and suggest the involvement of additional TRIM proteins in regulating host antiviral activities.

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Related in: MedlinePlus

Summary of TRIM expression in mouse and human macrophages upon various stimuli and in silico promoter analysis.TRIM expression in human macrophages upon IFN treatment. This part of the table shows the comparison of TRIM gene expression in mouse macrophages treated with LPS or poly(I:C) [35], in human macrophages upon IFN-γ and LPS treatment [35], [47], and in human macrophages stimulated with either type I or type II (γ) IFN (our study). In silico promoter analysis. Table illustrating potential transcription factor binding sites based on sequence analysis of 1 kb of genomic DNA upstream of each TRIM protein. IRF sites were scored using the PROMO virtual laboratory using matrices specific to selected human transcription factors (TFs). Highest scoring TF binding sites (+++) had dissimilarity values of less than 0.1 and random expectation values (noted RE within the table key) of less than 0.01. Calculated sites meeting only one of the above criteria (++) or neither (+) are indicated. ISRE/IRF sites were further corroborated with MatInspector. Highest scoring TF binding sites (+++) had similarity values above 0.9, (++) values between 0.85–0.89, and (+) values between 0.80–0.84. Numerous positive genomic controls (OAS2, MX1, STAT1, APOBEC3G, APOBEC3F, etc.) and their calculated TF profiles were used to evaluate the stringency of hits. Negative genomic controls GAPDH and ACTB were used to evaluate the stringency of the programs.
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pone-0004894-g005: Summary of TRIM expression in mouse and human macrophages upon various stimuli and in silico promoter analysis.TRIM expression in human macrophages upon IFN treatment. This part of the table shows the comparison of TRIM gene expression in mouse macrophages treated with LPS or poly(I:C) [35], in human macrophages upon IFN-γ and LPS treatment [35], [47], and in human macrophages stimulated with either type I or type II (γ) IFN (our study). In silico promoter analysis. Table illustrating potential transcription factor binding sites based on sequence analysis of 1 kb of genomic DNA upstream of each TRIM protein. IRF sites were scored using the PROMO virtual laboratory using matrices specific to selected human transcription factors (TFs). Highest scoring TF binding sites (+++) had dissimilarity values of less than 0.1 and random expectation values (noted RE within the table key) of less than 0.01. Calculated sites meeting only one of the above criteria (++) or neither (+) are indicated. ISRE/IRF sites were further corroborated with MatInspector. Highest scoring TF binding sites (+++) had similarity values above 0.9, (++) values between 0.85–0.89, and (+) values between 0.80–0.84. Numerous positive genomic controls (OAS2, MX1, STAT1, APOBEC3G, APOBEC3F, etc.) and their calculated TF profiles were used to evaluate the stringency of hits. Negative genomic controls GAPDH and ACTB were used to evaluate the stringency of the programs.

Mentions: Interestingly, our data partially overlap with a recent study performed on mouse TRIM genes [35] (Figure 5). For instance, TRIM6, 14, 19/PML, 20/MEFV, 21, 25, 26 and 34 were up-regulated in response to IFNs in our study and classified to cluster 2 or 3 by Rajsbaum et al. These two clusters comprise TRIM genes found to be highly expressed in macrophages and dendritic cells (DC) and whose expression is further induced following influenza virus infection in an IFN-dependent manner [35]. We also identified human TRIM5, 22, 31, 38, 56, 58 or 69 as additional genes induced by type I IFN, but these genes were not analyzed or have no homologue in mouse [35]. Our two studies also show that both constitutive expression and IFN-inducibility of TRIM genes are cell type dependent, which may have an impact on the antiviral properties of individual TRIM family members [35]. Our data also largely confirm a gene expression study performed by Martinez and colleagues [47] and re-analyzed by Rajsbaum et al. in order to examine TRIM gene expression in human macrophages stimulated with IFN-γ and LPS [35]. Despite different experimental conditions, a good overall agreement can be observed (Figure 5). The main discrepancies concern a number of TRIM genes (including TRIM2, 3, 10, 13, 17, 18, 29, 45, 46, 48 and 62) which were found to be up-regulated by IFN-γ/LPS treatment by Martinez et al., although they did not respond to IFNs in our study. It has to be noted that the study by Martinez et al. was performed on M-CSF-treated MDM, further activated for 18 h with LPS and IFN-γ [47]. In contrast, we avoided the use of exogenous cytokines, such as M-CSF, for differentiating monocytes into macrophages, since it may directly induce the expression of several genes [48], [49] and even influence retroviral replication [50]. In addition, we identified TRIM20/MEFV as being highly up-regulated by both type I and type II IFN, in accordance with another study [26], whereas Martinez et al. did not [35].


Human TRIM gene expression in response to interferons.

Carthagena L, Bergamaschi A, Luna JM, David A, Uchil PD, Margottin-Goguet F, Mothes W, Hazan U, Transy C, Pancino G, Nisole S - PLoS ONE (2009)

Summary of TRIM expression in mouse and human macrophages upon various stimuli and in silico promoter analysis.TRIM expression in human macrophages upon IFN treatment. This part of the table shows the comparison of TRIM gene expression in mouse macrophages treated with LPS or poly(I:C) [35], in human macrophages upon IFN-γ and LPS treatment [35], [47], and in human macrophages stimulated with either type I or type II (γ) IFN (our study). In silico promoter analysis. Table illustrating potential transcription factor binding sites based on sequence analysis of 1 kb of genomic DNA upstream of each TRIM protein. IRF sites were scored using the PROMO virtual laboratory using matrices specific to selected human transcription factors (TFs). Highest scoring TF binding sites (+++) had dissimilarity values of less than 0.1 and random expectation values (noted RE within the table key) of less than 0.01. Calculated sites meeting only one of the above criteria (++) or neither (+) are indicated. ISRE/IRF sites were further corroborated with MatInspector. Highest scoring TF binding sites (+++) had similarity values above 0.9, (++) values between 0.85–0.89, and (+) values between 0.80–0.84. Numerous positive genomic controls (OAS2, MX1, STAT1, APOBEC3G, APOBEC3F, etc.) and their calculated TF profiles were used to evaluate the stringency of hits. Negative genomic controls GAPDH and ACTB were used to evaluate the stringency of the programs.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2654144&req=5

pone-0004894-g005: Summary of TRIM expression in mouse and human macrophages upon various stimuli and in silico promoter analysis.TRIM expression in human macrophages upon IFN treatment. This part of the table shows the comparison of TRIM gene expression in mouse macrophages treated with LPS or poly(I:C) [35], in human macrophages upon IFN-γ and LPS treatment [35], [47], and in human macrophages stimulated with either type I or type II (γ) IFN (our study). In silico promoter analysis. Table illustrating potential transcription factor binding sites based on sequence analysis of 1 kb of genomic DNA upstream of each TRIM protein. IRF sites were scored using the PROMO virtual laboratory using matrices specific to selected human transcription factors (TFs). Highest scoring TF binding sites (+++) had dissimilarity values of less than 0.1 and random expectation values (noted RE within the table key) of less than 0.01. Calculated sites meeting only one of the above criteria (++) or neither (+) are indicated. ISRE/IRF sites were further corroborated with MatInspector. Highest scoring TF binding sites (+++) had similarity values above 0.9, (++) values between 0.85–0.89, and (+) values between 0.80–0.84. Numerous positive genomic controls (OAS2, MX1, STAT1, APOBEC3G, APOBEC3F, etc.) and their calculated TF profiles were used to evaluate the stringency of hits. Negative genomic controls GAPDH and ACTB were used to evaluate the stringency of the programs.
Mentions: Interestingly, our data partially overlap with a recent study performed on mouse TRIM genes [35] (Figure 5). For instance, TRIM6, 14, 19/PML, 20/MEFV, 21, 25, 26 and 34 were up-regulated in response to IFNs in our study and classified to cluster 2 or 3 by Rajsbaum et al. These two clusters comprise TRIM genes found to be highly expressed in macrophages and dendritic cells (DC) and whose expression is further induced following influenza virus infection in an IFN-dependent manner [35]. We also identified human TRIM5, 22, 31, 38, 56, 58 or 69 as additional genes induced by type I IFN, but these genes were not analyzed or have no homologue in mouse [35]. Our two studies also show that both constitutive expression and IFN-inducibility of TRIM genes are cell type dependent, which may have an impact on the antiviral properties of individual TRIM family members [35]. Our data also largely confirm a gene expression study performed by Martinez and colleagues [47] and re-analyzed by Rajsbaum et al. in order to examine TRIM gene expression in human macrophages stimulated with IFN-γ and LPS [35]. Despite different experimental conditions, a good overall agreement can be observed (Figure 5). The main discrepancies concern a number of TRIM genes (including TRIM2, 3, 10, 13, 17, 18, 29, 45, 46, 48 and 62) which were found to be up-regulated by IFN-γ/LPS treatment by Martinez et al., although they did not respond to IFNs in our study. It has to be noted that the study by Martinez et al. was performed on M-CSF-treated MDM, further activated for 18 h with LPS and IFN-γ [47]. In contrast, we avoided the use of exogenous cytokines, such as M-CSF, for differentiating monocytes into macrophages, since it may directly induce the expression of several genes [48], [49] and even influence retroviral replication [50]. In addition, we identified TRIM20/MEFV as being highly up-regulated by both type I and type II IFN, in accordance with another study [26], whereas Martinez et al. did not [35].

Bottom Line: We found that 27 of the 72 human TRIM genes are sensitive to IFN.Our analysis identifies 9 additional TRIM genes that are up-regulated by IFNs, among which only 3 have previously been found to display an antiviral activity.Our results present the first comprehensive TRIM gene expression analysis in primary human immune cells, and suggest the involvement of additional TRIM proteins in regulating host antiviral activities.

View Article: PubMed Central - PubMed

Affiliation: Département des Maladies Infectieuses, Institut Cochin, Université Paris Descartes, CNRS, UMR 8104, Paris, France.

ABSTRACT

Background: Tripartite motif (TRIM) proteins constitute a family of proteins that share a conserved tripartite architecture. The recent discovery of the anti-HIV activity of TRIM5alpha in primate cells has stimulated much interest in the potential role of TRIM proteins in antiviral activities and innate immunity.

Principal findings: To test if TRIM genes are up-regulated during antiviral immune responses, we performed a systematic analysis of TRIM gene expression in human primary lymphocytes and monocyte-derived macrophages in response to interferons (IFNs, type I and II) or following FcgammaR-mediated activation of macrophages. We found that 27 of the 72 human TRIM genes are sensitive to IFN. Our analysis identifies 9 additional TRIM genes that are up-regulated by IFNs, among which only 3 have previously been found to display an antiviral activity. Also, we found 2 TRIM proteins, TRIM9 and 54, to be specifically up-regulated in FcgammaR-activated macrophages.

Conclusions: Our results present the first comprehensive TRIM gene expression analysis in primary human immune cells, and suggest the involvement of additional TRIM proteins in regulating host antiviral activities.

Show MeSH
Related in: MedlinePlus