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Najm M, Cornet M, Albergante L, Zinovyev A, Sermet-Gaudelus I, Stoven V, Calzone L, Martignetti L. Representation and quantification of module activity from omics data with rROMA. NPJ Syst Biol Appl 2024; 10:8. [PMID: 38242871 PMCID: PMC10799004 DOI: 10.1038/s41540-024-00331-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/03/2024] [Indexed: 01/21/2024] Open
Abstract
The efficiency of analyzing high-throughput data in systems biology has been demonstrated in numerous studies, where molecular data, such as transcriptomics and proteomics, offers great opportunities for understanding the complexity of biological processes. One important aspect of data analysis in systems biology is the shift from a reductionist approach that focuses on individual components to a more integrative perspective that considers the system as a whole, where the emphasis shifted from differential expression of individual genes to determining the activity of gene sets. Here, we present the rROMA software package for fast and accurate computation of the activity of gene sets with coordinated expression. The rROMA package incorporates significant improvements in the calculation algorithm, along with the implementation of several functions for statistical analysis and visualizing results. These additions greatly expand the package's capabilities and offer valuable tools for data analysis and interpretation. It is an open-source package available on github at: www.github.com/sysbio-curie/rROMA . Based on publicly available transcriptomic datasets, we applied rROMA to cystic fibrosis, highlighting biological mechanisms potentially involved in the establishment and progression of the disease and the associated genes. Results indicate that rROMA can detect disease-related active signaling pathways using transcriptomic and proteomic data. The results notably identified a significant mechanism relevant to cystic fibrosis, raised awareness of a possible bias related to cell culture, and uncovered an intriguing gene that warrants further investigation.
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Affiliation(s)
- Matthieu Najm
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Matthieu Cornet
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Luca Albergante
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Andrei Zinovyev
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Isabelle Sermet-Gaudelus
- Faculté de Médecine, Université de Paris, Paris, France
- Institut Necker Enfants Malades, INSERM U1151, Paris, France
- AP-HP. Centre - Université Paris Cité; Hôpital Necker Enfants Malades, Centre de Référence Maladie Rare - Mucoviscidose, Paris, France
| | - Véronique Stoven
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Laurence Calzone
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Loredana Martignetti
- INSERM U900, 75428, Paris, France.
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France.
- Institut Curie, PSL Research University, 75248, Paris, France.
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Wetzel KS, Illouz M, Abad L, Aull HG, Russell DA, Garlena RA, Cristinziano M, Malmsheimer S, Chalut C, Hatfull GF, Kremer L. Therapeutically useful mycobacteriophages BPs and Muddy require trehalose polyphleates. Nat Microbiol 2023; 8:1717-1731. [PMID: 37644325 PMCID: PMC10465359 DOI: 10.1038/s41564-023-01451-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Mycobacteriophages show promise as therapeutic agents for non-tuberculous mycobacterium infections. However, little is known about phage recognition of Mycobacterium cell surfaces or mechanisms of phage resistance. We show here that trehalose polyphleates (TPPs)-high-molecular-weight, surface-exposed glycolipids found in some mycobacterial species-are required for infection of Mycobacterium abscessus and Mycobacterium smegmatis by clinically useful phages BPs and Muddy. TPP loss leads to defects in adsorption and infection and confers resistance. Transposon mutagenesis shows that TPP disruption is the primary mechanism for phage resistance. Spontaneous phage resistance occurs through TPP loss by mutation, and some M. abscessus clinical isolates are naturally phage-insensitive due to TPP synthesis gene mutations. Both BPs and Muddy become TPP-independent through single amino acid substitutions in their tail spike proteins, and M. abscessus mutants resistant to TPP-independent phages reveal additional resistance mechanisms. Clinical use of BPs and Muddy TPP-independent mutants should preempt phage resistance caused by TPP loss.
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Affiliation(s)
- Katherine S Wetzel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Morgane Illouz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haley G Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Madison Cristinziano
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Silke Malmsheimer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France.
- INSERM, IRIM, Montpellier, France.
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Soret P, Vandenborght LE, Francis F, Coron N, Enaud R, Avalos M, Schaeverbeke T, Berger P, Fayon M, Thiebaut R, Delhaes L. Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis. Sci Rep 2020; 10:3589. [PMID: 32108159 PMCID: PMC7046743 DOI: 10.1038/s41598-020-60015-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Lung infections play a critical role in cystic fibrosis (CF) pathogenesis. CF respiratory tract is now considered to be a polymicrobial niche and advances in high-throughput sequencing allowed to analyze its microbiota and mycobiota. However, no NGS studies until now have characterized both communities during CF pulmonary exacerbation (CFPE). Thirty-three sputa isolated from patients with and without CFPE were used for metagenomic high-throughput sequencing targeting 16S and ITS2 regions of bacterial and fungal rRNA. We built inter-kingdom network and adapted Phy-Lasso method to highlight correlations in compositional data. The decline in respiratory function was associated with a decrease in bacterial diversity. The inter-kingdom network revealed three main clusters organized around Aspergillus, Candida, and Scedosporium genera. Using Phy-Lasso method, we identified Aspergillus and Malassezia as relevantly associated with CFPE, and Scedosporium plus Pseudomonas with a decline in lung function. We corroborated in vitro the cross-domain interactions between Aspergillus and Streptococcus predicted by the correlation network. For the first time, we included documented mycobiome data into a version of the ecological Climax/Attack model that opens new lines of thoughts about the physiopathology of CF lung disease and future perspectives to improve its therapeutic management.
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Affiliation(s)
- Perrine Soret
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
| | - Louise-Eva Vandenborght
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- Genoscreen Society, 59000, Lille, France
| | - Florence Francis
- CHU Bordeaux, Department of Public Health, F-33000, Bordeaux, France
| | - Noémie Coron
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, F-33000, Bordeaux, France
| | - Raphael Enaud
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France
| | - Marta Avalos
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
| | | | - Patrick Berger
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
| | - Michael Fayon
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France
| | - Rodolphe Thiebaut
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
- CHU Bordeaux, Department of Public Health, F-33000, Bordeaux, France
| | - Laurence Delhaes
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France.
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France.
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, F-33000, Bordeaux, France.
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France.
- University and CHU of Lille, F-59000, Lille, France.
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Sana TG, Lomas R, Gimenez MR, Laubier A, Soscia C, Chauvet C, Conesa A, Voulhoux R, Ize B, Bleves S. Differential Modulation of Quorum Sensing Signaling through QslA in Pseudomonas aeruginosa Strains PAO1 and PA14. J Bacteriol 2019; 201:e00362-19. [PMID: 31405911 PMCID: PMC6779463 DOI: 10.1128/jb.00362-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/06/2019] [Indexed: 11/20/2022] Open
Abstract
Two clinical isolates of the opportunist pathogen Pseudomonas aeruginosa named PAO1 and PA14 are commonly studied in research laboratories. Despite the isolates being closely related, PA14 exhibits increased virulence compared to that of PAO1 in various models. To determine which players are responsible for the hypervirulence phenotype of the PA14 strain, we elected a transcriptomic approach through RNA sequencing. We found 2,029 genes that are differentially expressed between the two strains, including several genes that are involved with or regulated by quorum sensing (QS), known to control most of the virulence factors in P. aeruginosa Among them, we chose to focus our study on QslA, an antiactivator of QS whose expression was barely detectable in the PA14 strain according our data. We hypothesized that lack of expression of qslA in PA14 could be responsible for higher QS expression in the PA14 strain, possibly explaining its hypervirulence phenotype. After confirming that QslA protein was highly produced in PAO1 but not in the PA14 strain, we obtained evidence showing that a PAO1 deletion strain of qslA has faster QS gene expression kinetics than PA14. Moreover, known virulence factors activated by QS, such as (i) pyocyanin production, (ii) H2-T6SS (type VI secretion system) gene expression, and (iii) Xcp-T2SS (type II secretion system) machinery production and secretion, were all lower in PAO1 than in PA14, due to higher qslA expression. However, biofilm formation and cytotoxicity toward macrophages, although increased in PA14 compared to PAO1, were independent of QslA control. Together, our findings implicated differential qslA expression as a major determinant of virulence factor expression in P. aeruginosa strains PAO1 and PA14.IMPORTANCEPseudomonas aeruginosa is an opportunistic pathogen responsible for acute nosocomial infections and chronic pulmonary infections. P. aeruginosa strain PA14 is known to be hypervirulent in different hosts. Despite several studies in the field, the underlining molecular mechanisms sustaining this phenotype remain enigmatic. Here we provide evidence that the PA14 strain has faster quorum sensing (QS) kinetics than the PAO1 strain, due to the lack of QslA expression, an antiactivator of QS. QS is a major regulator of virulence factors in P. aeruginosa; therefore, we propose that the hypervirulent phenotype of the PA14 strain is, at least partially, due to the lack of QslA expression. This mechanism could be of great importance, as it could be conserved among other P. aeruginosa isolates.
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Affiliation(s)
- T G Sana
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires-UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille University and CNRS, Marseille, France
| | - R Lomas
- Genomics of Gene Expression Laboratory, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - M R Gimenez
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires-UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille University and CNRS, Marseille, France
| | - A Laubier
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires-UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille University and CNRS, Marseille, France
| | - C Soscia
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires-UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille University and CNRS, Marseille, France
| | - C Chauvet
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires-UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille University and CNRS, Marseille, France
| | - A Conesa
- Microbiology and Cell Science, IFAS, Genetics Insitute, University of Florida, Gainesville, Florida, USA
| | - R Voulhoux
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires-UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille University and CNRS, Marseille, France
| | - B Ize
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires-UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille University and CNRS, Marseille, France
| | - S Bleves
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires-UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille University and CNRS, Marseille, France
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Gimenez MR, Chandra G, Van Overvelt P, Voulhoux R, Bleves S, Ize B. Genome wide identification and experimental validation of Pseudomonas aeruginosa Tat substrates. Sci Rep 2018; 8:11950. [PMID: 30093651 PMCID: PMC6085387 DOI: 10.1038/s41598-018-30393-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/30/2018] [Indexed: 11/13/2022] Open
Abstract
In bacteria, the twin-arginine translocation (Tat) pathway allows the export of folded proteins through the inner membrane. Proteins targeted to this system are synthesized with N-terminal signal peptides bearing a conserved twin-arginine motif. The Tat pathway is critical for many bacterial processes including pathogenesis and virulence. However, the full set of Tat substrates is unknown in many bacteria, and the reliability of in silico prediction methods largely uncertain. In this work, we performed a combination of in silico analysis and experimental validation to identify a core set of Tat substrates in the opportunistic pathogen Pseudomonas aeruginosa. In silico analysis predicted 44 putative Tat signal peptides in the P. aeruginosa PA14 proteome. We developed an improved amidase-based Tat reporter assay to show that 33 of these are real Tat signal peptides. In addition, in silico analysis of the full translated genome revealed a Tat candidate with a missassigned start codon. We showed that it is a new periplasmic protein in P. aeruginosa. Altogether we discovered and validated 34 Tat substrates. These show little overlap with Escherichia coli Tat substrates, and functional analysis points to a general role for the P. aeruginosa Tat system in the colonization of environmental niches and pathogenicity.
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Affiliation(s)
- Maxime Rémi Gimenez
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM-UMR7255), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Univ., 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille cedex 09, France
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Perrine Van Overvelt
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM-UMR7255), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Univ., 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille cedex 09, France
| | - Romé Voulhoux
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM-UMR7255), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Univ., 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille cedex 09, France
| | - Sophie Bleves
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM-UMR7255), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Univ., 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille cedex 09, France
| | - Bérengère Ize
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM-UMR7255), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Univ., 31 Chemin Joseph Aiguier, CS 70071, 13402 Marseille cedex 09, France.
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