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Article ; Online: Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies.

Simopoulos, Caitlin M A / Figeys, Daniel / Lavallée-Adam, Mathieu

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2456, Page(s) 319–338

Abstract: Constant improvements in mass spectrometry technologies and laboratory workflows have enabled the proteomics investigation of biological samples of growing complexity. Microbiomes represent such complex samples for which metaproteomics analyses are ... ...

Abstract	Constant improvements in mass spectrometry technologies and laboratory workflows have enabled the proteomics investigation of biological samples of growing complexity. Microbiomes represent such complex samples for which metaproteomics analyses are becoming increasingly popular. Metaproteomics experimental procedures create large amounts of data from which biologically relevant signal must be efficiently extracted to draw meaningful conclusions. Such a data processing requires appropriate bioinformatics tools specifically developed for, or capable of handling metaproteomics data. In this chapter, we outline current and novel tools that can perform the most commonly used steps in the analysis of cutting-edge metaproteomics data, such as peptide and protein identification and quantification, as well as data normalization, imputation, mining, and visualization. We also provide details about the experimental setups in which these tools should be used.
MeSH term(s)	Computational Biology/methods ; Gastrointestinal Microbiome ; Microbiota ; Proteomics/methods ; Software
Language	English
Publishing date	2022-05-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2124-0_22
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Article ; Online: PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics.

Nadeau, Rachel / Byvsheva, Anastasiia / Lavallée-Adam, Mathieu

BMC bioinformatics

2021 Volume 22, Issue 1, Page(s) 302

Abstract: Background: Quantitative proteomics studies are often used to detect proteins that are differentially expressed across different experimental conditions. Functional enrichment analyses are then typically used to detect annotations, such as biological ... ...

Abstract	Background: Quantitative proteomics studies are often used to detect proteins that are differentially expressed across different experimental conditions. Functional enrichment analyses are then typically used to detect annotations, such as biological processes that are significantly enriched among such differentially expressed proteins to provide insights into the molecular impacts of the studied conditions. While common, this analytical pipeline often heavily relies on arbitrary thresholds of significance. However, a functional annotation may be dysregulated in a given experimental condition, while none, or very few of its proteins may be individually considered to be significantly differentially expressed. Such an annotation would therefore be missed by standard approaches. Results: Herein, we propose a novel graph theory-based method, PIGNON, for the detection of differentially expressed functional annotations in different conditions. PIGNON does not assess the statistical significance of the differential expression of individual proteins, but rather maps protein differential expression levels onto a protein-protein interaction network and measures the clustering of proteins from a given functional annotation within the network. This process allows the detection of functional annotations for which the proteins are differentially expressed and grouped in the network. A Monte-Carlo sampling approach is used to assess the clustering significance of proteins in an expression-weighted network. When applied to a quantitative proteomics analysis of different molecular subtypes of breast cancer, PIGNON detects Gene Ontology terms that are both significantly clustered in a protein-protein interaction network and differentially expressed across different breast cancer subtypes. PIGNON identified functional annotations that are dysregulated and clustered within the network between the HER2+, triple negative and hormone receptor positive subtypes. We show that PIGNON's results are complementary to those of state-of-the-art functional enrichment analyses and that it highlights functional annotations missed by standard approaches. Furthermore, PIGNON detects functional annotations that have been previously associated with specific breast cancer subtypes. Conclusion: PIGNON provides an alternative to functional enrichment analyses and a more comprehensive characterization of quantitative datasets. Hence, it contributes to yielding a better understanding of dysregulated functions and processes in biological samples under different experimental conditions.
MeSH term(s)	Biological Phenomena ; Cluster Analysis ; Humans ; Protein Interaction Maps ; Proteins ; Proteomics
Chemical Substances	Proteins
Language	English
Publishing date	2021-06-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-021-04042-6
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Article ; Online: Proximity Interactome Map of the Vac14-Fig4 Complex Using BioID.

Qiu, Shirley / Lavallée-Adam, Mathieu / Côté, Marceline

Journal of proteome research

2021 Volume 20, Issue 11, Page(s) 4959–4973

Abstract: Conversion between phosphatidylinositol-3-phosphate and phosphatidylinositol-3,5-bisphosphate on endosomal membranes is critical for the maturation of early endosomes to late endosomes/lysosomes and is regulated by the PIKfyve-Vac14-Fig4 complex. Despite ...

Abstract	Conversion between phosphatidylinositol-3-phosphate and phosphatidylinositol-3,5-bisphosphate on endosomal membranes is critical for the maturation of early endosomes to late endosomes/lysosomes and is regulated by the PIKfyve-Vac14-Fig4 complex. Despite the importance of this complex for endosomal homeostasis and vesicular trafficking, there is little known about how its activity is regulated or how it interacts with other cellular proteins. Here, we screened for the cellular interactome of Vac14 and Fig4 using proximity-dependent biotin labeling (BioID). After independently screening the interactomes of Vac14 and Fig4, we identified 89 high-confidence protein hits shared by both proteins. Network analysis of these hits revealed pathways with known involvement of the PIKfyve-Vac14-Fig4 complex, including vesicular organization and PI3K/Akt signaling, as well as novel pathways including cell cycle and mitochondrial regulation. We also identified subunits of coatomer complex I (COPI), a Golgi-associated complex with an emerging role in endosomal dynamics. Using proximity ligation assays, we validated the interaction between Vac14 and COPI subunit COPB1 and between Vac14 and Arf1, a GTPase required for COPI assembly. In summary, this study used BioID to comprehensively map the Vac14-Fig4 interactome, revealing potential roles for these proteins in diverse cellular processes and pathways, including preliminary evidence of an interaction between Vac14 and COPI. Data are available
MeSH term(s)	Endosomes/metabolism ; Flavoproteins/metabolism ; HEK293 Cells ; Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Membrane Proteins/metabolism ; Phosphoric Monoester Hydrolases/metabolism
Chemical Substances	Flavoproteins ; Intracellular Signaling Peptides and Proteins ; Membrane Proteins ; VAC14 protein, human ; FIG4 protein, human (EC 3.1.3.-) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
Language	English
Publishing date	2021-09-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00408
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Article ; Online: Polyphosphate kinase regulates LPS structure and polymyxin resistance during starvation in E. coli.

Baijal, Kanchi / Abramchuk, Iryna / Herrera, Carmen M / Mah, Thien-Fah / Trent, M Stephen / Lavallée-Adam, Mathieu / Downey, Michael

PLoS biology

2024 Volume 22, Issue 3, Page(s) e3002558

Abstract: Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1,000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. ... ...

Abstract	Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1,000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work, we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (Δppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and Δppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while Δppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of the required building blocks. From our data set, we were particularly interested in Arn and EptA proteins, which were down-regulated in Δppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins in K-12 strains and a uropathogenic isolate, and provide evidence that this mis-regulation in Δppk cells stems from a failure to induce the BasRS two-component system during starvation. We also show that Δppk mutants unable to up-regulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.
MeSH term(s)	Escherichia coli/metabolism ; Lipopolysaccharides/metabolism ; Lipid A/metabolism ; Polyphosphates/metabolism ; Phosphotransferases (Phosphate Group Acceptor)
Chemical Substances	polyphosphate kinase (EC 2.7.4.1) ; Lipopolysaccharides ; Lipid A ; Polyphosphates ; Phosphotransferases (Phosphate Group Acceptor) (EC 2.7.4.-)
Language	English
Publishing date	2024-03-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3002558
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Article ; Online: Modus operandi: Chromatin recognition by α-helical histone readers.

Davarinejad, Hossein / Arvanitis-Vigneault, Alexis / Nygard, Dallas / Lavallée-Adam, Mathieu / Couture, Jean-François

Structure (London, England : 1993)

2023 Volume 32, Issue 1, Page(s) 8–17

Abstract: Histone reader domains provide a mechanism for sensing states of coordinated nuclear processes marked by histone proteins' post-translational modifications (PTMs). Among a growing number of discovered histone readers, the 14-3-3s, ankyrin repeat domains ( ...

Abstract	Histone reader domains provide a mechanism for sensing states of coordinated nuclear processes marked by histone proteins' post-translational modifications (PTMs). Among a growing number of discovered histone readers, the 14-3-3s, ankyrin repeat domains (ARDs), tetratricopeptide repeats (TPRs), bromodomains (BRDs), and HEAT domains are a group of domains using various mechanisms to recognize unmodified or modified histones, yet they all are composed of an α-helical fold. In this review, we compare how these readers fold to create protein domains that are very diverse in their tertiary structures, giving rise to intriguing peptide binding mechanisms resulting in vastly different footprints of their targets.
MeSH term(s)	Chromatin ; Histones/metabolism ; Protein Processing, Post-Translational ; Protein Domains
Chemical Substances	Chromatin ; Histones
Language	English
Publishing date	2023-11-02
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2023.10.008
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Article: Proximity Interactome Map of the Vac14–Fig4 Complex Using BioID

Qiu, Shirley / Lavallée-Adam, Mathieu / Côté, Marceline

Journal of proteome research. 2021 Sept. 23, v. 20, no. 11

2021

Abstract	Conversion between phosphatidylinositol-3-phosphate and phosphatidylinositol-3,5-bisphosphate on endosomal membranes is critical for the maturation of early endosomes to late endosomes/lysosomes and is regulated by the PIKfyve–Vac14–Fig4 complex. Despite the importance of this complex for endosomal homeostasis and vesicular trafficking, there is little known about how its activity is regulated or how it interacts with other cellular proteins. Here, we screened for the cellular interactome of Vac14 and Fig4 using proximity-dependent biotin labeling (BioID). After independently screening the interactomes of Vac14 and Fig4, we identified 89 high-confidence protein hits shared by both proteins. Network analysis of these hits revealed pathways with known involvement of the PIKfyve–Vac14–Fig4 complex, including vesicular organization and PI3K/Akt signaling, as well as novel pathways including cell cycle and mitochondrial regulation. We also identified subunits of coatomer complex I (COPI), a Golgi-associated complex with an emerging role in endosomal dynamics. Using proximity ligation assays, we validated the interaction between Vac14 and COPI subunit COPB1 and between Vac14 and Arf1, a GTPase required for COPI assembly. In summary, this study used BioID to comprehensively map the Vac14–Fig4 interactome, revealing potential roles for these proteins in diverse cellular processes and pathways, including preliminary evidence of an interaction between Vac14 and COPI. Data are available via ProteomeXchange with the identifier PXD027917.
Keywords	biotin ; cell cycle ; endosomes ; guanosinetriphosphatase ; homeostasis ; lysosomes ; mitochondria ; proteome ; research
Language	English
Dates of publication	2021-0923
Size	p. 4959-4973.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00408
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Ddp1 Cooperates with Ppx1 to Counter a Stress Response Initiated by Nonvacuolar Polyphosphate.

McCarthy, Liam / Abramchuk, Iryna / Wafy, Gamal / Denoncourt, Alix / Lavallée-Adam, Mathieu / Downey, Michael

mBio

2022 Volume 13, Issue 4, Page(s) e0039022

Abstract: In diverse cells from bacterial to mammalian species, inorganic phosphate is stored in long chains called polyphosphate (polyP). These nearly universal polymers, ranging from three to thousands of phosphate moieties in length, are associated with ... ...

Abstract	In diverse cells from bacterial to mammalian species, inorganic phosphate is stored in long chains called polyphosphate (polyP). These nearly universal polymers, ranging from three to thousands of phosphate moieties in length, are associated with molecular functions, including energy homeostasis, protein folding, and cell signaling. In many cell types, polyphosphate is concentrated in subcellular compartments or organelles. In the budding yeast Saccharomyces cerevisiae, polyP synthesis by the membrane-bound
MeSH term(s)	Animals ; Biological Phenomena ; DNA-Binding Proteins/metabolism ; Humans ; Mammals/metabolism ; Polyphosphates/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factors/metabolism
Chemical Substances	DNA-Binding Proteins ; MSN2 protein, S cerevisiae ; MSN4 protein, S cerevisiae ; Polyphosphates ; Saccharomyces cerevisiae Proteins ; Transcription Factors
Language	English
Publishing date	2022-07-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00390-22
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Article ; Online: METAbolomics data Balancing with Over-sampling Algorithms (META-BOA): an online resource for addressing class imbalance.

Hashimoto-Roth, Emily / Surendra, Anuradha / Lavallée-Adam, Mathieu / Bennett, Steffany A L / Čuperlović-Culf, Miroslava

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 23, Page(s) 5326–5327

Abstract: Motivation: Class imbalance, or unequal sample sizes between classes, is an increasing concern in machine learning for metabolomic and lipidomic data mining, which can result in overfitting for the over-represented class. Numerous methods have been ... ...

Abstract	Motivation: Class imbalance, or unequal sample sizes between classes, is an increasing concern in machine learning for metabolomic and lipidomic data mining, which can result in overfitting for the over-represented class. Numerous methods have been developed for handling class imbalance, but they are not readily accessible to users with limited computational experience. Moreover, there is no resource that enables users to easily evaluate the effect of different over-sampling algorithms. Results: METAbolomics data Balancing with Over-sampling Algorithms (META-BOA) is a web-based application that enables users to select between four different methods for class balancing, followed by data visualization and classification of the sample to observe the augmentation effects. META-BOA outputs a newly balanced dataset, generating additional samples in the minority class, according to the user's choice of Synthetic Minority Over-sampling Technique (SMOTE), Borderline-SMOTE (BSMOTE), Adaptive Synthetic (ADASYN) or Random Over-Sampling Examples (ROSE). To present the effect of over-sampling on the data META-BOA further displays both principal component analysis and t-distributed stochastic neighbor embedding visualization of data pre- and post-over-sampling. Random forest classification is utilized to compare sample classification in both the original and balanced datasets, enabling users to select the most appropriate method for their further analyses. Availability and implementation: META-BOA is available at https://complimet.ca/meta-boa. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Algorithms ; Machine Learning ; Data Mining ; Metabolomics
Language	English
Publishing date	2022-10-11
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac649
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Article: Proteomics analysis reveals a role for

Baijal, Kanchi / Abramchuk, Iryna / Herrera, Carmen M / Stephen Trent, M / Lavallée-Adam, Mathieu / Downey, Michael

bioRxiv : the preprint server for biology

2023

Abstract: Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1000 residues in length. ... ...

Abstract	Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1000 residues in length. In
Language	English
Publishing date	2023-07-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.06.546892
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Article: MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening.

Simopoulos, Caitlin M A / Ning, Zhibin / Li, Leyuan / Khamis, Mona M / Zhang, Xu / Lavallée-Adam, Mathieu / Figeys, Daniel

mSystems

2022 Volume 7, Issue 4, Page(s) e0038122

Abstract: Metaproteomics is used to explore the functional dynamics of microbial communities. However, acquiring metaproteomic data by tandem mass spectrometry (MS/MS) is time-consuming and resource-intensive, and there is a demand for computational methods that ... ...

Abstract	Metaproteomics is used to explore the functional dynamics of microbial communities. However, acquiring metaproteomic data by tandem mass spectrometry (MS/MS) is time-consuming and resource-intensive, and there is a demand for computational methods that can be used to reduce these resource requirements. We present MetaProClust-MS1, a computational framework for microbiome feature screening developed to prioritize samples for follow-up MS/MS. In this proof-of-concept study, we tested and compared MetaProClust-MS1 results on gut microbiome data, from fecal samples, acquired using short 15-min MS1-only chromatographic gradients and MS1 spectra from longer 60-min gradients to MS/MS-acquired data. We found that MetaProClust-MS1 identified robust gut microbiome responses caused by xenobiotics with significantly correlated cluster topologies of comparable data sets. We also used MetaProClust-MS1 to reanalyze data from both a clinical MS/MS diagnostic study of pediatric patients with inflammatory bowel disease and an experiment evaluating the therapeutic effects of a small molecule on the brain tissue of Alzheimer's disease mouse models. MetaProClust-MS1 clusters could distinguish between inflammatory bowel disease diagnoses (ulcerative colitis and Crohn's disease) using samples from mucosal luminal interface samples and identified hippocampal proteome shifts of Alzheimer's disease mouse models after small-molecule treatment. Therefore, we demonstrate that MetaProClust-MS1 can screen both microbiomes and single-species proteomes using only MS1 profiles, and our results suggest that this approach may be generalizable to any proteomics experiment. MetaProClust-MS1 may be especially useful for large-scale metaproteomic screening for the prioritization of samples for further metaproteomic characterization, using MS/MS, for instance, in addition to being a promising novel approach for clinical diagnostic screening.
Language	English
Publishing date	2022-08-11
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/msystems.00381-22
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