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Article: H2B Type 1-K Accumulates in Senescent Fibroblasts with Persistent DNA Damage along with Methylated and Phosphorylated Forms of HMGA1.

Contrepois, Kévin / Mann, Carl / Fenaille, François

2021 Volume 9, Issue 2

Abstract: Cellular senescence is a state of terminal proliferative arrest that plays key roles in aging by preventing stem cell renewal and by inducing the expression of a series of inflammatory factors including many secreted proteins with paracrine effects. The ... ...

Abstract	Cellular senescence is a state of terminal proliferative arrest that plays key roles in aging by preventing stem cell renewal and by inducing the expression of a series of inflammatory factors including many secreted proteins with paracrine effects. The in vivo identification of senescent cells is difficult due to the absence of universal biomarkers. Chromatin modifications are key aspects of the senescence transition and may provide novel biomarkers. We used a combined protein profiling and bottom-up mass spectrometry approach to characterize the isoforms and post-translational modifications of chromatin proteins over time in post-mitotic human fibroblasts in vitro. We show that the H2B type 1-K variant is specifically enriched in deep senescent cells with persistent DNA damage. This accumulation was not observed in quiescent cells or in cells induced into senescence without DNA damage by expression of the RAF kinase. Similarly, HMGA1a di-methylated and HMGA1b tri-phosphorylated forms accumulated exclusively in the chromatin of cells in deep senescent conditions with persistent DNA damage. H2B type 1-K and modified HMGA1 may thus represent novel biomarkers of senescent cells containing persistent DNA damage.
Language	English
Publishing date	2021-06-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720995-7
ISSN	2227-7382
ISSN	2227-7382
DOI	10.3390/proteomes9020030
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices With Zeno SWATH Data-Independent Acquisition.

Sun, Weiwen / Lin, Yuan / Huang, Yue / Chan, Josolyn / Terrillon, Sonia / Rosenbaum, Anton I / Contrepois, Kévin

Molecular & cellular proteomics : MCP

2023 Volume 22, Issue 6, Page(s) 100562

Abstract: Modern mass spectrometers routinely allow deep proteome coverage in a single experiment. These methods are typically operated at nanoflow and microflow regimes, but they often lack throughput and chromatographic robustness, which is critical for large- ... ...

Abstract	Modern mass spectrometers routinely allow deep proteome coverage in a single experiment. These methods are typically operated at nanoflow and microflow regimes, but they often lack throughput and chromatographic robustness, which is critical for large-scale studies. In this context, we have developed, optimized, and benchmarked LC-MS methods combining the robustness and throughput of analytical flow chromatography with the added sensitivity provided by the Zeno trap across a wide range of cynomolgus monkey and human matrices of interest for toxicological studies and clinical biomarker discovery. Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectra (SWATH) data-independent acquisition (DIA) experiments with Zeno trap activated (Zeno SWATH DIA) provided a clear advantage over conventional SWATH DIA in all sample types tested with improved sensitivity, quantitative robustness, and signal linearity as well as increased protein coverage by up to 9-fold. Using a 10-min gradient chromatography, up to 3300 proteins were identified in tissues at 2 μg peptide load. Importantly, the performance gains with Zeno SWATH translated into better biological pathway representation and improved the ability to identify dysregulated proteins and pathways associated with two metabolic diseases in human plasma. Finally, we demonstrate that this method is highly stable over time with the acquisition of reliable data over the injection of 1000+ samples (14.2 days of uninterrupted acquisition) without the need for human intervention or normalization. Altogether, Zeno SWATH DIA methodology allows fast, sensitive, and robust proteomic workflows using analytical flow and is amenable to large-scale studies.
MeSH term(s)	Animals ; Humans ; Tandem Mass Spectrometry/methods ; Macaca fascicularis ; Proteomics/methods ; Software ; Chromatography, Liquid/methods ; Proteome
Chemical Substances	Proteome
Language	English
Publishing date	2023-05-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2023.100562
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Article: Correction: Chaby et al. Cross-Platform Evaluation of Commercially Targeted and Untargeted Metabolomics Approaches to Optimize the Investigation of Psychiatric Disease.

Chaby, Lauren E / Lasseter, Heather C / Contrepois, Kévin / Salek, Reza M / Turck, Christoph W / Thompson, Andrew / Vaughan, Timothy / Haas, Magali / Jeromin, Andreas

Metabolites

2023 Volume 13, Issue 8

Abstract: In the original publication [ ... ]. ...

Abstract	In the original publication [...].
Language	English
Publishing date	2023-08-09
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo13080933
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Article ; Online: Challenging obesity and sex based differences in resting energy expenditure using allometric modeling, a sub-study of the DIETFITS clinical trial

Haddad, Francois / Li, Xiao / Perelman, Dalia / Santana, Everton Jose / Kuznetsova, Tatiana / Cauwenberghs, Nicholas / Busque, Vincent / Contrepois, Kevin / Snyder, Michael P. / Leonard, Mary B. / Gardner, Christopher

Clinical Nutrition ESPEN. 2023 Feb., v. 53 p.43-52

2023

Abstract: Resting energy expenditure (REE) is a major component of energy balance. While REE is usually indexed to total body weight (BW), this may introduce biases when assessing REE in obesity or during weight loss intervention. The main objective of the study ... ...

Abstract	Resting energy expenditure (REE) is a major component of energy balance. While REE is usually indexed to total body weight (BW), this may introduce biases when assessing REE in obesity or during weight loss intervention. The main objective of the study was to quantify the bias introduced by ratiometric scaling of REE using BW both at baseline and following weight loss intervention. Participants in the DIETFITS Study (Diet Intervention Examining The Factors Interacting with Treatment Success) who completed indirect calorimetry and dual-energy X-ray absorptiometry (DXA) were included in the study. Data were available in 438 participants at baseline, 340 at 6 months and 323 at 12 months. We used multiplicative allometric modeling based on lean body mass (LBM) and fat mass (FM) to derive body size independent scaling of REE. Longitudinal changes in indexed REE were then assessed following weight loss intervention. A multiplicative model including LBM, FM, age, Black race and the double product (DP) of systolic blood pressure and heart rate explained 79% of variance in REE. REE indexed to [LBM⁰.⁶⁶ × FM⁰.⁰⁶⁶] was body size and sex independent (p = 0.91 and p = 0.73, respectively) in contrast to BW based indexing which showed a significant inverse relationship to BW (r = −0.47 for female and r = −0.44 for male, both p < 0.001). When indexed to BW, significant baseline differences in REE were observed between male and female (p < 0.001) and between individuals who are overweight and obese (p < 0.001) while no significant differences were observed when indexed to REE/[LBM⁰.⁶⁶ × FM⁰.⁰⁶⁶], p > 0.05). Percentage predicted REE adjusted for LBM, FM and DP remained stable following weight loss intervention (p = 0.614). Allometric scaling of REE based on LBM and FM removes body composition-associated biases and should be considered in obesity and weight-based intervention studies.
Keywords	allometry ; body size ; calorimetry ; clinical nutrition ; clinical trials ; dual-energy X-ray absorptiometry ; energy expenditure ; females ; heart rate ; lean body mass ; males ; models ; nutritional intervention ; obesity ; systolic blood pressure ; variance ; weight loss ; Resting energy expenditure ; Scaling ; Body composition ; Diet intervention ; ALM ; BF ; BMI ; BW ; DP ; DXA ; FM ; LBM ; REE
Language	English
Dates of publication	2023-02
Size	p. 43-52.
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ISSN	2405-4577
DOI	10.1016/j.clnesp.2022.11.015
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Robust identification of temporal biomarkers in longitudinal omics studies.

Metwally, Ahmed A / Zhang, Tom / Wu, Si / Kellogg, Ryan / Zhou, Wenyu / Contrepois, Kevin / Tang, Hua / Snyder, Michael

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 15, Page(s) 3802–3811

Abstract: Motivation: Longitudinal studies increasingly collect rich 'omics' data sampled frequently over time and across large cohorts to capture dynamic health fluctuations and disease transitions. However, the generation of longitudinal omics data has preceded ...

Abstract	Motivation: Longitudinal studies increasingly collect rich 'omics' data sampled frequently over time and across large cohorts to capture dynamic health fluctuations and disease transitions. However, the generation of longitudinal omics data has preceded the development of analysis tools that can efficiently extract insights from such data. In particular, there is a need for statistical frameworks that can identify not only which omics features are differentially regulated between groups but also over what time intervals. Additionally, longitudinal omics data may have inconsistencies, including non-uniform sampling intervals, missing data points, subject dropout and differing numbers of samples per subject. Results: In this work, we developed OmicsLonDA, a statistical method that provides robust identification of time intervals of temporal omics biomarkers. OmicsLonDA is based on a semi-parametric approach, in which we use smoothing splines to model longitudinal data and infer significant time intervals of omics features based on an empirical distribution constructed through a permutation procedure. We benchmarked OmicsLonDA on five simulated datasets with diverse temporal patterns, and the method showed specificity greater than 0.99 and sensitivity greater than 0.87. Applying OmicsLonDA to the iPOP cohort revealed temporal patterns of genes, proteins, metabolites and microbes that are differentially regulated in male versus female subjects following a respiratory infection. In addition, we applied OmicsLonDA to a longitudinal multi-omics dataset of pregnant women with and without preeclampsia, and OmicsLonDA identified potential lipid markers that are temporally significantly different between the two groups. Availability and implementation: We provide an open-source R package (https://bioconductor.org/packages/OmicsLonDA), to enable widespread use. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Pregnancy ; Humans ; Female ; Male ; Biomarkers ; Longitudinal Studies ; Proteins ; Research Design
Chemical Substances	Biomarkers ; Proteins
Language	English
Publishing date	2022-06-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac403
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Article ; Online: Untargeted metabolomic profiling in children identifies novel pathways in asthma and atopy.

Lejeune, Stéphanie / Kaushik, Abhinav / Parsons, Ella S / Chinthrajah, Sharon / Snyder, Michael / Desai, Manisha / Manohar, Monali / Prunicki, Mary / Contrepois, Kévin / Gosset, Philippe / Deschildre, Antoine / Nadeau, Kari

The Journal of allergy and clinical immunology

2023 Volume 153, Issue 2, Page(s) 418–434

Abstract: Background: Asthma and other atopic disorders can present with varying clinical phenotypes marked by differential metabolomic manifestations and enriched biological pathways.: Objective: We sought to identify these unique metabolomic profiles in ... ...

Abstract	Background: Asthma and other atopic disorders can present with varying clinical phenotypes marked by differential metabolomic manifestations and enriched biological pathways. Objective: We sought to identify these unique metabolomic profiles in atopy and asthma. Methods: We analyzed baseline nonfasted plasma samples from a large multisite pediatric population of 470 children aged <13 years from 3 different sites in the United States and France. Atopy positivity (At Results: Two hundred ten children were classified as At Conclusion: The At
MeSH term(s)	Child ; Humans ; Asthma/epidemiology ; Metabolomics/methods ; Hypersensitivity, Immediate ; Metabolome ; Immunoglobulin E
Chemical Substances	Immunoglobulin E (37341-29-0)
Language	English
Publishing date	2023-10-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	121011-7
ISSN	1097-6825 ; 1085-8725 ; 0091-6749
ISSN (online)	1097-6825 ; 1085-8725
ISSN	0091-6749
DOI	10.1016/j.jaci.2023.09.040
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Article ; Online: metID: an R package for automatable compound annotation for LC-MS-based data.

Shen, Xiaotao / Wu, Si / Liang, Liang / Chen, Songjie / Contrepois, Kévin / Zhu, Zheng-Jiang / Snyder, Michael

Bioinformatics (Oxford, England)

2021 Volume 38, Issue 2, Page(s) 568–569

Abstract: Summary: Accurate and efficient compound annotation is a long-standing challenge for LC-MS-based data (e.g. untargeted metabolomics and exposomics). Substantial efforts have been devoted to overcoming this obstacle, whereas current tools are limited by ... ...

Abstract	Summary: Accurate and efficient compound annotation is a long-standing challenge for LC-MS-based data (e.g. untargeted metabolomics and exposomics). Substantial efforts have been devoted to overcoming this obstacle, whereas current tools are limited by the sources of spectral information used (in-house and public databases) and are not automated and streamlined. Therefore, we developed metID, an R package that combines information from all major databases for comprehensive and streamlined compound annotation. metID is a flexible, simple and powerful tool that can be installed on all platforms, allowing the compound annotation process to be fully automatic and reproducible. A detailed tutorial and a case study are provided in Supplementary Materials. Availability and implementation: https://jaspershen.github.io/metID. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Chromatography, Liquid ; Tandem Mass Spectrometry ; Software ; Metabolomics ; Databases, Factual
Language	English
Publishing date	2021-08-16
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/btab583
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Article ; Online: Multi-omic profiling of primary mouse neutrophils predicts a pattern of sex and age-related functional regulation.

Lu, Ryan J / Taylor, Shalina / Contrepois, Kévin / Kim, Minhoo / Bravo, Juan I / Ellenberger, Mathew / Sampathkumar, Nirmal K / Benayoun, Bérénice A

Nature aging

2021 Volume 1, Issue 8, Page(s) 715–733

Abstract: Neutrophils are the most abundant human white blood cell and constitute a first line of defense in the innate immune response. Neutrophils are short-lived cells, and thus the impact of organismal aging on neutrophil biology, especially as a function of ... ...

Abstract	Neutrophils are the most abundant human white blood cell and constitute a first line of defense in the innate immune response. Neutrophils are short-lived cells, and thus the impact of organismal aging on neutrophil biology, especially as a function of biological sex, remains poorly understood. Here, we describe a multi-omic resource of mouse primary bone marrow neutrophils from young and old female and male mice, at the transcriptomic, metabolomic and lipidomic levels. We identify widespread regulation of neutrophil 'omics' landscapes with organismal aging and biological sex. In addition, we leverage our resource to predict functional differences, including changes in neutrophil responses to activation signals. To date, this dataset represents the largest multi-omics resource for neutrophils across sex and ages. This resource identifies neutrophil characteristics which could be targeted to improve immune responses as a function of sex and/or age.
MeSH term(s)	Humans ; Male ; Female ; Animals ; Mice ; Neutrophils ; Multiomics ; Immunity, Innate ; Aging/genetics ; Gene Expression Profiling
Language	English
Publishing date	2021-07-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2662-8465
ISSN (online)	2662-8465
DOI	10.1038/s43587-021-00086-8
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Article ; Online: In-depth triacylglycerol profiling using MS

Cabruja, Matias / Priotti, Josefina / Domizi, Pablo / Papsdorf, Katharina / Kroetz, Deanna L / Brunet, Anne / Contrepois, Kévin / Snyder, Michael P

Analytica chimica acta

2021 Volume 1184, Page(s) 339023

Abstract: Total triacylglycerol (TAG) level is a key clinical marker of metabolic and cardiovascular diseases. However, the roles of individual TAGs have not been thoroughly explored in part due to their extreme structural complexity. We present a targeted mass ... ...

Abstract	Total triacylglycerol (TAG) level is a key clinical marker of metabolic and cardiovascular diseases. However, the roles of individual TAGs have not been thoroughly explored in part due to their extreme structural complexity. We present a targeted mass spectrometry-based method combining multiple reaction monitoring (MRM) and multiple stage mass spectrometry (MS
MeSH term(s)	Chromatography, Reverse-Phase ; Humans ; Mass Spectrometry ; Plasma ; Reproducibility of Results ; Triglycerides
Chemical Substances	Triglycerides
Language	English
Publishing date	2021-09-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1483436-4
ISSN	1873-4324 ; 0003-2670
ISSN (online)	1873-4324
ISSN	0003-2670
DOI	10.1016/j.aca.2021.339023
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Article: Cross-Platform Evaluation of Commercially Targeted and Untargeted Metabolomics Approaches to Optimize the Investigation of Psychiatric Disease.

Chaby, Lauren E / Lasseter, Heather C / Contrepois, Kévin / Salek, Reza M / Turck, Christoph W / Thompson, Andrew / Vaughan, Timothy / Haas, Magali / Jeromin, Andreas

Metabolites

2021 Volume 11, Issue 9

Abstract: Metabolomics methods often encounter trade-offs between quantification accuracy and coverage, with truly comprehensive coverage only attainable through a multitude of complementary assays. Due to the lack of standardization and the variety of ... ...

Abstract	Metabolomics methods often encounter trade-offs between quantification accuracy and coverage, with truly comprehensive coverage only attainable through a multitude of complementary assays. Due to the lack of standardization and the variety of metabolomics assays, it is difficult to integrate datasets across studies or assays. To inform metabolomics platform selection, with a focus on posttraumatic stress disorder (PTSD), we review platform use and sample sizes in psychiatric metabolomics studies and then evaluate five prominent metabolomics platforms for coverage and performance, including intra-/inter-assay precision, accuracy, and linearity. We found performance was variable between metabolite classes, but comparable across targeted and untargeted approaches. Within all platforms, precision and accuracy were highly variable across classes, ranging from 0.9-63.2% (coefficient of variation) and 0.6-99.1% for accuracy to reference plasma. Several classes had high inter-assay variance, potentially impeding dissociation of a biological signal, including glycerophospholipids, organooxygen compounds, and fatty acids. Coverage was platform-specific and ranged from 16-70% of PTSD-associated metabolites. Non-overlapping coverage is challenging; however, benefits of applying multiple metabolomics technologies must be weighed against cost, biospecimen availability, platform-specific normative levels, and challenges in merging datasets. Our findings and open-access cross-platform dataset can inform platform selection and dataset integration based on platform-specific coverage breadth/overlap and metabolite-specific performance.
Language	English
Publishing date	2021-09-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo11090609
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