Proteins and Metabolites fingerprints of Gestational Diabetes Mellitus forming Protein‐Metabolite Interactomes are its potential biomarkers

Proteomics (Wiley)

Wiley: PROTEOMICS: Table of Contents

Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues.

Proteins and Metabolites fingerprints of Gestational Diabetes Mellitus forming Protein‐Metabolite Interactomes are its potential biomarkers

Abstract

Gestational diabetes mellitus (GDM) is a consequence of glucose intolerance with an inadequate production of insulin that happens during pregnancy and leads to adverse health consequences for both mother and fetus. GDM patients are at higher risk for preeclampsia, and developing diabetes mellitus type 2 in later life, while the child born to GDM mothers are more prone to macrosomia, and hypoglycemia. The universally accepted diagnostic criteria for GDM are lacking, therefore there is a need for a diagnosis of GDM that can identify GDM at its early stage (first trimester). We have reviewed the literature on proteins and metabolites fingerprints of GDM. Further, we have performed protein-protein, metabolite-metabolite, and protein-metabolite interaction network studies on GDM proteins and metabolites fingerprints. Notably, some proteins and metabolites fingerprints are forming strong interaction networks at high confidence scores. Therefore, we have suggested that those proteins and metabolites that are forming protein-metabolite interactomes are the potential biomarkers of GDM. The protein-metabolite biomarkers interactome may help in a deep understanding of the prognosis, pathogenesis of GDM and also detection of GDM. The protein-metabolites interactome may be further applied in planning future therapeutic strategies to promote long-term health benefits in GDM mothers and their children.

This article is protected by copyright. All rights reserved

Bhaswati Chatterjee,
Suman S. Thakur
March 16, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200257?af=R

Quantitative proteomics I.: Concept, design, and planning of quantitative proteomics experiments

Journal of Mass Spectrometry

Wiley: Journal of Mass Spectrometry: Table of Contents

Table of Contents for Journal of Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Quantitative proteomics I.: Concept, design, and planning of quantitative proteomics experiments

Journal of Mass Spectrometry, Volume 58, Issue 4, April 2023.

Simon SugĂĄr,
Laszlo Drahos,
Karoly Vekey
March 16, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jms.4907?af=R

[ASAP] Definitive Screening Designs to Optimize Library-Free DIA-MS Identification and Quantification of Neuropeptides

Journal of Proteome Research

Journal of Proteome Research: Latest Articles (ACS Publications)

latest articles published in Journal of Proteome Research

[ASAP] Definitive Screening Designs to Optimize Library-Free DIA-MS Identification and Quantification of Neuropeptides

TOC Graphic

Journal of Proteome Research
DOI: 10.1021/acs.jproteome.3c00088

Ashley Phetsanthad, Austin V. Carr, Lauren Fields, and Lingjun Li
March 16, 2023
http://dx.doi.org/10.1021/acs.jproteome.3c00088

[ASAP] Serum Bile Acid Metabolites Predict the Therapeutic Effect of Mesalazine in Patients with Ulcerative Colitis

Journal of Proteome Research

Journal of Proteome Research: Latest Articles (ACS Publications)

latest articles published in Journal of Proteome Research

[ASAP] Serum Bile Acid Metabolites Predict the Therapeutic Effect of Mesalazine in Patients with Ulcerative Colitis

TOC Graphic

Journal of Proteome Research
DOI: 10.1021/acs.jproteome.2c00820

Qiaoli Sun, Yingjue Tang, Liang Dai, Zhipeng Tang, Wenjun Zhou, Tao Wu, and Guang Ji
March 15, 2023
http://dx.doi.org/10.1021/acs.jproteome.2c00820

Proteomic and phosphoproteomic analyses of Jurkat T-cell treated with 2′3′ cGAMP reveals various signaling axes impacted by cyclic dinucleotides

Journal of Proteomics

ScienceDirect Publication: Journal of Proteomics

ScienceDirect RSS

Proteomic and phosphoproteomic analyses of Jurkat T-cell treated with 2′3′ cGAMP reveals various signaling axes impacted by cyclic dinucleotides

Publication date: 15 May 2023

Source: Journal of Proteomics, Volume 279

Author(s): Kenneth I. Onyedibe, Rodrigo Mohallem, Modi Wang, Uma K. Aryal, Herman O. Sintim

March 15, 2023
https://www.sciencedirect.com/science/article/pii/S1874391923000581?dgcid=rss_sd_all

[ASAP] Investigation of 2‑Hydroxypropyl-β-Cyclodextrin Treatment in a Neuronal-Like Cell Model of Niemann–Pick Type C Using Quantitative Proteomics

Journal of The American Society for Mass Spectrometry

Journal of the American Society for Mass Spectrometry: Latest Articles (ACS Publications)

latest articles published in Journal of the American Society for Mass Spectrometry

[ASAP] Investigation of 2‑Hydroxypropyl-β-Cyclodextrin Treatment in a Neuronal-Like Cell Model of Niemann–Pick Type C Using Quantitative Proteomics

TOC Graphic

Journal of the American Society for Mass Spectrometry
DOI: 10.1021/jasms.2c00342

Antony Cougnoux, Melissa R. Pergande, Fidel Serna-Perez, and Stephanie M. Cologna
March 15, 2023
http://dx.doi.org/10.1021/jasms.2c00342

Metabolomic interplay between gut microbiome and plasma metabolome in cardiac surgery‐associated acute kidney injury

Rapid Communications in Mass Spectrometry

Wiley: Rapid Communications in Mass Spectrometry: Table of Contents

Table of Contents for Rapid Communications in Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Metabolomic interplay between gut microbiome and plasma metabolome in cardiac surgery‐associated acute kidney injury

Rational

Cardiac surgery-associated acute kidney injury (CSA-AKI) is a prevalent complication of cardiac surgery, which may be associated with a great risk of developing chronic kidney disease and mortality. This study aimed to investigate the possible links between gut microbiota metabolism and CSA-AKI.

Methods

A prospective cohort of patients who underwent cardiac surgery was continuously recruited, who were further divided into CSA-AKI group and Non-AKI group based on the clinical outcomes. Their faecal and plasma samples were collected before the surgery and were separately analysed by non-targeted and targeted metabolomics. The differential metabolites related to CSA-AKI were screened out using statistical methods, and altered metabolic pathways were determined by examining the Kyoto Encyclopedia of Genes and Genomes database.

Results

Nearly 1000 faecal metabolites were detected through high-resolution mass spectrometry (MS) and bioinformatics at high and mid confidence levels, and 49 differential metabolites at high confidence level may perform essential biological functions and provide potential diagnostic indicators. Compared with the Non-AKI group, the patients in the CSA-AKI group displayed dramatic changes in gut microbiota metabolism, including amino acid metabolism, nicotinate and nicotinamide metabolism, purine metabolism, and ABC transporters. Meanwhile, 188 plasma metabolites were identified and quantified by tandem MS, and 34 differential plasma metabolites were screened out between the two groups using univariate statistical analysis. These differential plasma metabolites were primarily enriched in the following metabolic pathways: sulphur metabolism, amino acid biosynthesis, tryptophan metabolism, and ABC transporters. Furthermore, the content of indole metabolites in the faecal and plasma samples of the CSA-AKI group was higher than that of the Non-AKI group.

Conclusions

Patients with CSA-AKI may have dysbiosis of their intestinal microbiota and metabolic abnormalities in their gut system before cardiac surgery. Thus, some metabolites and related metabolic pathways may be potential biomarkers and new therapeutic targets for the disease.

Yunpeng Bai,
Wendong Huang,
Xinyi Jiang,
Wang Xu,
Ying Li,
Yirong Wang,
Sumei Huang,
Kunyong Wu,
Linhui Hu,
Chunbo Chen
March 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9504?af=R

Quantitative proteomics identifies and validates urinary biomarkers of rhabdomyosarcoma in children

Clinical Proteomics

Most Recent Articles: Clinical Proteomics

Most Recent Articles: Clinical Proteomics

Quantitative proteomics identifies and validates urinary biomarkers of rhabdomyosarcoma in children

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma with poor prognosis in children. The 5-year survival rate for early RMS has improved, whereas it remains unsatisfactory for advanced patients. Urin…

Na Xu, Yuncui Yu, Chao Duan, Jing Wei, Wei Sun, Chiyi Jiang, Binglin Jian, Wang Cao, Lulu Jia and Xiaoli Ma
March 15, 2023
https://clinicalproteomicsjournal.biomedcentral.com/articles/10.1186/s12014-023-09401-4

Front Cover

Proteomics (Wiley)

Wiley: PROTEOMICS: Table of Contents

Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues.

Front Cover

Front Cover

Cover Image Š Wiley-VCH GmbH. The image is part of a figure in the article DOI: 10.1002/pmic.201900203 by Lei Li, Yong Jiang et al.

March 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202370041?af=R

Molecular methods to study protein trafficking between organs

Proteomics (Wiley)

Wiley: PROTEOMICS: Table of Contents

Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues.

Molecular methods to study protein trafficking between organs

Abstract

Interorgan communication networks are key regulators of organismal homeostasis, and their dysregulation is associated with a variety of pathologies. While mass spectrometry proteomics identifies circulating proteins and can correlate their abundance with disease phenotypes, the tissues of origin and destinations of these secreted proteins remain largely unknown. In vitro approaches to study protein secretion are valuable, however, they may not mimic the complexity of in vivo environments. More recently, the development of engineered promiscuous BirA* biotin ligase derivatives has enabled tissue-specific tagging of cellular secreted proteomes in vivo. The use of biotin as a molecular tag provides information on the tissue of origin and destination, and enables the enrichment of low-abundance hormone proteins. Therefore, promiscuous protein biotinylation is a valuable tool to study protein secretion in vivo.

Felix K. Kreissl,
Michael A. Banki,
Ilia A. Droujinine
March 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202100331?af=R

Impact of wavelength and spot size on laser depth of focus: Considerations for mass spectrometry imaging of non‐flat samples

Journal of Mass Spectrometry

Wiley: Journal of Mass Spectrometry: Table of Contents

Table of Contents for Journal of Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Impact of wavelength and spot size on laser depth of focus: Considerations for mass spectrometry imaging of non‐flat samples

Abstract

Biospecimens with nearly flat surfaces on a flat stage are typically required for laser-based mass spectrometry imaging (MSI) techniques. However, sampling stages are rarely perfectly level, and accounting for this and the need to accommodate non-flat samples requires a deeper understanding of the laser beam depth of focus. In ablation-based MSI methods, a laser is focused on top of the sample surface, ensuring that the sample is at the focal point or remains within depth of focus. In general, the depth of focus of a given laser is related to the beam quality (M
2) and the wavelength (Îť). However, because laser is applied on a biological sample, other variables can also impact the depth of focus, which could affect the robustness of the MSI techniques for diverse sample types. When the height of a sample ranges outside of the depth of focus, ablated area and the corresponding ion abundances may vary as well, increasing the variability of results. In this tutorial, we examine the parameters and equations that describe the depth of focus of a Gaussian laser beam. Additionally, we describe several approaches that account for surface roughness exceeding the depth of focus of the laser.

Alena N. Joignant,
Ying Xi,
David C. Muddiman
March 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jms.4914?af=R

Localization of cyclopropyl groups and alkenes within glycerophospholipids using gas‐phase ion/ion chemistry

Journal of Mass Spectrometry

Wiley: Journal of Mass Spectrometry: Table of Contents

Table of Contents for Journal of Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Localization of cyclopropyl groups and alkenes within glycerophospholipids using gas‐phase ion/ion chemistry

Abstract

Shotgun lipid analysis using electrospray ionization tandem mass spectrometry (ESI-MS/MS) is a common approach for the identification and characterization of glycerophohspholipids GPs. ESI-MS/MS, with the aid of collision-induced dissociation (CID), enables the characterization of GP species at the headgroup and fatty acyl sum compositional levels. However, important structural features that are often present, such as carbon–carbon double bond(s) and cyclopropane ring(s), can be difficult to determine. Here, we report the use of gas-phase charge inversion reactions that, in combination with CID, allow for more detailed structural elucidation of GPs. CID of a singly deprotonated GP, [GP − H]−, generates FA anions, [FA − H]−. The fatty acid anions can then react with doubly charged cationic magnesium tris-phenanthroline complex, [Mg(Phen)3]2+, to form charge inverted complex cations of the form [FA − H + MgPhen2]+. CID of the complex generates product ion spectral patterns that allow for the identification of carbon–carbon double bond position(s) as well as the sites of cyclopropyl position(s) in unsaturated lipids. This approach to determining both double bond and cyclopropane positions is demonstrated with GPs for the first time using standards and is applied to lipids extracted from Escherichia coli.

De’Shovon M. Shenault,
Scott A. McLuckey,
Elissia T. Franklin
March 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jms.4913?af=R

Mass spectrometry molecular fingerprinting of mineral and synthetic lubricant oils

Journal of Mass Spectrometry

Wiley: Journal of Mass Spectrometry: Table of Contents

Table of Contents for Journal of Mass Spectrometry. List of articles from both the latest and EarlyView issues.

Mass spectrometry molecular fingerprinting of mineral and synthetic lubricant oils

Abstract

The molecular composition of lubricating oils has a strong impact on how automotive engines function, but the techniques used to monitor the quality parameters of these oils only inspect their gross physical–chemical properties such as viscosity, color, and bulk spectroscopy profiles; hence, bad-quality, adulterated, or counterfeit oils are hard to detect. Herein, we investigated the ability of direct infusion electrospray ionization mass spectrometry (ESI-MS) to provide simple, rapid but characteristic fingerprint profiles for such oils of the mineral and synthetic types. After a simple aqueous extraction, ESI-MS analyses, particularly in the positive ion mode, did indeed show characteristic molecular markers with unique profiles, which were confirmed and more clearly visualized by partial least squares-discriminant analysis (PLS-DA). Nuclear magnetic resonance and Fourier transform infrared-attenuated total reflection spectroscopy were also tested for the bulk samples but showed nearly identical spectra, thus failing to reveal their distinct molecular composition and to differentiate the oil samples. To simulate adulteration, mixtures of mineral and synthetic oils were also analyzed by ESI(+)-MS, and additions as low as 1% of mineral oil to synthetic oil could be detected. The technique therefore offers a simple and fast but powerful tool to monitor the molecular composition of lubricant oils, particularly vias their more polar constituents.

Caroline P. Carvalho,
Adriano J. R. Silva,
Rosineide C. Lima,
Marcos N. Eberlin
March 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jms.4906?af=R

Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG

In individuals with Down syndrome (DS), cardiovascular and pulmonary diseases are the most common health problem and result in increased mortality and morbidity. Although these clinical comorbidities are well described, no preclinical models for DS are fully characterized for cardiopulmonary alterations, preventing research to understanding the development and pharmacological modulation of lungs, heart and immune system. Our objective is to characterize the cardiopulmonary and immunological phenotype in Ts65Dn mice and investigate the modulatory effects green tea extract enriched in epigallocatechin 3 gallate (GTE-EGCG). GTE-EGCG administration started at embryonic day 9 and was discontinued at postnatal day (PD) 180. Newborns were longitudinally monitored until PD210 using micro-computed tomography. At endpoint, we characterized the structural, functional and immunological alterations and persistent effects of GTE-EGCG administration. This study revealed normal lung development in the Ts65Dn mice and highlighted RV hypertrophy and immunological alterations. GTE-EGCG administration resulted in genotype-specific and genotype-independent alterations resulting in lung immaturation and airway hyperreactivity. Our results highlight the cardiovascular and immunological phenotype of Ts65Dn mice and potential use for safety studies of therapeutic agents in a DS-specific context.
Tielemans, B., Llambrich, S., Seldeslachts, L., Cremer, J., Tsui, H.-C., Jonckheere, A.-C., Marain, F., Riedel, M., Wouters, J., Herzen, J., Leszczynski, B., Verbeken, E., Vanoirbeek, J., Vande Velde, G.
March 15, 2023
http://biorxiv.org/cgi/content/short/2023.03.13.532396v1?rss=1

In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models

In vitro models of Mycobacterium tuberculosis (Mtb) infection are a valuable tool to examine host-pathogen interactions and screen drugs. With the development of more complex in vitro models, there is a need for tools to help analyze and integrate data from these models. We introduce an agent-based model (ABM) representation of the interactions between immune cells and bacteria in an in vitro setting. This in silico model was used to independently simulate both traditional and spheroid cell culture models by changing the movement rules and initial spatial layout of the cells. These two setups were calibrated to published experimental data in a paired manner, by using the same parameters in both simulations. Within the calibrated set, heterogeneous outputs are seen for outputs of interest including bacterial count and T cell infiltration into the macrophage core of the spheroid. The simulations are also able to predict many outputs with high time resolution, including spatial structure. The structure of a single spheroid can be followed across the time course of the simulation, allowing the relationship between cell localization and immune activation to be explored. Uncertainty analyses are performed for both model setups using latin hypercube sampling and partial rank correlation coefficients to allow for easier comparison, which can provide insight into ideal use cases for the independent setups. Future model iterations can be guided by the limitations of the current model, specifically which parts of the output space were harder to reach. This ABM can be used to represent more in vitro Mtb infection models due to its flexible structure, providing a powerful analysis tool that can be used in tandem with experiments.
Petrucciani, A., Hoerter, A., Kotze, L., Du Plessis, N., Pienaar, E.
March 15, 2023
http://biorxiv.org/cgi/content/short/2023.03.13.532338v1?rss=1

TimeTeller: a tool to probe the circadian clock as a multigene dynamical system

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

TimeTeller: a tool to probe the circadian clock as a multigene dynamical system

Recent studies have established that the circadian clock influences onset, progression and therapeutic outcomes in a number of diseases including cancer and heart diseases. Therefore, there is a need for tools to measure the functional state of the molecular circadian clock and its downstream targets in patients. Moreover, the clock is a multi-dimensional stochastic oscillator and there are few tools for analysing it as a system. In this paper we consider the methodology behind TimeTeller, a machine learning tool that analyses the clock as a system and aims to estimate circadian clock function from a single transcriptome by modelling the multi-dimensional state of the clock. We demonstrate its potential for clock systems assessment by applying it to mouse, baboon and human microarray and RNA-seq data and show how to visualise and quantify the global structure of the clock, quantitatively stratify individual transcriptomic samples by clock dysfunction and globally compare clocks across individuals, conditions and tissues thus highlighting its potential relevance for advancing circadian medicine.
Vlachou, D., Veretennikova, M., Usselmann, L., Vasilyev, V., Ott, S., Bjarnason, G. A., Dallmann, R., Levi, F., Rand, D. A.
March 15, 2023
http://biorxiv.org/cgi/content/short/2023.03.14.532177v1?rss=1

Distilling identifiable and interpretable dynamic models from biological data

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Distilling identifiable and interpretable dynamic models from biological data

Mechanistic dynamical models allow us to study the behavior of complex biological systems. They can provide an objective and quantitative understanding that would be difficult to achieve through other means. However, the systematic development of these models is a non-trivial exercise and an open problem in computational biology. Currently, many research efforts are focused on model discovery, i.e. automating the development of interpretable models from data. One of the main frameworks is sparse regression, where the sparse identification of nonlinear dynamics (SINDy) algorithm and its variants have enjoyed great success. SINDy-PI is an extension which allows the discovery of rational nonlinear terms, thus enabling the identification of kinetic functions common in biochemical networks, such as Michaelis-Menten. SINDy-PI also pays special attention to the recovery of parsimonious models (Occam’s razor). Here we focus on biological models composed of sets of deterministic nonlinear ordinary differential equations. We present a methodology that, combined with SINDy-PI, allows the automatic discovery of structurally identifiable and observable models which are also mechanistically interpretable. The lack of structural identifiability and observability makes it impossible to uniquely infer parameter and state variables, which can compromise the usefulness of a model by distorting its mechanistic significance and hampering its ability to produce biological insights. We illustrate the performance of our method with six case studies. We find that, despite enforcing sparsity, SINDy-PI sometimes yields models that are unidentifiable. In these cases we show how our method transforms their equations in order to obtain a structurally identifiable and observable model which is also interpretable.
Banga, J. R., Massonis, G., Villaverde, A. F.
March 15, 2023
http://biorxiv.org/cgi/content/short/2023.03.13.532340v1?rss=1