International Journal of Molecular Sciences

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14 pages, 3679 KiB

Open AccessArticle

Golgi Reassembly Stacking Protein 2 Modulates Myometrial Contractility during Labor by Affecting ATP Production

by Fan Yang, Lina Chen, Bolun Wen, Xiaodi Wang, Lele Wang, Kaiyuan Ji and Huishu Liu

Int. J. Mol. Sci. 2023, 24(12), 10116; https://doi.org/10.3390/ijms241210116 - 14 Jun 2023

Viewed by 1346

Abstract

The mechanism of maintaining myometrial contractions during labor remains unclear. Autophagy has been reported to be activated in laboring myometrium, along with the high expression of Golgi reassembly stacking protein 2 (GORASP2), a protein capable of regulating autophagy activation. This study aimed to [...] Read more.

The mechanism of maintaining myometrial contractions during labor remains unclear. Autophagy has been reported to be activated in laboring myometrium, along with the high expression of Golgi reassembly stacking protein 2 (GORASP2), a protein capable of regulating autophagy activation. This study aimed to investigate the role and mechanism of GORASP2 in uterine contractions during labor. Western blot confirmed the increased expression of GORASP2 in laboring myometrium. Furthermore, the knockdown of GORASP2 in primary human myometrial smooth muscle cells (hMSMCs) using siRNA resulted in reduced cell contractility. This phenomenon was independent of the contraction-associated protein and autophagy. Differential mRNAs were analyzed using RNA sequencing. Subsequently, KEGG pathway analysis identified that GORASP2 knockdown suppressed several energy metabolism pathways. Furthermore, reduced ATP levels and aerobic respiration impairment were observed in measuring the oxygen consumption rate (OCR). These findings suggest that GORASP2 is up-regulated in the myometrium during labor and modulates myometrial contractility mainly by maintaining ATP production. Full article

(This article belongs to the Special Issue Proteomics and Metabolomics Investigation of Cell Lines, Tissues and Biological Fluids)

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15 pages, 2786 KiB

Open AccessArticle

Proteomic and miRNA Profiles of Exosomes Derived from Myometrial Tissue in Laboring Women

by Wenfeng Deng, Xiaodi Wang, Lina Chen, Bolun Wen, Yunshan Chen, Kaiyuan Ji and Huishu Liu

Int. J. Mol. Sci. 2022, 23(20), 12343; https://doi.org/10.3390/ijms232012343 - 15 Oct 2022

Cited by 2 | Viewed by 2510

Abstract

Myometrial contraction is essential for successful delivery. Recent studies have highlighted the vital roles of tissue-derived exosomes in disease diagnostic, prognostic, and therapeutic applications; however, the characteristics of uterine myometrium-derived exosomes are unclear. Here, we successfully isolated exosomes from myometrial tissues, human myometrial [...] Read more.

Myometrial contraction is essential for successful delivery. Recent studies have highlighted the vital roles of tissue-derived exosomes in disease diagnostic, prognostic, and therapeutic applications; however, the characteristics of uterine myometrium-derived exosomes are unclear. Here, we successfully isolated exosomes from myometrial tissues, human myometrial smooth muscle cells (HMSMCs), and human umbilical vein endothelial cells (HUVECs), then performed quantitative liquid chromatography-tandem mass spectrometry and miRNA sequencing to investigate the cargo of the exosomes. Fifty-two proteins and five miRNAs were differentially expressed (DE) in term non-labor and term labor myometrium-derived exosomes. Among them, seven proteins (SERPINE1, THBS1, MGAT1, VIM, FGB, FGG, and VWF) were differentially expressed both in the myometrial exosomes and tissues, three miRNAs (miR-363-3p, miR-203a-3p, and miR-205-5p) target 13 DE genes. The top three miRNA derived from HMSMCs (miR-125b-1-3p, miR-337-5p, and miR-503-5p) and HUVECs (miR-663a, miR-4463, and miR-3622a-5p) were identified. Two proteins, GJA1 and SLC39A14, exist in female blood exosomes and are highly expressed in HMSMCs exosomes, are also upregulated in the laboring myometrium, which verified increased in laboring blood samples, might be novel potential biomarkers for myometrial activation. The proteomic and miRNA profile of exosomes derived from laboring myometrium revealed some molecules in the exosomes that affect the intercellular communication and the function of the myometrium. Full article

(This article belongs to the Special Issue Proteomics and Metabolomics Investigation of Cell Lines, Tissues and Biological Fluids)

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18 pages, 3602 KiB

Open AccessArticle

STABILON, a Novel Sequence Motif That Enhances the Expression and Accumulation of Intracellular and Secreted Proteins

by Zsuzsanna Rethi-Nagy, Edit Abraham, Katalin Udvardy, Eva Klement, Zsuzsanna Darula, Margit Pal, Robert L. Katona, Vilmos Tubak, Tibor Pali, Zoltan Kota, Rita Sinka, Andor Udvardy and Zoltan Lipinszki

Int. J. Mol. Sci. 2022, 23(15), 8168; https://doi.org/10.3390/ijms23158168 - 25 Jul 2022

Cited by 4 | Viewed by 3066

Abstract

The dynamic balance of transcriptional and translational regulation together with degron-controlled proteolysis shapes the ever-changing cellular proteome. While a large variety of degradation signals has been characterized, our knowledge of cis-acting protein motifs that can in vivo stabilize otherwise short-lived proteins is [...] Read more.

The dynamic balance of transcriptional and translational regulation together with degron-controlled proteolysis shapes the ever-changing cellular proteome. While a large variety of degradation signals has been characterized, our knowledge of cis-acting protein motifs that can in vivo stabilize otherwise short-lived proteins is very limited. We have identified and characterized a conserved 13-mer protein segment derived from the p54/Rpn10 ubiquitin receptor subunit of the Drosophila 26S proteasome, which fulfills all the characteristics of a protein stabilization motif (STABILON). Attachment of STABILON to various intracellular as well as medically relevant secreted model proteins resulted in a significant increase in their cellular or extracellular concentration in mammalian cells. We demonstrate that STABILON acts as a universal and dual function motif that, on the one hand, increases the concentration of the corresponding mRNAs and, on the other hand, prevents the degradation of short-lived fusion proteins. Therefore, STABILON may lead to a breakthrough in biomedical recombinant protein production. Full article

(This article belongs to the Special Issue Proteomics and Metabolomics Investigation of Cell Lines, Tissues and Biological Fluids)

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11 pages, 692 KiB

Open AccessArticle

Dried Blood Spots as Matrix for Evaluation of Valproate Levels and the Immediate and Delayed Metabolomic Changes Induced by Single Valproate Dose Treatment

by Sing Teang Kong, Hai-Shu Lin, Jianhong Ching, Huiqing Xie and Paul C. Ho

Int. J. Mol. Sci. 2022, 23(13), 7083; https://doi.org/10.3390/ijms23137083 - 25 Jun 2022

Cited by 5 | Viewed by 1859

Abstract

The immediate and delayed metabolic changes in rats treated with valproate (VPA), a drug used for the treatment of epilepsy, were profiled. An established approach using dried blood spots (DBS) as sample matrices for gas chromatography/mass spectrometry-based metabolomics profiling was modified using double [...] Read more.

The immediate and delayed metabolic changes in rats treated with valproate (VPA), a drug used for the treatment of epilepsy, were profiled. An established approach using dried blood spots (DBS) as sample matrices for gas chromatography/mass spectrometry-based metabolomics profiling was modified using double solvents in the extraction of analytes. With the modified method, some of the previously undetectable metabolites were recovered and subtle differences in the metabolic changes upon exposure to a single dose of VPA between males and female rats were identified. In male rats, changes in 2-hydroxybutyric acid, pipecolic acid, tetratriacontane and stearic acid were found between the control and treatment groups at various time points from 2.5 h up to 24 h. In contrast, such differences were not observed in female rats, which could be caused by the vast inter-individual variations in metabolite levels within the female group. Based on the measured DBS drug concentrations, clearance and apparent volume of distribution of VPA were estimated and the values were found to be comparable to those estimated previously from full blood drug concentrations. The current study indicated that DBS is a powerful tool to monitor drug levels and metabolic changes in response to drug treatment. Full article

(This article belongs to the Special Issue Proteomics and Metabolomics Investigation of Cell Lines, Tissues and Biological Fluids)

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23 pages, 2271 KiB

Open AccessArticle

Proteolytic Profiling of Streptococcal Pyrogenic Exotoxin B (SpeB) by Complementary HPLC-MS Approaches

by Constantin Blöchl, Christoph Holzner, Michela Luciano, Renate Bauer, Jutta Horejs-Hoeck, Ulrich Eckhard, Hans Brandstetter and Christian G. Huber

Int. J. Mol. Sci. 2022, 23(1), 412; https://doi.org/10.3390/ijms23010412 - 30 Dec 2021

Cited by 9 | Viewed by 3937

Abstract

Streptococcal pyrogenic exotoxin B (SpeB) is a cysteine protease expressed during group A streptococcal infection that represents a major virulence factor. Although subject to several studies, its role during infection is still under debate, and its proteolytic properties remain insufficiently characterized. Here, we [...] Read more.

Streptococcal pyrogenic exotoxin B (SpeB) is a cysteine protease expressed during group A streptococcal infection that represents a major virulence factor. Although subject to several studies, its role during infection is still under debate, and its proteolytic properties remain insufficiently characterized. Here, we revisited this protease through a set of complementary approaches relying on state of-the-art HPLC-MS methods. After conceiving an efficient protocol to recombinantly express SpeB, the zymogen of the protease and its activation were characterized. Employing proteome-derived peptide libraries, a strong preference for hydrophobic and aromatic residues at P2 alongside negatively charged amino acids at P3′ to P6′ was revealed. To identify relevant in vivo substrates, native proteins were obtained from monocytic secretome and plasma to assess their cleavage under physiological conditions. Besides corroborating our findings concerning specificity, more than 200 cleaved proteins were identified, including proteins of the extracellular matrix, proteins of the immune system, and proteins involved in inflammation. Finally, the cleavage of IgG subclasses was studied in detail. This study precisely depicts the proteolytic properties of SpeB and provides a library of potential host substrates, including their exact cleavage positions, as a valuable source for further research to unravel the role of SpeB during streptococcal infection. Full article

(This article belongs to the Special Issue Proteomics and Metabolomics Investigation of Cell Lines, Tissues and Biological Fluids)

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28 pages, 3122 KiB

Open AccessArticle

NMR Hydrophilic Metabolomic Analysis of Bacterial Resistance Pathways Using Multivalent Antimicrobials with Challenged and Unchallenged Wild Type and Mutated Gram-Positive Bacteria

by Michelle L. Aries and Mary J. Cloninger

Int. J. Mol. Sci. 2021, 22(24), 13606; https://doi.org/10.3390/ijms222413606 - 19 Dec 2021

Cited by 7 | Viewed by 2682

Abstract

Multivalent membrane disruptors are a relatively new antimicrobial scaffold that are difficult for bacteria to develop resistance to and can act on both Gram-positive and Gram-negative bacteria. Proton Nuclear Magnetic Resonance (¹H NMR) metabolomics is an important method for studying resistance [...] Read more.

Multivalent membrane disruptors are a relatively new antimicrobial scaffold that are difficult for bacteria to develop resistance to and can act on both Gram-positive and Gram-negative bacteria. Proton Nuclear Magnetic Resonance (¹H NMR) metabolomics is an important method for studying resistance development in bacteria, since this is both a quantitative and qualitative method to study and identify phenotypes by changes in metabolic pathways. In this project, the metabolic differences between wild type Bacillus cereus (B. cereus) samples and B. cereus that was mutated through 33 growth cycles in a nonlethal dose of a multivalent antimicrobial agent were identified. For additional comparison, samples for analysis of the wild type and mutated strains of B. cereus were prepared in both challenged and unchallenged conditions. A C₁₆-DABCO (1,4-diazabicyclo-2,2,2-octane) and mannose functionalized poly(amidoamine) dendrimer (DABCOMD) were used as the multivalent quaternary ammonium antimicrobial for this hydrophilic metabolic analysis. Overall, the study reported here indicates that B. cereus likely change their peptidoglycan layer to protect themselves from the highly positively charged DABCOMD. This membrane fortification most likely leads to the slow growth curve of the mutated, and especially the challenged mutant samples. The association of these sample types with metabolites associated with energy expenditure is attributed to the increased energy required for the membrane fortifications to occur as well as to the decreased diffusion of nutrients across the mutated membrane. Full article

(This article belongs to the Special Issue Proteomics and Metabolomics Investigation of Cell Lines, Tissues and Biological Fluids)

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13 pages, 2080 KiB

Open AccessArticle

Integrated Systems Analysis of Mixed Neuroglial Cultures Proteome Post Oxycodone Exposure

by Rahul S. Guda, Katherine E. Odegaard, Chengxi Tan, Victoria L. Schaal, Sowmya V. Yelamanchili and Gurudutt Pendyala

Int. J. Mol. Sci. 2021, 22(12), 6421; https://doi.org/10.3390/ijms22126421 - 15 Jun 2021

Cited by 5 | Viewed by 2799

Abstract

Opioid abuse has become a major public health crisis that affects millions of individuals across the globe. This widespread abuse of prescription opioids and dramatic increase in the availability of illicit opioids have created what is known as the opioid epidemic. Pregnant women [...] Read more.

Opioid abuse has become a major public health crisis that affects millions of individuals across the globe. This widespread abuse of prescription opioids and dramatic increase in the availability of illicit opioids have created what is known as the opioid epidemic. Pregnant women are a particularly vulnerable group since they are prescribed for opioids such as morphine, buprenorphine, and methadone, all of which have been shown to cross the placenta and potentially impact the developing fetus. Limited information exists regarding the effect of oxycodone (oxy) on synaptic alterations. To fill this knowledge gap, we employed an integrated system approach to identify proteomic signatures and pathways impacted on mixed neuroglial cultures treated with oxy for 24 h. Differentially expressed proteins were mapped onto global canonical pathways using ingenuity pathway analysis (IPA), identifying enriched pathways associated with ephrin signaling, semaphorin signaling, synaptic long-term depression, endocannabinoid signaling, and opioid signaling. Further analysis by ClueGO identified that the dominant category of differentially expressed protein functions was associated with GDP binding. Since opioid receptors are G-protein coupled receptors (GPCRs), these data indicate that oxy exposure perturbs key pathways associated with synaptic function. Full article

(This article belongs to the Special Issue Proteomics and Metabolomics Investigation of Cell Lines, Tissues and Biological Fluids)

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17 pages, 930 KiB

Open AccessReview

Precision Medicine Approaches with Metabolomics and Artificial Intelligence

by Elettra Barberis, Shahzaib Khoso, Antonio Sica, Marco Falasca, Alessandra Gennari, Francesco Dondero, Antreas Afantitis and Marcello Manfredi

Int. J. Mol. Sci. 2022, 23(19), 11269; https://doi.org/10.3390/ijms231911269 - 24 Sep 2022

Cited by 22 | Viewed by 5684

Abstract

Recent technological innovations in the field of mass spectrometry have supported the use of metabolomics analysis for precision medicine. This growth has been allowed also by the application of algorithms to data analysis, including multivariate and machine learning methods, which are fundamental to [...] Read more.

Recent technological innovations in the field of mass spectrometry have supported the use of metabolomics analysis for precision medicine. This growth has been allowed also by the application of algorithms to data analysis, including multivariate and machine learning methods, which are fundamental to managing large number of variables and samples. In the present review, we reported and discussed the application of artificial intelligence (AI) strategies for metabolomics data analysis. Particularly, we focused on widely used non-linear machine learning classifiers, such as ANN, random forest, and support vector machine (SVM) algorithms. A discussion of recent studies and research focused on disease classification, biomarker identification and early diagnosis is presented. Challenges in the implementation of metabolomics–AI systems, limitations thereof and recent tools were also discussed. Full article

(This article belongs to the Special Issue Proteomics and Metabolomics Investigation of Cell Lines, Tissues and Biological Fluids)

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