Proteins in Health and Diseases: New Knowledge and Practical Applications

Topic Information

Dear Colleagues,

Proteins are of great importance in the diagnosis and understanding of most diseases and pathological disturbances that occur, thus having an impact on biomarkers. This Topic will focus on studies which offer new knowledge about proteins and their role and applications in health and disease. It will welcome contributions about the following topics:

• applicative studies about the use of proteins as biomarkers;
• the identification of new proteins that can be of interest in physiological and pathological problems;
• the development of new assays or validation studies for detection of proteins of clinical interest;
• advances in the studies of proteins in non-invasive samples such as saliva or feces;
• omics studies involving proteins;
• the establishment of reference ranges or physiological values of proteins and analytes of clinical interest;
• acute phase proteins and proteins of inflammation and immune system, such as cytokines and interleukins.

Prof. Dr. José Joaquín Cerón
Dr. Alberto Muñoz-Prieto
Dr. Vladimir Mrljak
Dr. Lorena Franco-Martinez
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Cells cells	5.1	10.5	2012	17 Days	CHF 2700
Diseases diseases	2.9	3.7	2013	21.4 Days	CHF 1800
International Journal of Molecular Sciences ijms	4.9	9.0	2000	16.8 Days	CHF 2900
Journal of Clinical Medicine jcm	3.0	5.2	2012	16 Days	CHF 2600
Nutrients nutrients	4.8	9.1	2009	13.5 Days	CHF 2900

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Published Papers (32 papers)

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Open AccessArticle

Food Sources of Animal Protein in Relation to Overall and Cause-Specific Mortality—Causal Associations or Confounding? An Analysis of the EPIC-Heidelberg Cohort

by Rashmita Bajracharya, Rudolf Kaaks and Verena Katzke

Nutrients 2023, 15(15), 3322; https://doi.org/10.3390/nu15153322 - 26 Jul 2023

Cited by 1 | Viewed by 5644

Abstract

While prior prospective iso-caloric substitution studies show a robust association between higher intake of animal protein and risk of mortality, associations observed for mortality risk in relation to major food sources of animal protein have been generally more diverse. We used the EPIC-Heidelberg [...] Read more.

While prior prospective iso-caloric substitution studies show a robust association between higher intake of animal protein and risk of mortality, associations observed for mortality risk in relation to major food sources of animal protein have been generally more diverse. We used the EPIC-Heidelberg cohort to examine if confounding, notably, by smoking, adiposity, or alcohol intake, could cause inconsistencies in estimated mortality hazard ratios (HR) related to intake levels of different types of meat and dairy products. Higher intakes of red or processed meats, and lower intakes of milk or cheese, were observed among current heavy smokers, participants with obesity, or heavy alcohol drinkers. Adjusting for age, sex, and total energy intake, risk models showed increased all-cause, cardiovascular, and cancer-related mortality with higher red or processed meat intakes (HR ranging from 1.25 [95% confidence interval = 1.15–1.36] to 1.76 [1.46–2.12] comparing highest to lowest tertiles), but reduced risks for poultry, milk, or cheese (HR ranging from 0.55 [0.43–0.72] to 0.88 [0.81–0.95]). Adjusting further for smoking history, adiposity indices, alcohol consumption, and physical activity levels, the statistical significance of all these observed was erased, except for the association of processed meat intake with cardiovascular mortality (HR = 1.36 [CI = 1.13–1.64]) and cheese intake with cancer mortality (HR = 0.86 [0.76–0.98]), which, however, were substantially attenuated. These findings suggest heavy confounding and provide little support for the hypothesis that animal protein, as a nutrient, is a major determinant of mortality risk. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

18 pages, 1255 KiB  

Open AccessReview

Revisiting PINI Scoring in Light of Recent Biological Advances

by Yves Ingenbleek

Nutrients 2023, 15(8), 1846; https://doi.org/10.3390/nu15081846 - 12 Apr 2023

Cited by 5 | Viewed by 4047

Abstract

The prognostic inflammatory and nutritional index (PINI) is a simple scoring formula allowing the follow-up of dietary protein restriction and infectious complications affecting critically ill patients hospitalized in medical and surgical wards. The World Health organization (WHO) has recently recommended using the binary [...] Read more.

The prognostic inflammatory and nutritional index (PINI) is a simple scoring formula allowing the follow-up of dietary protein restriction and infectious complications affecting critically ill patients hospitalized in medical and surgical wards. The World Health organization (WHO) has recently recommended using the binary CRP (C-reactive protein) and AGP (α₁-acid glycoprotein) numerators of the PINI formula in underprivileged inhabitants of developing countries to evaluate their (sub)clinical infectious states making their chronic malnutrition worse. These studies, mainly located in Africa and Asia, demonstrate that children and women enduring the combined effects of infectious burden and (micro)nutrient deprivation (principally retinol and iron) usually manifest persistent refractoriness and slackened recovery throughout dietary rehabilitation. The additive measurement of ALB (albumin) and TTR (transthyretin) composing the denominator of the PINI formula is shown to be helpful in grading the downsizing of lean body mass (LBM), a cornerstone of bodybuilding. The confrontation of these four objective parameters thus allows the quantification of the respective importance of nutritional and inflammatory components of any disease process, taking into account that TTR is the sole plasma protein remaining highly correlated to the fluctuations of LBM. The below review highlights the prevailing roles played by protein nutritional states in the release of plasma retinol to target tissues and to the restoration of iron-deficient anemias. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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11 pages, 1088 KiB  

Open AccessOpinion

Secreted Protein Acidic and Rich in Cysteine (SPARC)—Mediated Exercise Effects: Illustrative Molecular Pathways against Various Diseases

by Abdelaziz Ghanemi, Mayumi Yoshioka and Jonny St-Amand

Diseases 2023, 11(1), 33; https://doi.org/10.3390/diseases11010033 - 13 Feb 2023

Cited by 6 | Viewed by 3505

Abstract

The strong benefits of exercise, in addition to the development of both the therapeutic applications of physical activity and molecular biology tools, means that it has become very important to explore the underlying molecular patterns linking exercise and its induced phenotypic changes. Within [...] Read more.

The strong benefits of exercise, in addition to the development of both the therapeutic applications of physical activity and molecular biology tools, means that it has become very important to explore the underlying molecular patterns linking exercise and its induced phenotypic changes. Within this context, secreted protein acidic and rich in cysteine (SPARC) has been characterized as an exercise-induced protein that would mediate and induce some important effects of exercise. Herein, we suggest some underlying pathways to explain such SPARC-induced exercise-like effects. Such mechanistic mapping would not only allow us to understand the molecular processes of exercise and SPARC effects but would also highlight the potential to develop novel molecular therapies. These therapies would be based on mimicking the exercise benefits via either introducing SPARC or pharmacologically targeting the SPARC-related pathways to produce exercise-like effects. This is of a particular importance for those who do not have the ability to perform the required physical activity due to disabilities or diseases. The main objective of this work is to highlight selected potential therapeutic applications deriving from SPARC properties that have been reported in various publications. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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13 pages, 2779 KiB  

Open AccessArticle

Proteomic Analysis of Dupuytren’s Contracture-Derived Sweat Glands Revealed the Synthesis of Connective Tissue Growth Factor and Initiation of Epithelial-Mesenchymal Transition as Major Pathogenetic Events

by Claudia Griselda Cárdenas-León, Kristina Mäemets-Allas, Mariliis Klaas, Katre Maasalu and Viljar Jaks

Int. J. Mol. Sci. 2023, 24(2), 1081; https://doi.org/10.3390/ijms24021081 - 5 Jan 2023

Cited by 2 | Viewed by 2192

Abstract

Dupuytren’s contracture (DC) is a chronic and progressive fibroproliferative disorder restricted to the palmar fascia of the hands. Previously, we discovered the presence of high levels of connective tissue growth factor in sweat glands in the vicinity of DC nodules and hypothesized that [...] Read more.

Dupuytren’s contracture (DC) is a chronic and progressive fibroproliferative disorder restricted to the palmar fascia of the hands. Previously, we discovered the presence of high levels of connective tissue growth factor in sweat glands in the vicinity of DC nodules and hypothesized that sweat glands have an important role in the formation of DC lesions. Here, we shed light on the role of sweat glands in the DC pathogenesis by proteomic analysis and immunofluorescence microscopy. We demonstrated that a fraction of sweat gland epithelium underwent epithelial-mesenchymal transition illustrated by negative regulation of E-cadherin. We hypothesized that the increase in connective tissue growth factor expression in DC sweat glands has both autocrine and paracrine effects in sustaining the DC formation and inducing pathological changes in DC-associated sweat glands. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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11 pages, 1023 KiB  

Open AccessArticle

Evaluation of the Usefulness of a Serological Test for Diagnosis of Celiac Disease Simultaneously Detecting Specific Antibodies and Total IgA

by Emilia Majsiak, Bożena Cukrowska, Magdalena Choina, Kornel Bielawski, Joanna Cielecka-Kuszyk, Ewa Konopka, Mariusz Wysokiński and Joanna Beata Bierła

Nutrients 2023, 15(1), 202; https://doi.org/10.3390/nu15010202 - 31 Dec 2022

Cited by 6 | Viewed by 3920

Abstract

The diagnosis of celiac disease (CD) at the first diagnostic step requires the detection of specific class A antibodies to tissue transglutaminase type-2 (TG2 IgA) and the measurement of total immunoglobulin A (tIgA) to exclude IgA deficiency. The aim of the study was [...] Read more.

The diagnosis of celiac disease (CD) at the first diagnostic step requires the detection of specific class A antibodies to tissue transglutaminase type-2 (TG2 IgA) and the measurement of total immunoglobulin A (tIgA) to exclude IgA deficiency. The aim of the study was to evaluate the new quantitative immunoassay panel allowing for the detection of celiac-specific antibodies with the simultaneous determination of tIgA from the same sample of blood at one time. This retrospective study included 104 pediatric patients divided into groups with recognized CD and IgA deficiency (n = 20; 19%), immunocompetent children with CD (n = 28; 27%), children with IgA deficiency and without CD (n = 28; 27%), and the control group of immunocompetent children without CD (n = 28; 27%). Intestinal biopsy with histopathological evaluation (except five patients with CD who were diagnosed without biopsy) and measurement of reference celiac specific antibodies were performed in all children. Multiparametric quantitative immunoassay Polycheck^® Celiac IgA plus total IgA test was used to evaluate its usefulness in CD screening and IgA deficiency diagnosis. The statistical analysis showed the high sensitivity and specificity of both TG2 IgA and tIgA on the multiparametric panel (sensitivity 96% and 100%; specificity 100% and 79%, respectively). The accuracy and area under the ROC curve for tIgA were 0.904 and 0.955, while for TG2 IgA they were 0.982 and 1.000, respectively. Although the sensitivity of IgA antibodies against deaminated gliadin peptides was low (20%), the specificity reached 100%. The study showed that Polycheck^® Celiac IgA plus total IgA test is a specific and sensitive tool for simultaneous serological CD screening and recognition of IgA deficiency. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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11 pages, 498 KiB  

Open AccessArticle

Effect of Different Nutritional Education Based on Healthy Eating Index for HemoDialysis Patients on Dietary Quality and Muscle Mass

by Yun-Han Chen, Wan-Lin Liu, Tuyen Van Duong, Te-Chih Wong, Hsi-Hsien Chen, Tso-Hsiao Chen, Yung-Ho Hsu, Sheng-Jeng Peng and Shwu-Huey Yang

Nutrients 2022, 14(21), 4617; https://doi.org/10.3390/nu14214617 - 2 Nov 2022

Cited by 4 | Viewed by 3544

Abstract

Background: Hemodialysis patients are at high risk of muscle loss as a result of aging and disease, and combined with inadequate dietary intake. The Healthy Eating Index for HemoDialysis patients (HEI-HD) was developed to assess the dietary quality of hemodialysis patients. The purposes [...] Read more.

Background: Hemodialysis patients are at high risk of muscle loss as a result of aging and disease, and combined with inadequate dietary intake. The Healthy Eating Index for HemoDialysis patients (HEI-HD) was developed to assess the dietary quality of hemodialysis patients. The purposes of this study were to examine the effects of different nutritional education models using HEI-HD-based education on dietary quality and muscle mass in hemodialysis patients. Methods: A quasi-experimental study was conducted from May 2019 to April 2021, with four groups, including no course for patients and nurses (Non-C), course for nurses (CN), course for patients (CP), and course for patients and nurses (CPN). The courses were delivered by registered dietitians. The data of 94 patients were collected and analyzed at baseline, after 2 months of intervention, and 2 months follow-up, including demographics, body composition, 3-day dietary records, and hemodialysis dietary knowledge. The HEI-HD index score was calculated. Results: Patients aged 58.3 ± 10.1 years. The dietary quality change in the CPN group was improved as compared with the Non-C group (−3.4 ± 9.5 vs. 3.0 ± 5.5, 0.04). The skeletal muscle mass of the Non-C group at intervention was also significantly lower than baseline, but the CPN group was not. Conclusions: The HEI-HD-based nutritional education for both patients and nurses showed a positive effect on improving the dietary quality and maintaining muscle mass in hemodialysis patients. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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36 pages, 53617 KiB  

Open AccessArticle

NSP4 and ORF9b of SARS-CoV-2 Induce Pro-Inflammatory Mitochondrial DNA Release in Inner Membrane-Derived Vesicles

by Md Imam Faizan, Rituparna Chaudhuri, Shakti Sagar, Sarah Albogami, Nisha Chaudhary, Iqbal Azmi, Areej Akhtar, Syed Mansoor Ali, Rohit Kumar, Jawed Iqbal, Mohan C. Joshi, Gaurav Kharya, Pankaj Seth, Soumya Sinha Roy and Tanveer Ahmad

Cells 2022, 11(19), 2969; https://doi.org/10.3390/cells11192969 - 23 Sep 2022

Cited by 39 | Viewed by 6155

Abstract

Circulating cell-free mitochondrial DNA (cf-mtDNA) has been found in the plasma of severely ill COVID-19 patients and is now known as a strong predictor of mortality. However, the underlying mechanism of mtDNA release is unexplored. Here, we show a novel mechanism of SARS-CoV-2-mediated [...] Read more.

Circulating cell-free mitochondrial DNA (cf-mtDNA) has been found in the plasma of severely ill COVID-19 patients and is now known as a strong predictor of mortality. However, the underlying mechanism of mtDNA release is unexplored. Here, we show a novel mechanism of SARS-CoV-2-mediated pro-inflammatory/pro-apoptotic mtDNA release and a rational therapeutic stem cell-based approach to mitigate these effects. We systematically screened the effects of 29 SARS-CoV-2 proteins on mitochondrial damage and cell death and found that NSP4 and ORF9b caused extensive mitochondrial structural changes, outer membrane macropore formation, and the release of inner membrane vesicles loaded with mtDNA. The macropore-forming ability of NSP4 was mediated through its interaction with BCL2 antagonist/killer (BAK), whereas ORF9b was found to inhibit the anti-apoptotic member of the BCL2 family protein myeloid cell leukemia-1 (MCL1) and induce inner membrane vesicle formation containing mtDNA. Knockdown of BAK and/or overexpression of MCL1 significantly reversed SARS-CoV-2-mediated mitochondrial damage. Therapeutically, we engineered human mesenchymal stem cells (MSCs) with a simultaneous knockdown of BAK and overexpression of MCL1 (MSCshBAK+MCL1) and named these cells IMAT-MSCs (intercellular mitochondrial transfer-assisted therapeutic MSCs). Upon co-culture with SARS-CoV-2-infected or NSP4/ORF9b-transduced airway epithelial cells, IMAT-MSCs displayed functional intercellular mitochondrial transfer (IMT) via tunneling nanotubes (TNTs). The mitochondrial donation by IMAT-MSCs attenuated the pro-inflammatory and pro-apoptotic mtDNA release from co-cultured epithelial cells. Our findings thus provide a new mechanistic basis for SARS-CoV-2-induced cell death and a novel therapeutic approach to engineering MSCs for the treatment of COVID-19. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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15 pages, 1105 KiB  

Open AccessReview

A Scoping Analysis of Cathelicidin in Response to Organic Dust Exposure and Related Chronic Lung Illnesses

by Marcin Golec, Marta Kinga Lemieszek, Jacek Dutkiewicz, Janusz Milanowski and Sandra Barteit

Int. J. Mol. Sci. 2022, 23(16), 8847; https://doi.org/10.3390/ijms23168847 - 9 Aug 2022

Cited by 3 | Viewed by 8899

Abstract

Over two billion people worldwide are exposed to organic dust, which can cause respiratory disorders. The discovery of the cathelicidin peptide provides novel insights into the lung’s response to organic dust; however, its role in the lung’s response to organic dust exposure and [...] Read more.

Over two billion people worldwide are exposed to organic dust, which can cause respiratory disorders. The discovery of the cathelicidin peptide provides novel insights into the lung’s response to organic dust; however, its role in the lung’s response to organic dust exposure and chronic lung diseases remains limited. We conducted a scoping review to map the current evidence on the role of cathelicidin LL-37/CRAMP in response to organic dust exposure and related chronic lung diseases: hypersensitivity pneumonitis (HP), chronic obstructive pulmonary disease (COPD) and asthma. We included a total of n = 53 peer-reviewed articles in this review, following the process of (i) a preliminary screening; (ii) a systematic MEDLINE/PubMed database search; (iii) title, abstract and full-text screening; (iv) data extraction and charting. Cathelicidin levels were shown to be altered in all clinical settings investigated; its pleiotropic function was confirmed. It was found that cathelicidin contributes to maintaining homeostasis and participates in lung injury response and repair, in addition to exerting a positive effect against microbial load and infections. In addition, LL-37 was found to sustain continuous inflammation, increase mucus formation and inhibit microorganisms and corticosteroids. In addition, studies investigated cathelicidin as a treatment modality, such as cathelicidin inhalation in experimental HP, which had positive effects. However, the primary focus of the included articles was on LL-37’s antibacterial effect, leading to the conclusion that the beneficial LL-37 activity has not been adequately examined and that further research is required. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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17 pages, 3802 KiB  

Open AccessArticle

Regulation of Dietary Protein Solubility Improves Ruminal Nitrogen Metabolism In Vitro: Role of Bacteria–Protozoa Interactions

by Zhenbin Zhang, Wenjun Wei, Sihan Yang, Zeliang Huang, Chuang Li, Xiang Yu, Ruxin Qi, Wujun Liu, Juan J. Loor, Mengzhi Wang and Xin Zhang

Nutrients 2022, 14(14), 2972; https://doi.org/10.3390/nu14142972 - 20 Jul 2022

Cited by 16 | Viewed by 3765

Abstract

Precision dietary interventions (e.g., altering proportions of dietary protein fractions) has significant implications for the efficiency of nutrient use in ruminants, as well as lowering their environmental footprint, specifically nitrogen (N) emissions. Soluble protein (SP) is defined as the protein fraction that is [...] Read more.

Precision dietary interventions (e.g., altering proportions of dietary protein fractions) has significant implications for the efficiency of nutrient use in ruminants, as well as lowering their environmental footprint, specifically nitrogen (N) emissions. Soluble protein (SP) is defined as the protein fraction that is rapidly degraded in the rumen (e.g., non-protein N and true protein), and our previous study found that regulating SP levels could improve N efficiency in Hu sheep. Thus, the present study was conducted to explore in vitro how protein fractions with different SP levels modulate the rumen microbial community and its association with N metabolism. Four dietary treatments with different SP proportions and similar crude protein (CP) content (~14%) were formulated (% of CP): 20 (S20), 30 (S30), 40 (S40) and 50 (S50). Results showed that NH₃-N content increased with increasing SP levels at 4, 12 and 24 h; TVFA, acetate, propionate and valerate were higher in S30 and S40 (p < 0.05) and had quadratic effects (p < 0.05). Moreover, dry matter digestibility (DMD) and N digestibility (ND) were all decreased with S20 and S50 (p < 0.05). The S30 and S40 treatments increased the abundance of Bacteroidetes and Prevotella (Prevotella_ruminicola) but decreased the abundance of Firmicutes and Proteobacteria (p < 0.05). Bacterial pathways related to amino acid and fatty acid metabolism also were enriched with S30 and S40. The abundance of Entodinium was increased with S30 and S40 and had a positive correlation with Prevotella, and these two genera also played an important role in N metabolism and VFA synthesis of this study. In conclusion, bacterial and protozoal communities were altered by the level of SP (% of CP), with higher SP levels (~50% of CP) increasing the microbial diversity but being detrimental to rumen N metabolism. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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15 pages, 5775 KiB  

Open AccessArticle

Integrated Analysis of LncRNA-Mediated ceRNA Network in Calcific Aortic Valve Disease

by Long Chen, Ke Wei, Jun Li, Yue Li, Huiqing Cao and Zhe Zheng

Cells 2022, 11(14), 2204; https://doi.org/10.3390/cells11142204 - 14 Jul 2022

Cited by 13 | Viewed by 3851

Abstract

Background: The high morbidity and mortality of calcific aortic valve disease (CAVD) represents an unmet clinical need to investigate the molecular mechanisms involved. Evidence suggests that long non-coding RNAs (lncRNAs) can act as competitive endogenous RNAs (ceRNAs) by binding to microRNAs and regulating [...] Read more.

Background: The high morbidity and mortality of calcific aortic valve disease (CAVD) represents an unmet clinical need to investigate the molecular mechanisms involved. Evidence suggests that long non-coding RNAs (lncRNAs) can act as competitive endogenous RNAs (ceRNAs) by binding to microRNAs and regulating target genes in cardiovascular diseases. Nevertheless, the role of lncRNAs related ceRNA regulation in CAVD remains unclear. Methods: RNAseq data of human diseased aortic valves were downloaded from GEO data sets (GSE153555, GSE199718), and differentially expressed lncRNAs (DElncRNAs), mRNAs (DEmRNAs) between CAVD and non-calcific aortic valve tissues with limma R package. Gene Ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Set Enrichment analysis (GSEA) were performed with clusterProfiler and gesaplot2 R package. The pivotal microRNAs were predicted by three databases intersection including TargetScan, MiRwalk, miRDB according to the genes related to the crucial pathways. ENCORI was used to predict targeted lncRNAs of hub microRNAs. We constructed lncRNA-miRNA-mRNA ceRNA network with Cytoscape software. The lncRNAs in ceRNA network were verified by RT-qPCR in human 30 calcific and 20 noncalcified aortic valve tissues. Results: In total, 1739 DEmRNAs and 266 DElncRNAs were identified in CAVD. GO, KEGG pathway, GSEA annotations suggested that most of these genes are enriched in extracellular matrix (ECM)-reporter interaction pathways. The ceRNA networks associated with ECM-reporter interaction are constructed and related lncRNAs including H19, SNHG3 and ZNF436-AS1 were significant upregulated in human calcific aortic valve tissues, which might be potential therapeutic targets for CAVD. Conclusions: In this study, we proposed a novel lncRNA-miRNA-mRNA ceRNA network related to ECM-reporter interaction pathways, which potentially regulates CAVD progression. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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7 pages, 2819 KiB  

Open AccessBrief Report

A Potential Role of Cyclic Dependent Kinase 1 (CDK1) in Late Stage of Retinal Degeneration

by Jiaming Zhou and Per Ekström

Cells 2022, 11(14), 2143; https://doi.org/10.3390/cells11142143 - 7 Jul 2022

Cited by 2 | Viewed by 2337

Abstract

Cyclin dependent kinase 1 (CDK1) has long been known to drive the cell cycle and to regulate the division and differentiation of cells. Apart from its role in mitosis regulation, it also exerts multiple functions as a protein kinase, including engagement in cell [...] Read more.

Cyclin dependent kinase 1 (CDK1) has long been known to drive the cell cycle and to regulate the division and differentiation of cells. Apart from its role in mitosis regulation, it also exerts multiple functions as a protein kinase, including engagement in cell death, possibly via a cell cycle-independent mechanism. The latter is suggested, since CDK1 re-expression can be found in non-dividing and terminally differentiated neurons in several neurodegeneration models. However, the details of if and how CDK1 might be involved in the neurodegenerative condition, retinitis pigmentosa (RP), which displays progressive vision loss, are unclear. In the present study, we investigated CDK1 in degenerating RP photoreceptors of the rd1 RP model, including whether there is a link between this kinase and the cGMP-PKG system, which is regarded as a disease driver. With experiments performed using either in vivo retinal tissue or in vitro material, via organotypic retinal explants, our results showed that CDK1 appears in the photoreceptors at a late stage of their degeneration, and in such a position, it may be associated with the cGMP-PKG network. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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15 pages, 2519 KiB  

Open AccessArticle

Proteomic Analysis of Human Milk Reveals Nutritional and Immune Benefits in the Colostrum from Mothers with COVID-19

by Juanjuan Guo, Minjie Tan, Jing Zhu, Ye Tian, Huanyu Liu, Fan Luo, Jianbin Wang, Yanyi Huang, Yuanzhen Zhang, Yuexin Yang and Guanbo Wang

Nutrients 2022, 14(12), 2513; https://doi.org/10.3390/nu14122513 - 17 Jun 2022

Cited by 14 | Viewed by 4381

Abstract

Despite the well-known benefits of breastfeeding and the World Health Organization’s breastfeeding recommendations for COVID-19 infected mothers, whether these mothers should be encouraged to breastfeed is under debate due to concern about the risk of virus transmission and lack of evidence of breastmilk’s [...] Read more.

Despite the well-known benefits of breastfeeding and the World Health Organization’s breastfeeding recommendations for COVID-19 infected mothers, whether these mothers should be encouraged to breastfeed is under debate due to concern about the risk of virus transmission and lack of evidence of breastmilk’s protective effects against the virus. Here, we provide a molecular basis for the breastfeeding recommendation through mass spectrometry (MS)-based proteomics and glycosylation analysis of immune-related proteins in both colostrum and mature breastmilk collected from COVID-19 patients and healthy donors. The total protein amounts in the COVID-19 colostrum group were significantly higher than in the control group. While casein proteins in COVID-19 colostrum exhibited significantly lower abundances, immune-related proteins, especially whey proteins with antiviral properties against SARS-CoV-2, were upregulated. These proteins were detected with unique site-specific glycan structures and improved glycosylation diversity that are beneficial for recognizing epitopes and blocking viral entry. Such adaptive differences in milk from COVID-19 mothers tended to fade in mature milk from the same mothers one month postpartum. These results suggest that feeding infants colostrum from COVID-19 mothers confers both nutritional and immune benefits, and provide molecular-level insights that aid breastmilk feeding decisions in cases of active infection. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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16 pages, 2903 KiB  

Open AccessArticle

A Proteomic Approach to Elucidate the Changes in Saliva and Serum Proteins of Pigs with Septic and Non-Septic Inflammation

by María José López-Martínez, José Joaquín Cerón, Alba Ortín-Bustillo, Damián Escribano, Josipa Kuleš, Anđelo Beletić, Ivana Rubić, Juan Carlos González-Sánchez, Vladimir Mrljak, Silvia Martínez-Subiela and Alberto Muñoz-Prieto

Int. J. Mol. Sci. 2022, 23(12), 6738; https://doi.org/10.3390/ijms23126738 - 16 Jun 2022

Cited by 14 | Viewed by 2965

Abstract

Sepsis is a systemic inflammatory response triggered by an infectious agent and is recognized by the World Health Organization as a global concern, since it is one of the major causes of severe illness in humans and animals. The study of the changes [...] Read more.

Sepsis is a systemic inflammatory response triggered by an infectious agent and is recognized by the World Health Organization as a global concern, since it is one of the major causes of severe illness in humans and animals. The study of the changes that can occur in saliva and serum in sepsis can contribute to a better understanding of the pathophysiological mechanisms involved in the process and also to discover potential biomarkers that can help in its diagnosis and monitoring. The objective of this study was to characterize the changes that occur in the salivary and serum proteome of pigs with experimentally-induced sepsis. The study included five pigs with sepsis induced by LPS administration and five pigs with non-septic inflammation induced by turpentine for comparative purposes. In saliva, there were eighteen salivary proteins differentially expressed in the sepsis condition and nine in non-septic inflammation. Among these, significant increments in aldolase A and serpin B12 only occurred in the sepsis model. Changes in aldolase A were validated in a larger population of pigs with sepsis due to Streptococcus suis infection. In serum, there were 30 proteins differentially expressed in sepsis group and 26 proteins in the non-septic group, and most of the proteins that changed in both groups were related to non-specific inflammation. In the saliva of the septic animals there were some specific pathways activated, such as the organonitrogen compound metabolic process and lipid transport, whereas, in the serum, one of the main activated pathways was the regulation of protein secretion. Overall, saliva and serum showed different proteome variations in response to septic inflammation and could provide complementary information about the pathophysiological mechanisms occurring in this condition. Additionally, salivary aldolase A could be a potential biomarker of sepsis in pigs that should be confirmed in a larger population. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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12 pages, 2074 KiB  

Open AccessArticle

A Novel Antihypertensive Pentapeptide Identified in Quinoa Bran Globulin Hydrolysates: Purification, In Silico Characterization, Molecular Docking with ACE and Stability against Different Food-Processing Conditions

by Yonghua Wei, Yongjuan Liu, Yan Li, Xian Wang, Yajun Zheng, Jianguo Xu, Shen Sang and Yuxi Liu

Nutrients 2022, 14(12), 2420; https://doi.org/10.3390/nu14122420 - 10 Jun 2022

Cited by 13 | Viewed by 2680

Abstract

The addition of food derived antihypertensive peptides to the diet is considered a reasonable way to prevent and lower blood pressure. However, data about stability of antihypertensive peptides against different food-processing conditions are limited. In this study, through Sephadex G-15 gel chromatography and [...] Read more.

The addition of food derived antihypertensive peptides to the diet is considered a reasonable way to prevent and lower blood pressure. However, data about stability of antihypertensive peptides against different food-processing conditions are limited. In this study, through Sephadex G-15 gel chromatography and RP-HPLC separation, UPLC-ESI-MS/MS analysis and in silico screening, a novel ACE-inhibitory pentapeptide Ser-Ala-Pro-Pro-Pro (IC₅₀: 915.03 μmol/L) was identified in quinoa bran globulin hydrolysate. The inhibition patterns on angiotensin-I-converting enzyme and safety of SAPPP were studied using molecular docking and in silico predication, respectively. Results demonstrated that SAPPP could noncompetitively bind to active sites PRO519 and SER461 of ACE through short hydrogen bonds. SAPPP was resistant to different pH values (2.0–10.0), pasteurization conditions, addition of Na⁺, Mg²⁺, Fe³⁺ or K⁺, and the simulated gastrointestinal digestion. In contrast, SAPPP was unstable against heating at 100 °C for more than 50 min and the treatment of Zn²⁺ (5 mmol/L). These results indicated that peptides derived from quinoa globulin hydrolysates can be added into foods for antihypertension. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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14 pages, 4578 KiB  

Open AccessArticle

Lung Spatial Profiling Reveals a T Cell Signature in COPD Patients with Fatal SARS-CoV-2 Infection

by Chen Xi Yang, Michael Tomchaney, Manuel F. Landecho, Borja R. Zamacona, Marta Marin Oto, Javier Zulueta, Joshua Malo, Steve Knoper, Marco Contoli, Alberto Papi, Dragoş M. Vasilescu, Maor Sauler, Christof Straub, Cheryl Tan, Fernando D. Martinez, Deepta Bhattacharya, Ivan O. Rosas, Farrah Kheradmand, Tillie-Louise Hackett and Francesca Polverino

Cells 2022, 11(12), 1864; https://doi.org/10.3390/cells11121864 - 7 Jun 2022

Cited by 6 | Viewed by 4764

Abstract

People with pre-existing lung diseases such as chronic obstructive pulmonary disease (COPD) are more likely to get very sick from SARS-CoV-2 disease 2019 (COVID-19). Still, an interrogation of the immune response to COVID-19 infection, spatially throughout the lung structure, is lacking in patients [...] Read more.

People with pre-existing lung diseases such as chronic obstructive pulmonary disease (COPD) are more likely to get very sick from SARS-CoV-2 disease 2019 (COVID-19). Still, an interrogation of the immune response to COVID-19 infection, spatially throughout the lung structure, is lacking in patients with COPD. For this study, we characterized the immune microenvironment of the lung parenchyma, airways, and vessels of never- and ever-smokers with or without COPD, all of whom died of COVID-19, using spatial transcriptomic and proteomic profiling. The parenchyma, airways, and vessels of COPD patients, compared to control lungs had (1) significant enrichment for lung-resident CD45RO⁺ memory CD4⁺ T cells; (2) downregulation of genes associated with T cell antigen priming and memory T cell differentiation; and (3) higher expression of proteins associated with SARS-CoV-2 entry and primary receptor ubiquitously across the ROIs and in particular the lung parenchyma, despite similar SARS-CoV-2 structural gene expression levels. In conclusion, the lung parenchyma, airways, and vessels of COPD patients have increased T-lymphocytes with a blunted memory CD4 T cell response and a more invasive SARS-CoV-2 infection pattern and may underlie the higher death toll observed with COVID-19. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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17 pages, 606 KiB  

Open AccessArticle

Effect of Early Nutritional Support on Clinical Outcomes of Critically Ill Patients with Sepsis and Septic Shock: A Single-Center Retrospective Study

by Jun-Kwon Cha, Hyung-Sook Kim, Eun-Ji Kim, Eun-Sook Lee, Jae-Ho Lee and In-Ae Song

Nutrients 2022, 14(11), 2318; https://doi.org/10.3390/nu14112318 - 31 May 2022

Cited by 29 | Viewed by 7173

Abstract

The initial nutritional delivery policy for patients with sepsis admitted to the intensive care unit (ICU) has not been fully elucidated. We aimed to determine whether an initial adequate nutrition supply and route of nutrition delivery during the first week of sepsis onset [...] Read more.

The initial nutritional delivery policy for patients with sepsis admitted to the intensive care unit (ICU) has not been fully elucidated. We aimed to determine whether an initial adequate nutrition supply and route of nutrition delivery during the first week of sepsis onset improve clinical outcomes of critically ill patients with sepsis. We reviewed adult patients with sepsis and septic shock in the ICU in a single tertiary teaching hospital between 31 November 2013 and 20 May 2017. Poisson log-linear and Cox regressions were performed to assess the relationships between clinical outcomes and sex, modified nutrition risk in the critically ill score, sequential organ failure assessment score, route of nutrition delivery, acute physiology and chronic health evaluation score, and daily energy and protein delivery during the first week of sepsis onset. In total, 834 patients were included. Patients who had a higher protein intake during the first week of sepsis onset had a lower in-hospital mortality (adjusted hazard ratio (HR), 0.55; 95% confidence interval (CI), 0.39–0.78; p = 0.001). A higher energy intake was associated with a lower 30-day mortality (adjusted HR, 0.94; 95% CI, 0.90–0.98; p = 0.003). The route of nutrition delivery was not associated with 1-year mortality in the group which was underfed; however, in patients who met > 70% of their nutritional requirement, enteral feeding (EN) with supplemental parenteral nutrition (PN) was superior to only EN (p = 0.016) or PN (p = 0.042). In patients with sepsis and septic shock, a high daily average protein intake may lower in-hospital mortality, and a high energy intake may lower the 30-day mortality, especially in those with a high modified nutrition risk in the critically ill scores. In patients who receive adequate energy, EN with supplemental PN may be better than only EN or PN, but not in underfed patients. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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13 pages, 2407 KiB  

Open AccessArticle

Cytokine Pattern of Peripheral Blood Mononuclear Cells Isolated from Children Affected by Generalized Epilepsy Treated with Different Protein Fractions of Meat Sources

by Maria Giovanna Cilberti, Antonella Santillo, Anna N. Polito, Giovanni Messina, Antonella Della Malva, Mariangela Caroprese, Agostino Sevi and Marzia Albenzio

Nutrients 2022, 14(11), 2243; https://doi.org/10.3390/nu14112243 - 27 May 2022

Cited by 2 | Viewed by 2236

Abstract

The objective of the present study was the evaluation of cytokine patterns in terms of TNF-α, IL-10, IL-6, and IL-1β secretion in peripheral blood mononuclear cell (PBMC) supernatants isolated from blood of children affected by generalized epilepsy and treated in vitro with myofibrillar, [...] Read more.

The objective of the present study was the evaluation of cytokine patterns in terms of TNF-α, IL-10, IL-6, and IL-1β secretion in peripheral blood mononuclear cell (PBMC) supernatants isolated from blood of children affected by generalized epilepsy and treated in vitro with myofibrillar, sarcoplasmic, and total protein fractions of meat and fish sources. Children with generalized epilepsy (EC group, n = 16) and children without any clinical signs of disease, representing a control group (CC group n = 16), were recruited at the Complex Structure of Neuropsychiatry Childhood-Adolescence of Policlinico Riuniti (Foggia, Italy). Myofibrillar (MYO), sarcoplasmic (SA), and total (TOT) protein fractions were obtained from longissimus thoracis muscle of beef (BF) and lamb (LA); from pectoralis muscle of chicken (CH); and from dorsal white muscle of sole (Solea solea, SO), European hake (Merluccius merluccius, EH), and sea bass fish (Dicentrarchus labrax, SB), respectively. PBMCs were isolated from peripheral blood of EC and CC groups, and an in vitro stimulation in the presence of 100 μg/mL for each protein fraction from different meat sources was performed. Data were classified according to three different levels of cytokines produced from the EC group relative to the CC group. TNF-α, IL-10, and IL-6 levels were not affected by different meat fractions and meat sources; on the contrary, IL-1β levels were found to be significantly affected by the tested proteins fractions, as well as different meat sources, in high-level cytokine group. On average, the protein fractions obtained from LB, BF, and CH meat sources showed a higher level of IL-1β than the protein fractions obtained from EH and SB fish samples. When all cytokine classes were analyzed, on average, a significant effect was observed for IL-10, IL-1β, and TNF-α. Data obtained in the present study evidence that the nutritional strategy based on protein from fish and meat sources may modulate the immunological cytokine pattern of infants with generalized epilepsy. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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13 pages, 3285 KiB  

Open AccessArticle

Epigenomic Analysis Reveals the KCNK9 Potassium Channel as a Potential Therapeutic Target for Adenomyosis

by Ling-Hui Chu, Chi-Chun Liao, Phui-Ly Liew, Chien-Wen Chen, Po-Hsuan Su, Kuo-Chang Wen, Hung-Cheng Lai, Rui-Lan Huang and Lin-Yu Chen

Int. J. Mol. Sci. 2022, 23(11), 5973; https://doi.org/10.3390/ijms23115973 - 26 May 2022

Cited by 5 | Viewed by 2495

Abstract

Adenomyosis is linked to dysmenorrhea and infertility. The pathogenesis of adenomyosis remains unclear, and little is known of the genetic and epigenetic changes in the eutopic endometrium in adenomyosis, which may predispose patients to the invasion and migration of endometrial tissues into the [...] Read more.

Adenomyosis is linked to dysmenorrhea and infertility. The pathogenesis of adenomyosis remains unclear, and little is known of the genetic and epigenetic changes in the eutopic endometrium in adenomyosis, which may predispose patients to the invasion and migration of endometrial tissues into the myometrium. Transcriptome studies have identified genes related to various cell behaviors but no targets for therapeutic intervention. The epigenetics of the eutopic endometrium in adenomyosis have rarely been investigated. Endometrial tissue was obtained from premenopausal women with (n = 32) or without adenomyosis (n = 17) who underwent hysterectomy aged 34–57 years at a tertiary hospital. The methylome and transcriptome were assessed by using a Methylation 450 K BeadChip array and Affymetrix expression microarray. Protein expression was examined by immunohistochemistry. Differential methylation analysis revealed 53 lowly methylated genes and 176 highly methylated genes with consistent gene expression in adenomyosis, including three genes encoding potassium ion channels. High expression of KCNK9 in the eutopic and ectopic endometria in patients with adenomyosis but not in normal controls was observed. Hormone-free, antibody-based KCNK9 targeting is a potential therapeutic strategy for adenomyosis-related dysmenorrhea, menorrhagia, and infertility. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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21 pages, 1698 KiB  

Open AccessFeature PaperReview

Diagnostic and Therapeutic Perspectives Associated to Cobalamin-Dependent Metabolism and Transcobalamins’ Synthesis in Solid Cancers

by Valentin Lacombe, Guy Lenaers and Geoffrey Urbanski

Nutrients 2022, 14(10), 2058; https://doi.org/10.3390/nu14102058 - 14 May 2022

Cited by 13 | Viewed by 5361

Abstract

Cobalamin or vitamin B12 (B12) is a cofactor for methionine synthase and methylmalonyl-CoA mutase, two enzymes implicated in key pathways for cell proliferation: methylation, purine synthesis, succinylation and ATP production. Ensuring these functions in cancer cells therefore requires important cobalamin needs and its [...] Read more.

Cobalamin or vitamin B12 (B12) is a cofactor for methionine synthase and methylmalonyl-CoA mutase, two enzymes implicated in key pathways for cell proliferation: methylation, purine synthesis, succinylation and ATP production. Ensuring these functions in cancer cells therefore requires important cobalamin needs and its uptake through the transcobalamin II receptor (TCII-R). Thus, both the TCII-R and the cobalamin-dependent metabolic pathways constitute promising therapeutic targets to inhibit cancer development. However, the link between cobalamin and solid cancers is not limited to cellular metabolism, as it also involves the circulating transcobalamins I and II (TCI or haptocorrin and TCII) carrier proteins, encoded by TCN1 and TCN2, respectively. In this respect, elevations of B12, TCI and TCII concentrations in plasma are associated with cancer onset and relapse, and with the presence of metastases and worse prognosis. In addition, TCN1 and TCN2 overexpressions are associated with chemoresistance and a proliferative phenotype, respectively. Here we review the involvement of cobalamin and transcobalamins in cancer diagnosis and prognosis, and as potential therapeutic targets. We further detail the relationship between cobalamin-dependent metabolic pathways in cancer cells and the transcobalamins’ abundancies in plasma and tumors, to ultimately hypothesize screening and therapeutic strategies linking these aspects. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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12 pages, 1395 KiB  

Open AccessArticle

Beneficial Effects of Walnut Oligopeptides on Muscle Loss in Senescence-Accelerated Mouse Prone-8 (SAMP8) Mice: Focusing on Mitochondrial Function

by Rui Fan, Yuntao Hao, Qian Du, Jiawei Kang, Meihong Xu and Yong Li

Nutrients 2022, 14(10), 2051; https://doi.org/10.3390/nu14102051 - 13 May 2022

Cited by 8 | Viewed by 3233

Abstract

Aging-related muscle loss is a hallmark of aging and is the cause of some negative outcomes. An optimized diet and supplements have a positive effect in slowing down the process of muscle loss. This study was designed to evaluate the beneficial effects of [...] Read more.

Aging-related muscle loss is a hallmark of aging and is the cause of some negative outcomes. An optimized diet and supplements have a positive effect in slowing down the process of muscle loss. This study was designed to evaluate the beneficial effects of walnut oligopeptides (WOPs) on aging-related muscle loss and explore the possible underlying mechanism in Senescence-Accelerated Mouse Prone 8 (SAMP8) Mice. SAMP8 mice were randomly divided into four groups (n = 15/group), including one group which was the SAMP8 age control group and three groups those were WOP intervention groups. Meanwhile, Senescence Accelerated Resistant Mouse 1 (SAMR1) mice (n = 12), which had normal senescence rates, were used as model controls. During the six-month intervention period, the age control and normal control groups were given sterilized water, while the three WOP intervention groups were given WOP solution with low (110 mg/kg·bw), medium (220 mg/kg·bw) and high concentrations (440 mg/kg·bw), respectively. The results showed that WOPs could significantly increase muscle mass and improve physical performance (wire hang and catwalk behavioral tests) in aging mice. Moreover, WOPs could significantly reduce the levels of IL-1β, IL-6 and TNF-α in serum and gastrocnemius tissues and increase the mitochondrial DNA content, as well as the expression levels of AMPK, PGC-1α, NRF-1 and TFAM in the gastrocnemius muscle of aging mice, which was speculated to be the specific mechanism related to mitochondrial function improvement and inflammation reduction. These results indicate that WOPs can improve aging-related muscle loss, in term of both muscle mass and physical performance, and WOP supplements seems to be potentially effective in elderly individuals. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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17 pages, 1536 KiB  

Open AccessArticle

A Non-Invasive Neonatal Signature Predicts Later Development of Atopic Diseases

by Youssouf Sereme, Moïse Michel, Soraya Mezouar, Cheick Oumar Guindo, Lanceï Kaba, Ghiles Grine, Thibault Mura, Jean-Louis Mège, Tu Anh Tran, Pierre Corbeau, Anne Filleron and Joana Vitte

J. Clin. Med. 2022, 11(10), 2749; https://doi.org/10.3390/jcm11102749 - 12 May 2022

Cited by 4 | Viewed by 2561

Abstract

Background: Preterm birth is a major cause of morbidity and mortality in infants and children. Non-invasive methods for screening the neonatal immune status are lacking. Archaea, a prokaryotic life domain, comprise methanogenic species that are part of the neonatal human microbiota and contribute [...] Read more.

Background: Preterm birth is a major cause of morbidity and mortality in infants and children. Non-invasive methods for screening the neonatal immune status are lacking. Archaea, a prokaryotic life domain, comprise methanogenic species that are part of the neonatal human microbiota and contribute to early immune imprinting. However, they have not yet been characterized in preterm neonates. Objective: To characterize the gut immunological and methanogenic Archaeal (MA) signature in preterm neonates, using the presence or absence of atopic conditions at the age of one year as a clinical endpoint. Methods: Meconium and stool were collected from preterm neonates and used to develop a standardized stool preparation method for the assessment of mediators and cytokines and characterize the qPCR kinetics of gut MA. Analysis addressed the relationship between immunological biomarkers, Archaea abundance, and atopic disease at age one. Results: Immunoglobulin E, tryptase, calprotectin, EDN, cytokines, and MA were detectable in the meconium and later samples. Atopic conditions at age of one year were positively associated with neonatal EDN, IL-1β, IL-10, IL-6, and MA abundance. The latter was negatively associated with neonatal EDN, IL-1β, and IL-6. Conclusions: We report a non-invasive method for establishing a gut immunological and Archaeal signature in preterm neonates, predictive of atopic diseases at the age of one year. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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15 pages, 3177 KiB  

Open AccessArticle

Identification of Key Genes and Pathways Associated with PIEZO1 in Bone-Related Disease Based on Bioinformatics

by Yuanyuan Zhou, Chen Zhang, Zhongguo Zhou, Chao Zhang and Jiali Wang

Int. J. Mol. Sci. 2022, 23(9), 5250; https://doi.org/10.3390/ijms23095250 - 8 May 2022

Cited by 8 | Viewed by 4534

Abstract

PIEZO1 is a mechano-sensitive ion channel that can sense various forms of mechanical stimuli and convert them into biological signals, affecting bone-related diseases. The present study aimed to identify key genes and signaling pathways in Piezo1-regulated bone-related diseases and to explain the [...] Read more.

PIEZO1 is a mechano-sensitive ion channel that can sense various forms of mechanical stimuli and convert them into biological signals, affecting bone-related diseases. The present study aimed to identify key genes and signaling pathways in Piezo1-regulated bone-related diseases and to explain the potential mechanisms using bioinformatic analysis. The differentially expressed genes (DEGs) in tendon, femur, and humerus bone tissue; cortical bone; and bone-marrow-derived macrophages were identified with the criteria of |log2FC| > 1 and adjusted p-value < 0.05 analysis based on a dataset from GSE169261, GSE139121, GSE135282, and GSE133069, respectively, and visualized in a volcano plot. Venn diagram analyses were performed to identify the overlapping DEGs expressed in the above-mentioned tissues. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, protein–protein interaction (PPI) analysis, and module analysis were also conducted. Furthermore, qRT-PCR was performed to validate the above results using primary chondrocytes. As a result, a total of 222 overlapping DEGs and 12 mostly overlapping DEGs were identified. Key Piezo1-related genes, such as Lcn2, Dkk3, Obscn, and Tnnt1, were identified, and pathways, such as Wnt/β-catenin and PI3k-Akt, were also identified. The present informatic study provides insight, for the first time, into the potential therapeutic targets of Piezo1-regulated bone-related diseases Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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11 pages, 721 KiB  

Open AccessReview

A Narrative Review about Autism Spectrum Disorders and Exclusion of Gluten and Casein from the Diet

by Pablo José González-Domenech, Francisco Diaz-Atienza, Luis Gutiérrez-Rojas, María Luisa Fernández-Soto and Carmen María González-Domenech

Nutrients 2022, 14(9), 1797; https://doi.org/10.3390/nu14091797 - 25 Apr 2022

Cited by 7 | Viewed by 5809

Abstract

Objective: Autism spectrum disorders (ASDs) appear in the early stages of neurodevelopment, and they remain constant throughout life. Currently, due to limitations in ASDs treatment, alternative approaches, such as nutritional interventions, have frequently been implemented. The aim of this narrative review is to [...] Read more.

Objective: Autism spectrum disorders (ASDs) appear in the early stages of neurodevelopment, and they remain constant throughout life. Currently, due to limitations in ASDs treatment, alternative approaches, such as nutritional interventions, have frequently been implemented. The aim of this narrative review is to gather the most relevant and updated studies about dietary interventions related to ASDs etiopathogenesis. Results: Our literature search focused on the gluten- and casein-free (GFCF) diet. The literature found shows the inexistence of enough scientific evidence to support a general recommendation of dietary intervention in children with ASD. Protocols and procedures for assessing risk and safety are also needed. Future lines: Prospective and controlled research studies with larger sample sizes and longer follow-up times are scarce and needed. In addition, studies considering an assessment of intestinal permeability, bacterial population, enzymatic, and inflammatory gastrointestinal activity are interesting to identify possible responders. Besides brain imaging techniques, genetic tests can also contribute as markers to evaluate the comorbidity of gastrointestinal symptoms. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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16 pages, 3399 KiB  

Open AccessReview

Research Status of the Orphan G Protein Coupled Receptor 158 and Future Perspectives

by Xianan Fu, Shoupeng Wei, Tao Wang, Hengxin Fan, Ying Zhang, Clive Da Costa, Sebastian Brandner, Guang Yang, Yihang Pan, Yulong He and Ningning Li

Cells 2022, 11(8), 1334; https://doi.org/10.3390/cells11081334 - 14 Apr 2022

Cited by 10 | Viewed by 5779

Abstract

G-protein-coupled receptors (GPCRs) remain one of the most successful targets for therapeutic drugs approved by the US Food and Drug Administration (FDA). Many novel orphan GPCRs have been identified by human genome sequencing and considered as putative targets for refractory diseases. Of note, [...] Read more.

G-protein-coupled receptors (GPCRs) remain one of the most successful targets for therapeutic drugs approved by the US Food and Drug Administration (FDA). Many novel orphan GPCRs have been identified by human genome sequencing and considered as putative targets for refractory diseases. Of note, a series of studies have been carried out involving GPCR 158 (or GPR158) since its identification in 2005, predominantly focusing on the characterization of its roles in the progression of cancer and mental illness. However, advances towards an in-depth understanding of the biological mechanism(s) involved for clinical application of GPR158 are lacking. In this paper, we clarify the origin of the GPR158 evolution in different species and summarize the relationship between GPR158 and different diseases towards potential drug target identification, through an analysis of the sequences and substructures of GPR158. Further, we discuss how recent studies set about unraveling the fundamental features and principles, followed by future perspectives and thoughts, which may lead to prospective therapies involving GPR158. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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26 pages, 3407 KiB  

Open AccessArticle

Neither Incretin or Amino Acid Responses, nor Casein Content, Account for the Equal Insulin Response Following Iso-Lactose Loads of Natural Human and Cow Milk in Healthy Young Adults

by Paolo Tessari, Alessandro Toffolon, Monica Vettore, Elisabetta Iori, Anna Lante, Emiliano Feller, Elisabetta Alma Rocco, Monica Vedovato, Giovanna Verlato and Massimo Bellettato

Nutrients 2022, 14(8), 1624; https://doi.org/10.3390/nu14081624 - 13 Apr 2022

Cited by 1 | Viewed by 2591

Abstract

Human milk contains <50% less protein (casein) than cow milk, but is equally effective in insulin secretion despite lower postingestion hyperaminoacidemia. Such potency of human milk might be modulated either by incretins (glucagon-like polypeptide-1,GLP-1); glucose-inhibitory-polypeptide, GIP), and/or by milk casein content. Healthy volunteers [...] Read more.

Human milk contains <50% less protein (casein) than cow milk, but is equally effective in insulin secretion despite lower postingestion hyperaminoacidemia. Such potency of human milk might be modulated either by incretins (glucagon-like polypeptide-1,GLP-1); glucose-inhibitory-polypeptide, GIP), and/or by milk casein content. Healthy volunteers of both sexes were fed iso-lactose loads of two low-protein milks, i.e., human [Hum] (n = 8) and casein-deprived cow milk (Cow [↓Cas]) (n = 10), as well as loads of two high-protein milks, i.e., cow (n = 7), and casein-added human-milk (Hum [↑Cas]) (n = 7). Plasma glucose, insulin, C-peptide, incretins and amino acid concentrations were measured for 240′. All milks induced the same transient hyperglycemia. The early [20′–30′] insulin and C-peptide responses were comparable among all milk types apart from the low-protein (Cow [↓Cas]) milk, where they were reduced by <50% (p < 0.05 vs. others). When comparing the two high-protein milks, GLP-1 and GIP [5’–20’] responses with the (Hum [↑Cas]) milk were lower (by ≈2–3 fold, p < 0.007 and p < 0.03 respectively) than those with cow milk, whereas incretin secretion was substantially similar. Plasma amino acid increments largely reflected the milk protein content. Thus, neither casein milk content, nor incretin or amino acid concentrations, can account for the specific potency of human milk on insulin secretion, which remains as yet unresolved. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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17 pages, 2042 KiB  

Open AccessArticle

Type XX Collagen Is Elevated in Circulation of Patients with Solid Tumors

by Jeppe Thorlacius-Ussing, Christina Jensen, Emilie A. Madsen, Neel I. Nissen, Tina Manon-Jensen, Inna M. Chen, Julia S. Johansen, Hadi M. H. Diab, Lars N. Jørgensen, Morten A. Karsdal and Nicholas Willumsen

Int. J. Mol. Sci. 2022, 23(8), 4144; https://doi.org/10.3390/ijms23084144 - 8 Apr 2022

Cited by 17 | Viewed by 3668

Abstract

In the tumor microenvironment, the extracellular matrix (ECM) has been recognized as an important part of cancer development. The dominant ECM proteins are the 28 types of collagens, each with a unique function in tissue architecture. Type XX collagen, however, is poorly characterized, [...] Read more.

In the tumor microenvironment, the extracellular matrix (ECM) has been recognized as an important part of cancer development. The dominant ECM proteins are the 28 types of collagens, each with a unique function in tissue architecture. Type XX collagen, however, is poorly characterized, and little is known about its involvement in cancer. We developed an ELISA quantifying type XX collagen, named PRO-C20, using a monoclonal antibody raised against the C-terminus. PRO-C20 and PRO-C1, an ELISA targeting the N-terminal pro-peptide of type I collagen, was measured in sera of 219 patients with various solid cancer types and compared to sera levels of 33 healthy controls. PRO-C20 was subsequently measured in a separate cohort comprising 36 patients with pancreatic ductal adenocarcinoma (PDAC) and compared to 20 healthy controls and 11 patients with chronic pancreatitis. PRO-C20 was significantly elevated in all cancers tested: bladder, breast, colorectal, head and neck, kidney, lung, melanoma, ovarian, pancreatic, prostate, and stomach cancer (p < 0.01–p < 0.0001). PRO-C1 was only elevated in patients with ovarian cancer. PRO-C20 could discriminate between patients and healthy controls with AUROC values ranging from 0.76 to 0.92. Elevated levels were confirmed in a separate cohort of patients with PDAC (p < 0.0001). High PRO-C20 levels (above 2.57 nM) were predictive of poor survival after adjusting for the presence of metastasis, age, and sex (HR: 4.25, 95% CI: 1.52–11.9, p-value: 0.006). Circulating type XX collagen is elevated in sera of patients with various types of cancer and has prognostic value in PDAC. If validated, PRO-C20 may be a novel biomarker for patients with solid tumors and can help understand the ECM biology of cancer. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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27 pages, 887 KiB  

Open AccessEditor’s ChoiceReview

Faba Bean: An Untapped Source of Quality Plant Proteins and Bioactives

by Delphine Martineau-Côté, Allaoua Achouri, Salwa Karboune and Lamia L’Hocine

Nutrients 2022, 14(8), 1541; https://doi.org/10.3390/nu14081541 - 7 Apr 2022

Cited by 95 | Viewed by 13952

Abstract

Faba beans are emerging as sustainable quality plant protein sources, with the potential to help meet the growing global demand for more nutritious and healthy foods. The faba bean, in addition to its high protein content and well-balanced amino acid profile, contains bioactive [...] Read more.

Faba beans are emerging as sustainable quality plant protein sources, with the potential to help meet the growing global demand for more nutritious and healthy foods. The faba bean, in addition to its high protein content and well-balanced amino acid profile, contains bioactive constituents with health-enhancing properties, including bioactive peptides, phenolic compounds, GABA, and L-DOPA. Faba bean peptides released after gastrointestinal digestion have shown antioxidant, antidiabetic, antihypertensive, cholesterol-lowering, and anti-inflammatory effects, indicating a strong potential for this legume crop to be used as a functional food to help face the increasing incidences of non-communicable diseases. This paper provides a comprehensive review of the current body of knowledge on the nutritional and biofunctional qualities of faba beans, with a particular focus on protein-derived bioactive peptides and how they are affected by food processing. It further covers the adverse health effects of faba beans associated with the presence of anti-nutrients and potential allergens, and it outlines research gaps and needs. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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16 pages, 6494 KiB  

Open AccessArticle

The Role of N-Glycosylation in the Intracellular Trafficking and Functionality of Neuronal Growth Regulator 1

by Gyuri Sim, Moonkyung Jeong, Hyunseok Seo, Jangrae Kim and Soojin Lee

Cells 2022, 11(7), 1242; https://doi.org/10.3390/cells11071242 - 6 Apr 2022

Cited by 4 | Viewed by 3559

Abstract

Neuronal growth regulator 1 (NEGR1) is a brain-enriched membrane protein that is involved in neural cell communication and synapse formation. Accumulating evidence indicates that NEGR1 is a generic risk factor for various psychiatric diseases including autism and depression. Endoglycosidase digestion of single NEGR1 [...] Read more.

Neuronal growth regulator 1 (NEGR1) is a brain-enriched membrane protein that is involved in neural cell communication and synapse formation. Accumulating evidence indicates that NEGR1 is a generic risk factor for various psychiatric diseases including autism and depression. Endoglycosidase digestion of single NEGR1 mutants revealed that the wild type NEGR1 has six putative N-glycosylation sites partly organized in a Golgi-dependent manner. To understand the role of each putative N-glycan residue, we generated a series of multi-site mutants (2MT–6MT) with additive mutations. Cell surface staining and biotinylation revealed that NEGR1 mutants 1MT to 4MT were localized on the cell surface at different levels, whereas 5MT and 6MT were retained in the endoplasmic reticulum to form highly stable multimer complexes. This indicated 5MT and 6MT are less likely to fold correctly. Furthermore, the removal of two N-terminal sites N75 and N155 was sufficient to completely abrogate membrane targeting. An in vivo binding assay using the soluble NEGR1 protein demonstrated that glycans N286, N294 and N307 on the C-terminal immunoglobulin-like domain play important roles in homophilic interactions. Taken together, these results suggest that the N-glycan moieties of NEGR1 are closely involved in the folding, trafficking, and homodimer formation of NEGR1 protein in a site-specific manner. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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16 pages, 2881 KiB  

Open AccessFeature PaperArticle

High-Throughput Screening to Identify Inhibitors of Plasmodium falciparum Importin α

by Sujata B. Walunj, Manisha M. Dias, Chhaminder Kaur, Kylie M. Wagstaff, Vishakha Dey, Caroline Hick, Swati Patankar and David A. Jans

Cells 2022, 11(7), 1201; https://doi.org/10.3390/cells11071201 - 2 Apr 2022

Cited by 6 | Viewed by 4678

Abstract

The global burden of malaria and toxoplasmosis has been limited by the use of efficacious anti-parasitic agents, however, emerging resistance in Plasmodium species and Toxoplasma gondii threatens disease control worldwide, implying that new agents/therapeutic targets are urgently needed. Nuclear localization signal (NLS)-dependent transport [...] Read more.

The global burden of malaria and toxoplasmosis has been limited by the use of efficacious anti-parasitic agents, however, emerging resistance in Plasmodium species and Toxoplasma gondii threatens disease control worldwide, implying that new agents/therapeutic targets are urgently needed. Nuclear localization signal (NLS)-dependent transport into the nucleus, mediated by members of the importin (IMP) superfamily of nuclear transporters, has shown potential as a target for intervention to limit viral infection. Here, we show for the first time that IMPα from P. falciparum and T. gondii have promise as targets for small molecule inhibitors. We use high-throughput screening to identify agents able to inhibit P. falciparum IMPα binding to a P. falciparum NLS, identifying a number of compounds that inhibit binding in the µM-nM range, through direct binding to P. falciparum IMPα, as shown in thermostability assays. Of these, BAY 11-7085 is shown to be a specific inhibitor of P. falciparum IMPα-NLS recognition. Importantly, a number of the inhibitors limited growth by both P. falciparum and T. gondii. The results strengthen the hypothesis that apicomplexan IMPα proteins have potential as therapeutic targets to aid in identifying novel agents for two important, yet neglected, parasitic diseases. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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16 pages, 3128 KiB  

Open AccessArticle

The Methyltransferase HemK Regulates the Virulence and Nutrient Utilization of the Phytopathogenic Bacterium Xanthomonas citri Subsp. citri

by Yu Shi, Xiaobei Yang, Xiaoxin Ye, Jiaying Feng, Tianfang Cheng, Xiaofan Zhou, Ding Xiang Liu, Linghui Xu and Junxia Wang

Int. J. Mol. Sci. 2022, 23(7), 3931; https://doi.org/10.3390/ijms23073931 - 1 Apr 2022

Cited by 7 | Viewed by 3157

Abstract

Citrus canker, caused by the bacterium Xanthomonas citri subsp. citri (Xcc), seriously affects fruit quality and yield, leading to significant economic losses around the world. Understanding the mechanism of Xcc virulence is important for the effective control of Xcc infection. In [...] Read more.

Citrus canker, caused by the bacterium Xanthomonas citri subsp. citri (Xcc), seriously affects fruit quality and yield, leading to significant economic losses around the world. Understanding the mechanism of Xcc virulence is important for the effective control of Xcc infection. In this report, we investigate the role of a protein named HemK in the regulation of the virulence traits of Xcc. The hemK gene was deleted in the Xcc jx-6 background, and the ΔhemK mutant phenotypically displayed significantly decreased motility, biofilm formation, extracellular enzymes, and polysaccharides production, as well as increased sensitivity to oxidative stress and high temperatures. In accordance with the role of HemK in the regulation of a variety of virulence-associated phenotypes, the deletion of hemK resulted in reduced virulence on citrus plants as well as a compromised hypersensitive response on a non-host plant, Nicotiana benthamiana. These results indicated that HemK is required for the virulence of Xcc. To characterize the regulatory effect of hemK deletion on gene expression, RNA sequencing analysis was conducted using the wild-type Xcc jx-6 strain and its isogenic ΔhemK mutant strain, grown in XVM2 medium. Comparative transcriptome analysis of these two strains revealed that hemK deletion specifically changed the expression of several virulence-related genes associated with the bacterial secretion system, chemotaxis, and quorum sensing, and the expression of various genes related to nutrient utilization including amino acid metabolism, carbohydrate metabolism, and energy metabolism. In conclusion, our results indicate that HemK plays an essential role in virulence, the regulation of virulence factor synthesis, and the nutrient utilization of Xcc. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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14 pages, 2146 KiB  

Open AccessArticle

Effect of an Acute Insect Preload vs. an Almond Preload on Energy Intake, Subjective Food Consumption and Intestinal Health in Healthy Young Adults

by Alba Miguéns-Gómez, Marta Sierra-Cruz, Esther Rodríguez-Gallego, Raúl Beltrán-Debón, M Teresa Blay, Ximena Terra, Montserrat Pinent and Anna Ardévol

Nutrients 2022, 14(7), 1463; https://doi.org/10.3390/nu14071463 - 31 Mar 2022

Cited by 3 | Viewed by 3271

Abstract

Protein is considered the most satiating macronutrient, and its effect on satiety and food intake is source-dependent. For the first time, we compared the effect of the administration of an insect or almond preload, both containing 20 g of protein, on appetite and [...] Read more.

Protein is considered the most satiating macronutrient, and its effect on satiety and food intake is source-dependent. For the first time, we compared the effect of the administration of an insect or almond preload, both containing 20 g of protein, on appetite and food intake in human subjects. Participants consumed both foods and a vehicle as a liquid preload on three separate days. They were then offered a breakfast and lunch buffet meal at which food intake was measured. Visual analogue scale (VAS) questionnaires were completed following the three preloads to assess appetite and other sensations. At breakfast, reduced energy intake was observed for both preloads compared with vehicle. At lunch, food intake only differed in the insect group, which consumed more than the vehicle. Insect preload increased the total amount of protein ingested with a slight increase in total energy consumed, differently than almond, which significantly increased total protein and energy consumed. There was no correlation between indigestion-sensation ratings and food intake. Moreover, the insect preload resulted in lower sleepiness and tiredness ratings compared with the almond preload. Thus, insect-derived protein may be suitable as a safe ingredient for snacks intended for elderly or infirm patients who require increased protein intake. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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12 pages, 2177 KiB  

Open AccessArticle

Garvicin KS, a Broad-Spectrum Bacteriocin Protects Zebrafish Larvae against Lactococcus garvieae Infection

by Saurabh Dubey, Dzung B. Diep, Øystein Evensen and Hetron M. Munang’andu

Int. J. Mol. Sci. 2022, 23(5), 2833; https://doi.org/10.3390/ijms23052833 - 4 Mar 2022

Cited by 11 | Viewed by 4205

Abstract

Bacteriocins are emerging as a viable alternative to antibiotics due to their ability to inhibit growth or kill antibiotic resistant pathogens. Herein, we evaluated the ability of the bacteriocin Garvicin KS (GarKS) produced by Lactococcus garvieae KS1546 isolated from cow milk to inhibit [...] Read more.

Bacteriocins are emerging as a viable alternative to antibiotics due to their ability to inhibit growth or kill antibiotic resistant pathogens. Herein, we evaluated the ability of the bacteriocin Garvicin KS (GarKS) produced by Lactococcus garvieae KS1546 isolated from cow milk to inhibit the growth of fish and foodborne bacterial pathogens. We found that GarKS inhibited the growth of five fish L. garvieae strains isolated from infected trout and eels. Among fish pathogens, GarKS inhibited the growth of Streptococcus agalactiae serotypes Ia and Ib, and Aeromonas hydrophila but did not inhibit the growth of Edwardsiella tarda. In addition, it inhibited the growth of A. salmonicida strain 6421 but not A. salmonicida strain 6422 and Yersinia ruckeri. There was no inhibition of three foodborne bacterial species, namely Salmonella enterica, Klebsiella pneumoniae, and Escherichia coli. In vitro cytotoxicity tests using different GarKS concentrations showed that the highest concentration of 33 µg/mL exhibited low cytotoxicity, while concentrations ≤3.3 µg/mL had no cytotoxicity on CHSE-214 and RTG-2 cells. In vivo tests showed that zebrafish larvae treated with 33 µg/mL and 3.3 µg/mL GarKS prior to challenge had 53% and 48% survival, respectively, while concentrations ≤0.33 µg/mL were nonprotective. Altogether, these data show that GarKS has a broad inhibitory spectrum against Gram positive and negative bacteria and that it has potential applications as a therapeutic agent for a wide range of bacterial pathogens. Thus, future studies should include clinical trials to test the efficacy of GarKS against various bacterial pathogens in farmed fish. Full article

(This article belongs to the Topic Proteins in Health and Diseases: New Knowledge and Practical Applications)

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