S-Nitrosylation Proteome Profile of Peripheral Blood Mononuclear Cells in Human Heart Failure

Redox regulation of focal adhesions

Focal adhesions (FAs), multi-protein complexes that link the extracellular matrix to the intracellular cytoskeleton, are key mediators of cell adhesion, migration, and proliferation. These dynamic structures act as mechanical sensors, transmitting stimuli from the extracellular to intracellular environment activating in this way signaling pathways and enabling cells to adapt to environmental changes. As such, FAs are critical for tissue organization and serve as hubs governing cell spatial arrangement within the organism. The assembly, reactivity, and functional regulation of FAs are tightly controlled by post-translational modifications, including redox modulation by reactive oxygen and nitrogen species. Increasing evidence suggests that redox signaling plays a pivotal role in both the physiological and pathological functions of FAs and their downstream processes. Redox regulation affects various components of the FA complex, including integrins, focal adhesion kinase 1 (FAK1), SRC, adapter proteins, and cytoskeletal elements. In this review, we provide an updated overview of the complex interplay between redox signaling and post-translational modifications in FAs. We explore how redox reactions influence the structure, dynamics, and function of FAs, shedding light on their broader implications in health and disease.

Role of macrophage bioenergetics in N-acetylcysteine-mediated mitigation of lung injury and oxidative stress induced by nitrogen mustard

Nitrogen mustard (NM) is a toxic vesicant that causes acute injury to the respiratory tract. This is accompanied by an accumulation of activated macrophages in the lung and oxidative stress which have been implicated in tissue injury. In these studies, we analyzed the effects of N-acetylcysteine (NAC), an inhibitor of oxidative stress and inflammation on NM-induced lung injury, macrophage activation and bioenergetics. Treatment of rats with NAC (150 mg/kg, i.p., daily) beginning 30 min after administration of NM (0.125 mg/kg, i.t.) reduced histopathologic alterations in the lung including alveolar interstitial thickening, blood vessel hemorrhage, fibrin deposition, alveolar inflammation, and bronchiolization of alveolar walls within 3 d of exposure; damage to the alveolar-epithelial barrier, measured by bronchoalveolar lavage fluid protein and cells, was also reduced by NAC, along with oxidative stress as measured by heme oxygenase (HO)-1 and Ym-1 expression in the lung. Treatment of rats with NAC attenuated the accumulation of macrophages in the lung expressing proinflammatory genes including Ptgs2, Nos2, Il-6 and Il-12; macrophages expressing inducible nitric oxide synthase (iNOS), cyclooxygenase (COX)-2 and tumor necrosis factor (TNF)α protein were also reduced in histologic sections. Conversely, NAC had no effect on macrophages expressing the anti-inflammatory proteins arginase-1 or mannose receptor, or on NM-induced increases in matrix metalloproteinase (MMP)-9 or proliferating cell nuclear antigen (PCNA), markers of tissue repair. Following NM exposure, lung macrophage basal and maximal glycolytic activity increased, while basal respiration decreased indicating greater reliance on glycolysis to generate ATP. NAC increased both glycolysis and oxidative phosphorylation. Additionally, in macrophages from both control and NM treated animals, NAC treatment resulted in increased S-nitrosylation of ATP synthase, protecting the enzyme from oxidative damage. Taken together, these data suggest that alterations in NM-induced macrophage activation and bioenergetics contribute to the efficacy of NAC in mitigating lung injury.

Transcriptomics data integration and analysis to uncover hallmark genes in hypertrophic cardiomyopathy

INTRODUCTION

Hypertrophic cardiomyopathy (HCM) is a heterogeneous disease that mainly affects the myocardium. In the current study, we aim to explore HCM-related hub genes through the analysis of differentially expressed genes (DEGs) between HCM and normal sample groups.

METHODS

The GSE68316 and GSE36961 expression profiles were obtained from the Gene Expression Omnibus (GEO) database for the identification of DEGs, to explore hub genes, and to perform their expression analysis. Clinical HCM and control tissue samples were taken for expression and promoter methylation validation analysis via RNA-sequencing (RNA-seq) and targeted bisulfite sequencing (bisulfite-seq) analyses. Then, other different bioinformatics tools were employed to perform STRING, lncRNA-miRNA-mRNA regulatory networks, gene enrichment, and drug prediction analyses.

RESULTS

In total, the top 20 DEGs, including 10 up-regulated and 10 down-regulated, were obtained from GSE68316. Out of the 20 DEGs, we subsequently identified the 8 most important hub genes including 5 up-regulated genes (EPB42, UQCRH, CA1, PFDN5, and LSM5) and 3 down-regulated genes (RPS24, TNS1, and RPL26). Expression and promoter methylation dysregulation of these genes were further validated on clinical HCM samples paired with controls. Next, we further investigated hub genes' regulatory 6 miRNAs (has-mir-1-3p, has-mir-129-5p, has-mir-16-5p, has-mir-23b-3p, has-mir-27-3p, and has-mir-182-5p) and miRNAs regulatory 4 lncRNAs (NUTMB2-AS1, NEAT1, XIST, and GABPB1-AS1) in this study via the lncRNA-cricRNA-miRNA-mRNA regulatory network. Later on, gene enrichment analysis revealed that hub genes were enriched in various important pathways including Nitrogen metabolism, Ribosome, RNA degradation, Cardiac muscle contraction, and Coronavirus disease, etc. Finally, the drug prediction analysis highlighted different potential candidate drugs for altering the expression of hub genes in the treatment of HCM.

CONCLUSION

In summary, the identification of key hub genes and their enrichment analysis in the current study may shed light on the mechanisms behind the occurrence and development of HCM.

Global Proteome-Wide Analysis of Cysteine S-Nitrosylation in Toxoplasma gondii

Toxoplasma gondii transmits through various routes, rapidly proliferates during acute infection and causes toxoplasmosis, which is an important zoonotic disease in human and veterinary medicine. T. gondii can produce nitric oxide and derivatives, and S-nitrosylation contributes to their signaling transduction and post-translation regulation. To date, the S-nitrosylation proteome of T. gondii remains mystery. In this study, we reported the first S-nitrosylated proteome of T. gondii using mass spectrometry in combination with resin-assisted enrichment. We found that 637 proteins were S-nitrosylated, more than half of which were localized in the nucleus or cytoplasm. Motif analysis identified seven motifs. Of these motifs, five and two contained lysine and isoleucine, respectively. Gene Ontology enrichment revealed that S-nitrosylated proteins were primarily located in the inner membrane of mitochondria and other organelles. These S-nitrosylated proteins participated in diverse biological and metabolic processes, including organic acid binding, carboxylic acid binding ribose and phosphate biosynthesis. T. gondii S-nitrosylated proteins significantly contributed to glycolysis/gluconeogenesis and aminoacyl-tRNA biosynthesis. Moreover, 27 ribosomal proteins and 11 microneme proteins were identified as S-nitrosylated proteins, suggesting that proteins in the ribosome and microneme were predominantly S-nitrosylated. Protein-protein interaction analysis identified three subnetworks with high-relevancy ribosome, RNA transport and chaperonin complex components. These results imply that S-nitrosylated proteins of T. gondii are associated with protein translation in the ribosome, gene transcription, invasion and proliferation of T. gondii. Our research is the first to identify the S-nitrosylated proteomic profile of T. gondii and will provide direction to the ongoing investigation of the functions of S-nitrosylated proteins in T. gondii.

Dysfunctional network of hub genes in hypertrophic cardiomyopathy patients

BACKGROUND

Considering it is one of the major causes of sudden cardiac arrest, the proper management of hypertrophic cardiomyopathy (HCM) is essential. However, efficient treatment options for this disease are still lacking. The discovery of HCM-associated hub genes may help in diagnosis and offer a reliable tool for developing effective therapeutic strategies.

METHODS

We examined HCM-based gene expression datasets (GSE36961) from the Gene Expression Omnibus (GEO) database for the identification of differentially expressed genes (DEGs), PPI network development, module screening, and shortlisting of hub genes via GEOR2, STRING, and Cytoscape. Moreover, we also used another HCM-based gene expression dataset (GSE32453) for the expression validation of hub genes. Following this, we constructed the lncRNA-cricRNA-miRNA-mRNA regulatory network after retrieving information from the miRTarBase, miRDB, and MiRcode databases. Finally, we used DAVID to perform functional and pathway analysis of the hub genes.

RESULTS

From GSE36961, a total of the 262 most significant DEGs, including 162 down-regulated and 76 up-regulated, were identified between HCM patients and normal individuals. Among these DEGs, a total of 10 significantly down-regulated DEGs, including cluster of differentiation 14 (CD14), beta2 Integrin Gene (ITGB2), C1q subcomponent subunit B (C1QB), Cluster of Differentiation 163 (CD163), Hematopoietic Cell-Specific Lyn Substrate 1 (HCLS1), Arachidonate 5-Lipoxygenase Activating Protein (ALOX5AP), Pleckstrin (PLEK), Complement C1q C Chain (C1QC), Fc fragment Of IgE receptor Ig (FCER1G), and tyrosine kinase binding protein (TYROBP), were shortlisted as the hub genes. Pathway enrichment analysis showed that the identified hub genes were involved in the dysregulation of some diverse pathways in HCM patients. Such as, Pertussis, Complement and coagulation cascade, Legnionellosis, Asthma, Staphylococcus aureus infection, etc. Lastly, we also explored hub genes' regulatory 2 MicroRNAs (miRNAs, has-mir-7-5p and has-mir-27a-3p), one Long non-coding RNAs (lncRNA, OIP5-AS1-201), and one Circular RNA (cricRNA, CDR1as) via lncRNA-cricRNA-miRNA-mRNA regulatory network.

CONCLUSION

Our study revealed that ten hub genes (CD14, ITGB2, C1QB, CD163, HCLS1, ALOX5AP, PLEK, C1QC, FCER1G, and TYROBP) are involved in the development and progression of HCM. These genes can potentially be used as biomarkers and therapeutic targets for HCM patients.

Dysfunctional Network and Mutation Genes of Hypertrophic Cardiomyopathy

Background

Hypertrophic cardiomyopathy (HCM) is a group of heterogeneous diseases that affects the myocardium. It is also a common familial disease. The symptoms are not common and easy to find.

Objective

In this paper, we aim to explore and analyze the dysfunctional gene network related to hypertrophic cardiomyopathy, and the key target genes with diagnostic and therapeutic significance for HCM were screened.

Methods

The gene expression profiles of 37 samples (GSE130036) were downloaded from the GEO database. Differential analysis was used to identify the related dysregulated genes in patients with HCM. Enrichment analysis identified the biological function and signaling pathway of these differentially expressed genes. Then, PPI network was built and verified in the GSE36961 dataset. Finally, the gene of single-nucleotide variants (SNVs) in HCM samples was screened by means of maftools.

Results

In this study, 920 differentially expressed genes were obtained, and these genes were mainly related to metabolism-related signaling pathways. 187 interacting genes were identified by PPI network analysis, and the expression trends of C1QB, F13A1, CD163, FCN3, PLA2G2A, and CHRDL2 were verified by another dataset and quantitative real-time polymerase chain reaction. ROC curve analysis showed that they had certain clinical diagnostic ability, and they were the potential key dysfunctional genes of HCM. In addition, we found that PRMT5 mutation was the most frequent in HCM samples, which may affect the pathogenesis of HCM.

Conclusion

Therefore, the key genes and enrichment results identified by our analysis may provide a reference for the occurrence and development mechanism of HCM. In addition, mutations in PRMT5 may be a useful therapeutic and diagnostic target for HCM. Our results also provide an independent quantitative assessment of functional limitations in patients with unknown history.

Nitric oxide inhibits endothelial cell apoptosis by inhibiting cysteine-dependent SOD1 monomerization

Endothelial cell apoptosis is an important pathophysiology in many cardiovascular diseases. The gasotransmitter nitric oxide (NO) is known to regulate cell survival and apoptosis. However, the mechanism underlying the effect of NO remains unclear. In this research, by targeting cytosolic copper/zinc superoxide dismutase (SOD1) monomerization, we aimed to explore how NO inhibited endothelial cell apoptosis. We showed that treatment with the NO synthase (NOS) inhibitor nomega‐nitro‐l‐arginine methyl ester hydrochloride (L‐NAME) significantly decreased the endogenous NO content of endothelial cells, facilitated the formation of SOD1 monomers, inhibited dismutase activity, and promoted reactive oxygen species (ROS) accumulation in human umbilical vein endothelial cells (HUVECs); by contrast, supplementation with the NO donor sodium nitroprusside (SNP) upregulated NO content, prevented the formation of SOD1 monomers, enhanced dismutase activity, and reduced ROS accumulation in L‐NAME‐treated HUVECs. Mechanistically, tris(2‐carboxyethyl) phosphine hydrochloride (TCEP), a specific reducer of cysteine thiol, increased SOD1 monomer formation, thus preventing the NO‐induced increase in dismutase activity and the decrease in ROS. Furthermore, SNP inhibited HUVEC apoptosis caused by the decrease in endogenous NO, whereas TCEP abolished this protective effect of SNP. In summary, our data reveal that NO protects endothelial cells against apoptosis by inhibiting cysteine‐dependent SOD1 monomerization to enhance SOD1 activity and inhibit oxidative stress.

Gel-based fluorescent proteomic tools for investigating cell redox signaling. A mini-review

The specific chemical reactivity of thiol groups makes protein cysteines susceptible to reactions with reactive oxygen species (ROS) and reactive nitrogen species (RNS) resulting in the formation of various reversible and irreversible oxidative post-translational modifications (oxPTMs). This review highlights a number of gel-based redox proteomic approaches to detect protein oxPTMs, with particular emphasis on S-nitrosylation, which we believe are currently one of the most accurate way to analyze changes in the redox status of proteins. The information collected in this review relates to the recent progress regarding methods for the enrichment and identification of redox-modified proteins, with an emphasis on fluorescent gel proteomics. Gel-based fluorescent proteomic strategies are low-cost and easy-to-use tools for investigating the thiol proteome and can provide substantial information on redox signaling.

Unlocking the Value of White Blood Cells for Heart Failure Diagnosis

Cardiovascular disease (CVD) is the single greatest cause of mortality and morbidity worldwide. Inciting 85% of CVD fatalities is heart failure, often resulting in or from a myocardial infarction. Early detection along with pharmacological treatment and lifestyle adaptation can result in better prognosis. Biomarkers are molecular or physiological measures that indicate disease presence, status, and severity. However, not all forms of heart failure are created equal. Current mainstay biomarkers for heart failure, including NT-pro-BNP and ejection fraction, lack sensitivity for many patients. Circulating white blood cells and peripheral blood mononuclear cells (PBMCs) are emerging as surrogate biopsies, reflecting molecular changes in the heart. We discuss the advantages of PBMCs over other sources, as well as limitations and considerations. We urge medical center biobanks to collect, isolate and store circulating white blood cells as a rich source of biomarkers to catalyze the discovery of novel diagnostic tools for heart failure.

Potential Role of Antioxidants as Adjunctive Therapy in Chagas Disease

Chagas disease (CD) is one of the most important neglected tropical diseases in the American continent. Host-derived nitroxidative stress in response to Trypanosoma cruzi infection can induce tissue damage contributing to the progression of Chagas disease. Antioxidant supplementation has been suggested as adjuvant therapy to current treatment. In this article, we synthesize and discuss the current evidence regarding the use of antioxidants as adjunctive compounds to fight harmful reactive oxygen species and lower the tissue oxidative damage during progression of chronic Chagas disease. Several antioxidants evaluated in recent studies have shown potential benefits for the control of oxidative stress in the host's tissues. Melatonin, resveratrol, the combination of vitamin C/vitamin E (vitC/vitE) or curcumin/benznidazole, and mitochondria-targeted antioxidants seem to be beneficial in reducing plasma and cardiac levels of lipid peroxidation products. Nevertheless, further research is needed to validate beneficial effects of antioxidant therapies in Chagas disease.

Genes of the cGMP-PKG-Ca2+ signaling pathway are alternatively spliced in cardiomyopathy: Role of RBFOX2

Aberrations in the cGMP-PKG-Ca2+ pathway are implicated in cardiovascular complications of diverse etiologies, though involved molecular mechanisms are not understood. We performed RNA-Seq analysis to profile global changes in gene expression and exon splicing in Chagas disease (ChD) murine myocardium. Ingenuity-Pathway-Analysis of transcriptome dataset identified 26 differentially expressed genes associated with increased mobilization and cellular levels of Ca2+ in ChD hearts. Mixture-of-isoforms and Enrichr KEGG pathway analyses of the RNA-Seq datasets from ChD (this study) and diabetic (previous study) murine hearts identified alternative splicing (AS) in eleven genes (Arhgef10, Atp2b1, Atp2a3, Cacna1c, Itpr1, Mef2a, Mef2d, Pde2a, Plcb1, Plcb4, and Ppp1r12a) of the cGMP-PKG-Ca2+ pathway in diseased hearts. AS of these genes was validated by an exon exclusion-inclusion assay. Further, Arhgef10, Atp2b1, Mef2a, Mef2d, Plcb1, and Ppp1r12a genes consisted RBFOX2 (RNA-binding protein) binding-site clusters, determined by analyzing the RBFOX2 CLIP-Seq dataset. H9c2 rat heart cells transfected with Rbfox2 (vs. scrambled) siRNA confirmed that expression of Rbfox2 is essential for proper exon splicing of genes of the cGMP-PKG-Ca2+ pathway. We conclude that changes in gene expression may influence the Ca2+ mobilization pathway in ChD, and AS impacts the genes involved in cGMP/PKG/Ca2+ signaling pathway in ChD and diabetes. Our findings suggest that ChD patients with diabetes may be at increased risk of cardiomyopathy and heart failure and provide novel ways to restore cGMP-PKG regulated signaling networks via correcting splicing patterns of key factors using oligonucleotide-based therapies for the treatment of cardiovascular complications.

Integrated Functional Analysis of the Nuclear Proteome of Classically and Alternatively Activated Macrophages

Macrophages (Mφ) play a central role in coordinating host response to pathogens, cellular injury, and environmental stimuli. Herein, we report multidimensional, nuclear proteomic analyses of protein expression and posttranslational modifications (PTMs) that control biological processes during Mφ activation. For this, Mφ were incubated with IFN-γ/LPS and IL-4, and their differentiation to proinflammatory (M1) and anti-inflammatory (M2a, referred as M2 for simplicity throughtout the manuscript) phenotypes was confirmed by detection of CD64 and CD206 surface markers and TNF-α, arginase I, and iNOS-dependent nitrite levels. We used a sequential method of organellar enrichment and labeling of nuclear fractions with BODIPY FL-maleimide fluorescence dye followed by two-dimensional electrophoresis (2DE) to capture quantitative changes in abundance and S-nitrosylated (SNO) proteome signatures. Exact same gels were then labeled with Pro-Q Diamond to detect protein phosphorylation. MALDI-TOF/TOF MS analysis of the protein spots with fold change of ≥|1.5| in any of the groups yielded 229 identifications. We found that 145, 78, and 173 protein spots in M1 Mφ and 105, 81, and 164 protein spots in M2 Mφ were changed in abundance, S-nitrosylation, and phosphorylation, respectively, with respect to M0 controls (fold change: ≥|1.5|, p ≤ 0.05). Targeted analysis by immunoprecipitation and Western blotting was performed to verify the differential abundance and phosphorylation levels of two of the proteins in M1 and M2 (vs. M0) Mφ. Ingenuity Pathway Analysis of the nuclear proteome datasets showed that the abundance and posttranslational (SNO and Phosphor) modifications of the proteins predicted to be involved in cytoskeletal organization/cell movement, phagocytosis/endocytosis, and cell proliferation/cell death were differentially regulated with proinflammatory and anti-inflammatory activation of Mφ.

Potential Utility of Protein Targets of Cysteine-S-Nitrosylation in Identifying Clinical Disease Status in Human Chagas Disease

Trypanosoma cruzi (Tc) infection causes Chagas disease (ChD) presented by dilated cardiomyopathy and heart failure. During infection, oxidative and nitrosative stresses are elicited by the immune cells for control the pathogen; however, excess nitric oxide and superoxide production can result in cysteine S-nitrosylation (SNO) of host proteins that affects cellular homeostasis and may contribute to disease development. To identify the proteins with changes in SNO modification levels as a hallmark of ChD, we obtained peripheral blood mononuclear cells (PBMC) from seronegative, normal healthy (NH, n = 30) subjects, and from seropositive clinically asymptomatic (ChD CA, n = 25) or clinically symptomatic (ChD CS, n = 28) ChD patients. All samples were treated (Asc+) or not-treated (Asc⁻) with ascorbate (reduces nitrosylated thiols), labeled with the thiol-labeling BODIPY FL-maleimide dye, resolved by two-dimensional electrophoresis (total 166 gels), and the protein spots that yielded significant differences in abundance or SNO level at p-value of ≤ 0.05_{t−test/Welch/BH} were identified by MALDI-TOF/TOF MS or OrbiTrap LC-MS/MS. Targeted analysis of a new cohort of PBMC samples (n = 10–14/group) was conducted to verify the differential abundance/SNO levels of two of the proteins in ChD (vs. NH) subjects. The multivariate adaptive regression splines (MARS) modeling, comparing differences in relative SNO level (Asc⁻/Asc+ ratio) of the protein spots between any two groups yielded SNO biomarkers that exhibited ≥90% prediction success in classifying ChD CA (582-KRT1 and 884-TPM3) and ChD CS (426-PNP, 582-KRT1, 486-ALB, 662-ACTB) patients from NH controls. Ingenuity Pathway Analysis (IPA) of the SNO proteome dataset normalized to changes in protein abundance suggested the proteins belonging to the signaling networks of cell death and the recruitment and migration of immune cells were most affected in ChD CA and ChD CS (vs. NH) subjects. We propose that SNO modification of the select panel of proteins identified in this study have the potential to identify ChD severity in seropositive individuals exposed to Tc infection.

Proteome profiling of s-nitrosylated synaptosomal proteins by isobaric mass tags

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Protocol for quantitative proteomics of nitrosylation on synaptosomal proteins.

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Identification of endogenous nitrosylation independent of induction by NO donors.

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Use of iodoTMT sixplex mass tags for stable labeling, enrichment, identification, and multiplex quantitation.

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Applicable on low amounts of sample material of mouse and human brain tissue.