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Secreted immune proteases Rcr3 (Required for Cladosporium resistance-3) and Pip1 (Phytophthora- inhibited protease-1) of tomato (Solanum lycopersicum) are both inhibited by Avr2 from the fungal plant pathogen Cladosporium fulvum. However, only Rcr3 acts as a decoy co-receptor that detects Avr2 in the presence of the Cf-2 immune receptor. Here, we identified crucial residues in tomato Rcr3 that are required for Cf-2-mediated signalling and bioengineered various proteases to trigger Avr2/Cf-2-dependent immunity. Despite substantial divergence in Rcr3 orthologs from eggplant (Solanum melongena) and tobacco (Nicotiana spp.), minimal alterations were sufficient to trigger Avr2/Cf-2-mediated immune signalling. By contrast, tomato Pip1 was bioengineered with 16 Rcr3-specific residues to initiate Avr2/Cf-2-triggered immune signalling. These residues cluster on one side of the protein next to the substrate-binding groove, indicating a potential Cf-2 interaction site. Our findings also revealed that Rcr3 and Pip1 have distinct substrate preferences determined by two variant residues, and that both are suboptimal for binding Avr2. This study advances our understanding of Avr2 perception and opens avenues to bioengineer proteases to broaden pathogen recognition in other crops.
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BACKGROUND: Minimal change disease and primary focal segmental glomerulosclerosis in adults, along with idiopathic nephrotic syndrome in children, are immune-mediated podocytopathies that lead to nephrotic syndrome. Autoantibodies targeting nephrin have been found in patients with minimal change disease, but their clinical and pathophysiological roles are unclear. METHODS: We conducted a multicenter study to analyze antinephrin autoantibodies in adults with glomerular diseases, including minimal change disease, focal segmental glomerulosclerosis, membranous nephropathy, IgA nephropathy, antineutrophil cytoplasmic antibody-associated glomerulonephritis, and lupus nephritis, as well as in children with idiopathic nephrotic syndrome and in controls. We also created an experimental mouse model through active immunization with recombinant murine nephrin. RESULTS: The study included 539 patients (357 adults and 182 children) and 117 controls. Among the adults, antinephrin autoantibodies were found in 46 of the 105 patients (44%) with minimal change disease, 7 of 74 (9%) with primary focal segmental glomerulosclerosis, and only in rare cases among the patients with other conditions. Of the 182 children with idiopathic nephrotic syndrome, 94 (52%) had detectable antinephrin autoantibodies. In the subgroup of patients with active minimal change disease or idiopathic nephrotic syndrome who were not receiving immunosuppressive treatment, the prevalence of antinephrin autoantibodies was as high as 69% and 90%, respectively. At study inclusion and during follow-up, antinephrin autoantibody levels were correlated with disease activity. Experimental immunization induced a nephrotic syndrome, a minimal change disease-like phenotype, IgG localization to the podocyte slit diaphragm, nephrin phosphorylation, and severe cytoskeletal changes in mice. CONCLUSIONS: In this study, circulating antinephrin autoantibodies were common in patients with minimal change disease or idiopathic nephrotic syndrome and appeared to be markers of disease activity. Their binding at the slit diaphragm induced podocyte dysfunction and nephrotic syndrome, which highlights their pathophysiological significance. (Funded by Deutsche Forschungsgemeinschaft and others.).
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Autoanticuerpos , Proteínas de la Membrana , Síndrome Nefrótico , Podocitos , Proteínas de la Membrana/inmunología , Autoanticuerpos/sangre , Autoanticuerpos/inmunología , Humanos , Animales , Ratones , Niño , Podocitos/inmunología , Adulto , Síndrome Nefrótico/inmunología , Masculino , Femenino , Persona de Mediana Edad , Modelos Animales de Enfermedad , Adolescente , Nefrosis Lipoidea/inmunología , Preescolar , Glomeruloesclerosis Focal y Segmentaria/inmunología , Adulto Joven , AncianoRESUMEN
BACKGROUND: SGLT2 (sodium-glucose cotransporter 2) inhibitors (SGLT2i) can protect the kidneys and heart, but the underlying mechanism remains poorly understood. METHODS: To gain insights on primary effects of SGLT2i that are not confounded by pathophysiologic processes or are secondary to improvement by SGLT2i, we performed an in-depth proteomics, phosphoproteomics, and metabolomics analysis by integrating signatures from multiple metabolic organs and body fluids after 1 week of SGLT2i treatment of nondiabetic as well as diabetic mice with early and uncomplicated hyperglycemia. RESULTS: Kidneys of nondiabetic mice reacted most strongly to SGLT2i in terms of proteomic reconfiguration, including evidence for less early proximal tubule glucotoxicity and a broad downregulation of the apical uptake transport machinery (including sodium, glucose, urate, purine bases, and amino acids), supported by mouse and human SGLT2 interactome studies. SGLT2i affected heart and liver signaling, but more reactive organs included the white adipose tissue, showing more lipolysis, and, particularly, the gut microbiome, with a lower relative abundance of bacteria taxa capable of fermenting phenylalanine and tryptophan to cardiovascular uremic toxins, resulting in lower plasma levels of these compounds (including p-cresol sulfate). SGLT2i was detectable in murine stool samples and its addition to human stool microbiota fermentation recapitulated some murine microbiome findings, suggesting direct inhibition of fermentation of aromatic amino acids and tryptophan. In mice lacking SGLT2 and in patients with decompensated heart failure or diabetes, the SGLT2i likewise reduced circulating p-cresol sulfate, and p-cresol impaired contractility and rhythm in human induced pluripotent stem cell-derived engineered heart tissue. CONCLUSIONS: SGLT2i reduced microbiome formation of uremic toxins such as p-cresol sulfate and thereby their body exposure and need for renal detoxification, which, combined with direct kidney effects of SGLT2i, including less proximal tubule glucotoxicity and a broad downregulation of apical transporters (including sodium, amino acid, and urate uptake), provides a metabolic foundation for kidney and cardiovascular protection.
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Cresoles , Diabetes Mellitus Experimental , Diabetes Mellitus Tipo 2 , Células Madre Pluripotentes Inducidas , Inhibidores del Cotransportador de Sodio-Glucosa 2 , Ésteres del Ácido Sulfúrico , Humanos , Ratones , Animales , Inhibidores del Cotransportador de Sodio-Glucosa 2/farmacología , Transportador 2 de Sodio-Glucosa/metabolismo , Ácido Úrico , Triptófano , Diabetes Mellitus Experimental/tratamiento farmacológico , Diabetes Mellitus Experimental/complicaciones , Proteómica , Tóxinas Urémicas , Células Madre Pluripotentes Inducidas/metabolismo , Glucosa , Sodio/metabolismo , Diabetes Mellitus Tipo 2/complicacionesRESUMEN
OBJECTIVE: Appendiceal neoplasms (ANs) are rare tumors that are often discovered incidentally during histopathological examinations. The increasing incidence of ANs is a critical issue in the non-operative management of acute appendicitis. This study aimed to document the temporal trends over a 12-year period by analyzing the clinical presentation, imaging findings, and histopathological features of ANs. SUBJECTS AND METHODS: Health records of patients who underwent appendectomy from 2011 to 2022 were examined. Demographic and clinical data, laboratory results, imaging findings, and histopathological features were documented. The characteristics of both ANs and non-neoplastic cases were evaluated. RESULTS: A total of 22,304 cases were identified, of which 330 (1.5%) were diagnosed with ANs. The odds ratio for ANs increased with age, with the highest odds ratio observed in patients aged 70 or older. Receiver Operating Characteristic analysis showed that age and appendiceal diameter were significant predictors of ANs. An optimal age cut-off point of 28.5 years was determined, yielding a sensitivity of 72% and a specificity of 64%. For appendiceal diameter, the optimal cut-off was found to be 9.5 mm, exhibiting a sensitivity of 77% and a specificity of 56%. CONCLUSION: Although the incidence of ANs remains relatively low, a steady increase has been observed over the past decade. The increasing rate of ANs raises concerns regarding non-surgical management options. The results of this study highlight the importance of considering ANs as a potential diagnosis in older patients and in patients with an appendix diameter greater than 9.5 mm. These findings may have implications for treatment and management.
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Neoplasias del Apéndice , Apendicitis , Anciano , Humanos , Neoplasias del Apéndice/epidemiología , Neoplasias del Apéndice/terapia , Neoplasias del Apéndice/patología , Incidencia , Apendicectomía , Apendicitis/epidemiología , Apendicitis/terapia , Apendicitis/diagnóstico , Enfermedad Aguda , Estudios RetrospectivosRESUMEN
Plant legumains are crucial for processing seed storage proteins and are critical regulators of plant programmed cell death. Although research on legumains boosted recently, little is known about their activity regulation. In our study, we used pull-down experiments to identify AtCYT6 as a natural inhibitor of legumain isoform ß (AtLEGß) in Arabidopsis thaliana. Biochemical analysis revealed that AtCYT6 inhibits both AtLEGß and papain-like cysteine proteases through two separate cystatin domains. The N-terminal domain inhibits papain-like proteases, while the C-terminal domain inhibits AtLEGß. Furthermore, we showed that AtCYT6 interacts with legumain in a substrate-like manner, facilitated by a conserved asparagine residue in its reactive center loop. Complex formation was additionally stabilized by charged exosite interactions, contributing to pH-dependent inhibition. Processing of AtCYT6 by AtLEGß suggests a context-specific regulatory mechanism with implications for plant physiology, development, and programmed cell death. These findings enhance our understanding of AtLEGß regulation and its broader physiological significance.
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Arabidopsis , Papaína , Papaína/metabolismo , Arabidopsis/genética , Arabidopsis/metabolismo , Cisteína Endopeptidasas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Plantas/metabolismoRESUMEN
Kidney organoids are a promising model to study kidney disease, but their use is constrained by limited knowledge of their functional protein expression profile. Here, we define the organoid proteome and transcriptome trajectories over culture duration and upon exposure to TNFα, a cytokine stressor. Older organoids increase deposition of extracellular matrix but decrease expression of glomerular proteins. Single cell transcriptome integration reveals that most proteome changes localize to podocytes, tubular and stromal cells. TNFα treatment of organoids results in 322 differentially expressed proteins, including cytokines and complement components. Transcript expression of these 322 proteins is significantly higher in individuals with poorer clinical outcomes in proteinuric kidney disease. Key TNFα-associated protein (C3 and VCAM1) expression is increased in both human tubular and organoid kidney cell populations, highlighting the potential for organoids to advance biomarker development. By integrating kidney organoid omic layers, incorporating a disease-relevant cytokine stressor and comparing with human data, we provide crucial evidence for the functional relevance of the kidney organoid model to human kidney disease.
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Enfermedades Renales , Factor de Necrosis Tumoral alfa , Humanos , Factor de Necrosis Tumoral alfa/metabolismo , Proteoma/metabolismo , Riñón , Enfermedades Renales/genética , Enfermedades Renales/metabolismo , Organoides/metabolismoRESUMEN
BACKGROUND/AIM: Gastric carcinoma (GC) is a highly heterogeneous disease with many subtypes that have different morphologic and molecular characteristics. In the current study, we analyzed immunohistochemical (IHC) and in situ hybridization (ISH) features of GCs and evaluated their association with prognosis and clinicopathological features. MATERIALS AND METHODS: Three hundred cases analyzed by IHC and ISH for microsatellite stability, p53, e-cadherin, HER2, PD-L1 expression, and Epstein-Barr virus (EBV) status. Cases were classified into five subgroups based on expression profile. The relationships between subgroups, clinicopathological features, and survival were determined. RESULTS: Ten (3.3%) cases were classified as EBV-associated, 45 (15%) as microsatellite instable (MSI), 73 (24.3%) as EBV-/microsatellite-stable (MSS)/epithelial-mesenchymal-transformation (EMT)-like, 75 (25%) as EBV-/MSS/ non-EMT-like/p53+, and 97 (32.3%) as EBV-/MSS/non-EMT-like/p53-. The MSI subtype had the best overall survival (OS). In contrast, the EBV-/MSS/EMT-like subtype had the poorest OS. The MSI subtype was also related with old age of the patient and antrum-corpus localized tumors, whereas the EBV-/MSS/EMT-like was associated with young age, larger tumor size, and advanced stage presentation. PD-L1 positivity is highly correlated with MSI and EBV-associated subtypes. CONCLUSION: Our data demonstrated a link between IHC/ISH characteristics of GC and clinical outcomes. IHC/ISH based molecular classification may be helpful in predicting the survival.
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Carcinoma , Infecciones por Virus de Epstein-Barr , Neoplasias Gástricas , Humanos , Infecciones por Virus de Epstein-Barr/diagnóstico , Infecciones por Virus de Epstein-Barr/genética , Infecciones por Virus de Epstein-Barr/complicaciones , Herpesvirus Humano 4/genética , Herpesvirus Humano 4/metabolismo , Antígeno B7-H1/genética , Antígeno B7-H1/metabolismo , Pronóstico , Inmunohistoquímica , Proteína p53 Supresora de Tumor/genética , Inestabilidad de Microsatélites , Neoplasias Gástricas/diagnóstico , Neoplasias Gástricas/genética , Hibridación in Situ , Carcinoma/complicacionesRESUMEN
Increasing drought phenomena pose a serious threat to agricultural productivity. Although plants have multiple ways to respond to the complexity of drought stress, the underlying mechanisms of stress sensing and signaling remain unclear. The role of the vasculature, in particular the phloem, in facilitating inter-organ communication is critical and poorly understood. Combining genetic, proteomic and physiological approaches, we investigated the role of AtMC3, a phloem-specific member of the metacaspase family, in osmotic stress responses in Arabidopsis thaliana. Analyses of the proteome in plants with altered AtMC3 levels revealed differential abundance of proteins related to osmotic stress pointing into a role of the protein in water-stress-related responses. Overexpression of AtMC3 conferred drought tolerance by enhancing the differentiation of specific vascular tissues and maintaining higher levels of vascular-mediated transportation, while plants lacking the protein showed an impaired response to drought and inability to respond effectively to the hormone abscisic acid. Overall, our data highlight the importance of AtMC3 and vascular plasticity in fine-tuning early drought responses at the whole plant level without affecting growth or yield.
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Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Resistencia a la Sequía , Floema/metabolismo , Proteómica , Ácido Abscísico/farmacología , Ácido Abscísico/metabolismo , Sequías , Estrés Fisiológico/genética , Regulación de la Expresión Génica de las Plantas , Plantas Modificadas Genéticamente/metabolismoRESUMEN
BACKGROUND AND AIMS: Appendiceal neoplasms are uncommon entities that are usually determined incidentally during the histopathological examination. Different techniques used for the macroscopic sampling of appendectomy material may affect the determinating neoplasms. MATERIALS AND METHODS: H&E-stained slides of 1280 cases who underwent appendectomy between 2013 and 2018 were reviewed retrospectively for histopathological features. RESULTS: Neoplasms were determined in 28 cases (3.09%); 1 lesion was observed in the proximal part of the appendix, 1 covering the entire length from proximal to distal and 26 in the distal part. In the 26 cases that observed in the distal part, the lesion was seen on both sides of the longitudinal section of the distal appendix in 20 cases, while it was seen on only one distal longitudinal section in the remaining 6 cases. CONCLUSION: The vast majority of appendiceal neoplasms are seen in the distal part of the appendix, and, in some cases, neoplasms might be seen on only one side of the distal section. Sampling only one-half of the distal part of the appendix, where tumours are most often observed, could result in some neoplasms being missed. Therefore, sampling the whole distal part would be more beneficial to determine small diameter tumours that do not create macroscopic findings.
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Neoplasias del Apéndice , Humanos , Estudios Retrospectivos , ApendicectomíaRESUMEN
Aim: We aimed to examine the safety and effectiveness of a posterior approach alone in the surgical treatment of sacral-presacral tumors. In addition, we investigate factors that determine the selection of a posterior approach alone. Materials and Methods: Patients with sacral-presacral tumors who underwent surgery in our institution between 2007 and 2019 were examined in this study. Data regarding patient age, gender, tumor size (>6 cm and <6 cm), tumor localization (below or above S1), tumor pathology (benign or malignant), surgical approach (anterior alone, posterior alone, or combined), and extent of resection were recorded. The Spearman's correlation analyses were conducted between surgical approach and tumor size, localization, and pathology. Factors influencing the extent of resection were also examined. Results: Complete tumor resection was achieved in 18 of 20 patients. A posterior approach alone was used in 16. No strong or significant relation was detected between surgical approach and tumor size (r = 0.218; P = 0.355). There was no strong or significant relationship between surgical approach and tumor localization (r = 0.145; P = 0.541) or tumor pathology (r = 0.250; P = 0.288). Tumor size, localization, and pathology were not independent factors that determined surgical approach. The only significant independent determining factor for incomplete resection was tumor pathology (r = 0.688; P = 0.001). Conclusion: A posterior approach is safe and effective in the surgical treatment of sacral-presacral tumors independent of tumor localization, size, or pathology and is a feasible first-line treatment option.
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OBJECTIVE: Parasites and plant seeds may both be found in appendectomy specimens. Each plant seed has a different appearance and can thus exhibit wide variations under the microscope. Fragmented seeds may histologically mimic parasites. The differential diagnosis between seeds and parasites can be challenging in such cases. This study aimed to determine the incidence of parasites, seeds, and foreign bodies in appendectomy materials and highlight the most characteristic histopathological features associated with these structures. MATERIAL AND METHOD: In this study, pathology slides of 9,480 patients, who underwent appendectomy between 2010 and 2021, were reviewed, and cases that contained parasites, seeds, or foreign bodies were identified. We reviewed the literature on seeds and parasites in appendectomy specimens. RESULTS: Parasites were observed in 56 (0.6%) cases. Of these cases, 45 had Enterobius vermicularis (80%), and 11 had Taenia subspecies (20%). Plant seeds were observed in 47 cases (0.5%), and were macroscopically recognizable in 5 of them as olive, lemon, and cherry seeds. Parasites and seeds were usually observed in the lumen of appendix vermiformis, filled with abundant fecal materials. CONCLUSION: Seeds are seen in approximately 0.5% of the appendectomy specimens. Though rarely seen, the fragmented seed appearance may cause diagnostic difficulties. In this context, the key morphological features of parasites and plant seeds outlined in this study may be helpful in their differential diagnosis.
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Apendicitis , Apéndice , Enterobiasis , Cuerpos Extraños , Parásitos , Animales , Humanos , Apéndice/parasitología , Apéndice/patología , Apéndice/cirugía , Apendicitis/complicaciones , Apendicitis/epidemiología , Apendicitis/cirugía , Enterobiasis/diagnóstico , Enterobiasis/epidemiología , Enterobiasis/parasitología , Estudios Retrospectivos , Apendicectomía , Cuerpos Extraños/complicaciones , Cuerpos Extraños/patologíaRESUMEN
The lipid kinase VPS34 orchestrates autophagy, endocytosis, and metabolism and is implicated in cancer and metabolic disease. The proximal tubule in the kidney is a key metabolic organ that controls reabsorption of nutrients such as fatty acids, amino acids, sugars, and proteins. Here, by combining metabolomics, proteomics, and phosphoproteomics analyses with functional and superresolution imaging assays of mice with an inducible deficiency in proximal tubular cells, we revealed that VPS34 controlled the metabolome of the proximal tubule. In addition to inhibiting pinocytosis and autophagy, VPS34 depletion induced membrane exocytosis and reduced the abundance of the retromer complex necessary for proper membrane recycling and lipid retention, leading to a loss of fuel and biomass. Integration of omics data into a kidney cell metabolomic model demonstrated that VPS34 deficiency increased ß-oxidation, reduced gluconeogenesis, and enhanced the use of glutamine for energy consumption. Furthermore, the omics datasets revealed that VPS34 depletion triggered an antiviral response that included a decrease in the abundance of apically localized virus receptors such as ACE2. VPS34 inhibition abrogated SARS-CoV-2 infection in human kidney organoids and cultured proximal tubule cells in a glutamine-dependent manner. Thus, our results demonstrate that VPS34 adjusts endocytosis, nutrient transport, autophagy, and antiviral responses in proximal tubule cells in the kidney.
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COVID-19 , Glutamina , Humanos , Animales , Ratones , SARS-CoV-2 , Riñón , Nutrientes , Antivirales , LípidosRESUMEN
Background and Objectives: The multiple endoclip retraction technique (MERT) was developed based on our experience with suturing renal parenchyma in laparoscopic partial nephrectomy. In this study we prospectively evaluated the one-year results of cases treated by transperitoneal laparoscopic Burch with the MERT. Methods: The patients were evaluated with stress test, one-hour pad test, and were requested to complete the International Continence Society Incontinence Questionnaire short form (ICIQ-SF) in the postoperative period. The follow-up periods were postoperative 3, 6, and 12 months. Results: The primary outcome of this study was surgical success, defined as being cured of stress urinary incontinence (SUI) (no symptoms), experiencing improved symptoms of SUI in ICIQ-SF and negative stress test, and less than 2g urine leakage in a one-hour pad test.No statistically significant difference was found in terms of age, number of children, and body mass index (BMI) in patients according to the results of the 12 month postoperative stress test. We found statistically significant improvements at all control months in terms of stress test and pad weight. ICIQ-SF results showed a significant decrease at three months in patients who recovered after the operation. This rate has not changed in following control months. However, there was no statistical change in ICIQ-SF values in patients who did not recover after the operation. Conclusion: MERT seems to be one of the safe and effective modifications in the management of SUI with good one year outcomes when performed by suitably trained experienced surgeons.
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Laparoscopía , Incontinencia Urinaria de Esfuerzo , Incontinencia Urinaria , Niño , Humanos , Periodo Posoperatorio , Encuestas y Cuestionarios , Incontinencia Urinaria/cirugía , Incontinencia Urinaria de Esfuerzo/diagnóstico , Incontinencia Urinaria de Esfuerzo/cirugíaRESUMEN
Hypertension and kidney disease have been repeatedly associated with genomic variants and alterations of lysine metabolism. Here, we combined stable isotope labeling with untargeted metabolomics to investigate lysine's metabolic fate in vivo. Dietary 13C6 labeled lysine was tracked to lysine metabolites across various organs. Globally, lysine reacts rapidly with molecules of the central carbon metabolism, but incorporates slowly into proteins and acylcarnitines. Lysine metabolism is accelerated in a rat model of hypertension and kidney damage, chiefly through N-alpha-mediated degradation. Lysine administration diminished development of hypertension and kidney injury. Protective mechanisms include diuresis, further acceleration of lysine conjugate formation, and inhibition of tubular albumin uptake. Lysine also conjugates with malonyl-CoA to form a novel metabolite Nε-malonyl-lysine to deplete malonyl-CoA from fatty acid synthesis. Through conjugate formation and excretion as fructoselysine, saccharopine, and Nε-acetyllysine, lysine lead to depletion of central carbon metabolites from the organism and kidney. Consistently, lysine administration to patients at risk for hypertension and kidney disease inhibited tubular albumin uptake, increased lysine conjugate formation, and reduced tricarboxylic acid (TCA) cycle metabolites, compared to kidney-healthy volunteers. In conclusion, lysine isotope tracing mapped an accelerated metabolism in hypertension, and lysine administration could protect kidneys in hypertensive kidney disease.
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Hipertensión , Riñón , Lisina , Albúminas/metabolismo , Animales , Carbono/metabolismo , Modelos Animales de Enfermedad , Hipertensión/metabolismo , Riñón/metabolismo , Lisina/metabolismo , Malonil Coenzima A/metabolismo , RatasRESUMEN
The podocyte is a key cell in maintaining renal filtration barrier integrity. Several recent studies have analyzed the genome and transcriptome in the podocyte at deep resolution. This avenue of "podocyte-ome" research was enabled by a variety of techniques, including 1) single-cell transcriptomics, 2) FACS with and without genetically encoded markers, and 3) deep proteomics. However, data across various omics techniques and studies are currently not well integrated with each other. Here, we aimed to establish a common, simplified knowledge base for the mouse podocyte-ome by integrating bulk RNA sequencing, bulk proteomics of FACS-sorted podocytes, and single-cell transcriptomics. Three publicly available datasets of each omics technique from different laboratories were bioinformatically integrated and visualized. Our approach not only revealed conserved processes of podocytes but also sheds light on the benefits and limitations of the used technologies. We identified that high expression of glycan glycosylphosphatidylinositol anchor synthesis and turnover, as well as retinol metabolism, were relatively understudied features of podocytes. In addition, actin-binding molecules were organized in a podocyte-specific manner, as evidenced by differential expression in podocytes compared with other glomerular cells. We compiled a Web-based "PodIent" application that illustrates the features of the integrated dataset. This enables user-driven exploratory analysis by querying genes of interest for podocyte identity in absolute and relative quantification while also linking to functional annotation using keywords, Gene Ontology terms, and gene set enrichments. This consensus draft is a first step toward common molecular omics knowledge of kidney cells.NEW & NOTEWORTHY Podocytes are key components of glomerular filtration and are affected in various kidney diseases. Here, we present an integrated, robust definition of molecular identity across proteomic, single-cell transcriptomics, and bulk transcriptomic studies on native mouse podocytes. We created the "PodIdent" app, a novel knowledge base promoting access to the presence and expression of specific proteins for podocytes.
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Enfermedades Renales , Podocitos , Animales , Consenso , Riñón/metabolismo , Enfermedades Renales/metabolismo , Glomérulos Renales/metabolismo , Ratones , Podocitos/metabolismo , ProteómicaRESUMEN
Protein N-termini provide unique and distinguishing information on proteolytically processed or N-terminally modified proteoforms. Also splicing, use of alternative translation initiation sites, and a variety of co- and post-translational N-terminal modifications generate distinct proteoforms that are unambiguously identified by their N-termini. However, N-terminal peptides are only a small fraction among all peptides generated in a shotgun proteome digest, are often of low stoichiometric abundance, and therefore require enrichment. Various protocols for enrichment of N-terminal peptides have been established and successfully been used for protease substrate discovery and profiling of N-terminal modification, but often require large amounts of proteome. We have recently established the High-efficiency Undecanal-based N-Termini EnRichment (HUNTER) as a fast and sensitive method to enable enrichment of protein N-termini from limited sample sources with as little as a few microgram proteome. Here we present our current HUNTER protocol for sensitive plant N-terminome profiling, including sample preparation, enrichment of N-terminal peptides, and mass spectrometry data analysis.
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Proteoma , Proteómica , Péptidos/química , Procesamiento Proteico-Postraduccional , Proteolisis , Proteoma/metabolismo , Proteómica/métodosRESUMEN
Substrate sequence specificity is a fundamental characteristic of proteolytic enzymes. Hundreds of proteases are encoded in plant genomes, but the vast majority of them have not been characterized and their distinct specificity remains largely unknown. Here we present our current protocol for profiling sequence specificity of plant proteases using Proteomic Identification of Cleavage Sites (PICS). This simple, cost-effective protocol is suited for detailed, time-resolved specificity profiling of purified or enriched proteases. The isolated active protease or fraction with enriched protease activity together with a suitable control are incubated with split aliquots of proteome-derived peptide libraries, followed by identification of specifically cleaved peptides using quantitative mass spectrometry. Detailed specificity profiles are obtained by alignment of many individual cleavage sites. The chapter covers preparation of complementary peptide libraries from heterologous sources, the cleavage assay itself, as well as mass spectrometry data analysis.
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Biblioteca de Péptidos , Proteoma , Endopeptidasas , Péptido Hidrolasas/metabolismo , Proteolisis , Proteoma/análisis , Proteómica/métodos , Especificidad por Sustrato , Espectrometría de Masas en Tándem/métodosRESUMEN
A large variety of enrichment procedures for protein N-termini have been developed to trace protease activity and determine precise cleavage sites, as well as other N-terminal protein modifications. Typically, enriched N-terminal peptides are identified by tandem mass spectrometry using standard database search engines, in many cases the popular MaxQuant software package. MaxQuant Advanced N-termini Interpreter (MANTI) is a software package that helps to validate, annotate, and visualize peptide identifications in N-termini datasets in a rapid and straightforward manner. Usage of MANTI and especially its graphical interface Yogurtlu MANTI in detail are described to enable users to take full advantage of the software package and the multitude of options it has to offer.
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Proteoma , Proteómica , Péptidos/química , Procesamiento Proteico-Postraduccional , Proteolisis , Proteoma/metabolismo , Proteómica/métodos , Espectrometría de Masas en Tándem/métodosRESUMEN
The new type of coronavirus disease, which has spread from Wuhan, China since the beginning of 2020 called COVID-19, has caused many deaths and cases in most countries and has reached a global pandemic scale. In addition to test kits, imaging techniques with X-rays used in lung patients have been frequently used in the detection of COVID-19 cases. In the proposed method, a novel approach based on a deep learning model named DeepCovNet was utilized to classify chest X-ray images containing COVID-19, normal (healthy), and pneumonia classes. The convolutional-autoencoder model, which had convolutional layers in encoder and decoder blocks, was trained by using the processed chest X-ray images from scratch for deep feature extraction. The distinctive features were selected with a novel and robust algorithm named SDAR from the deep feature set. In the classification stage, an SVM classifier with various kernel functions was used to evaluate the classification performance of the proposed method. Also, hyperparameters of the SVM classifier were optimized with the Bayesian algorithm for increasing classification accuracy. Specificity, sensitivity, precision, and F-score, were also used as performance metrics in addition to accuracy which was used as the main criterion. The proposed method with an accuracy of 99.75 outperformed the other approaches based on deep learning.
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Parkinson's disease (PD), which is a slowly progressing neurodegenerative disorder, negatively affects people's daily lives. Early diagnosis is of great importance to minimize the effects of PD. One of the most important symptoms in the early diagnosis of PD disease is the monotony and distortion of speech. Artificial intelligence-based approaches can help specialists and physicians to automatically detect these disorders. In this study, a new and powerful approach based on multi-level feature selection was proposed to detect PD from features containing voice recordings of already-diagnosed cases. At the first level, feature selection was performed with the Chi-square and L1-Norm SVM algorithms (CLS). Then, the features that were extracted from these algorithms were combined to increase the representation power of the samples. At the last level, those samples that were highly distinctive from the combined feature set were selected with feature importance weights using the ReliefF algorithm. In the classification stage, popular classifiers such as KNN, SVM, and DT were used for machine learning, and the best performance was achieved with the KNN classifier. Moreover, the hyperparameters of the KNN classifier were selected with the Bayesian optimization algorithm, and the performance of the proposed approach was further improved. The proposed approach was evaluated using a 10-fold cross-validation technique on a dataset containing PD and normal classes, and a classification accuracy of 95.4% was achieved.