Translational Urinomics

Preface
	References
Acknowledgments
Contents
Contributors
About the Editor
1: Sample Preparation for High-Throughput Urine Proteomics Using 96-Well Polyvinylidene Fluoride (PVDF) Membranes.
	1.1	 Introduction
	1.2	 Experimental Section
		1.2.1	 Materials
			1.2.1.1	 Reagents for Digestion
			1.2.1.2	 Plates and Disposables for Digestion
		1.2.2	 Methods (Workflow Design Shown in Fig. 1.1)
			1.2.2.1	 Prepare Plate with Dry Urea
			1.2.2.2	 Protein Reduction and Alkylation
			1.2.2.3	 Protein Digestion
		1.2.3	 Data Analysis as Used for the Example Dataset (Monitoring Catabolism Post Thoracotomy by Urine Proteomics)
			1.2.3.1	 Spectral Library Construction with MaxQuant
			1.2.3.2	 DIA Sample Acquisition
			1.2.3.3	 DIA Data Analysis in Spectronaut
			1.2.3.4	 Data Processing and Statistical Analysis
		1.2.4	 Notes
		1.2.5	 Application: Monitoring Catabolism Post Thoracotomy by Urine Proteomics
	1.3	 Results
	1.4	 Conclusion
	References
2: Kidney Diseases: The Age of Molecular Markers
	2.1	 Introduction
		2.1.1	 Biomarkers
		2.1.2	 Liquid Biopsy
		2.1.3	 Nephrotic Syndrome
			2.1.3.1	 Diagnosis
		2.1.4	 Nephritic Syndrome
			2.1.4.1	 Diagnosis
		2.1.5	 Acute Kidney Injury
			2.1.5.1	 Diagnosis
		2.1.6	 Chronic Kidney Disease
		2.1.7	 Diabetic Nephropathy
			2.1.7.1	 Diagnosis
		2.1.8	 New Era of Biomarkers and Liquid Matrices
	References
3: Urinary Extracellular Vesicles Magic Particles for Biomarker Discovery
	3.1	 Introduction
	3.2	 Urinary EV Biology
	3.3	 Urinary Extracellular Vesicle Isolation
	3.4	 Inter- and Intra- Individual Variability in EVs Samples
	3.5	 Example of Experimental Setups Relevant in uEV Studies
	3.6	 uEV Omics Studies for Biomarker Research
	3.7	 Future of uEV Studies
	References
4: Cardiac Troponin T: The Impact of Posttranslational Modifications on Analytical Immunoreactivity in Blood up to the Excretion in Urine
	4.1	 Basic Primary Structure and Isoforms of cTnT
	4.2	 Isoforms of cTnT and Cross Reactivity
	4.3	 Structures of cTnT beyond Its Basic Primary Structure
	4.4	 Quaternary Structures: Biomolecular Complexes of cTnT
	4.5	 Posttranslational Modifications in the Basic Primary Structure of cTnT and Clearance of cTnT
	4.6	 Step 1: N-Terminal Initiator Methionine Removal, N-Acetylation and C-Terminal Proteolysis
	4.7	 Step 2: N-Ubiquinylation, N,S-Myristoylation and O-(N-Acetyl)-Glucosaminylation
	4.8	 Miscellaneous PTMs Related to Step 2: O-Phosphorylation and Advanced Glycation
	4.9	 Step 3: Proteolytic Degradation
	4.10	 Step 4: Excretion in Urine
	4.11	 Observed Proteoforms in Urine
	4.12	 Final Remarks
	4.13	 Conclusion
	References
5: Research Progress of Urine Biomarkers in the Diagnosis, Treatment, and Prognosis of Bladder Cancer
	5.1	 Introduction
		5.1.1	 Bladder Cancer (BC) Incidence, Epidemiology, and Risk Factors
		5.1.2	 Economic Burden of BC
		5.1.3	 Classical Classification of BC
		5.1.4	 Molecular Phenotyping of BC
	5.2	 Biomarker Discovery in BC
		5.2.1	 Proteomics-Based BC Biomarkers
		5.2.2	 Metabolomics-Based BC Biomarkers
		5.2.3	 Genomics-Based BC Biomarkers
			5.2.3.1	 DNA Methylation
			5.2.3.2	 miRNAs
	5.3	 Metabolomics and Metabolic Phenotypes of BC
	5.4	 Metabolomic Platforms
	5.5	 Metabolomics in BC Diagnosis and Prognosis and Predicting Response to Therapies
		5.5.1	 Tricarboxylic Acid Cycle
		5.5.2	 Lipid Metabolism
		5.5.3	 Amino Acid Metabolism
			5.5.3.1	 Glutathione Metabolism
			5.5.3.2	 Tryptophan Metabolism
			5.5.3.3	 Hippuric Acid & Taurine Metabolism
			5.5.3.4	 Nucleotide Metabolism
			5.5.3.5	 Glycolysis
	5.6	 Clinically Applicable BC Biomarkers-Based Tools
	5.7	 Conclusions and Perspectives
	References
6: Urinary Markers of Podocyte Dysfunction in Chronic Glomerulonephritis
	6.1	 Introduction
	6.2	 Podocyte Damage. Podocyte Damage Markers in Chronic Glomerulonephritis
		6.2.1	 Glomerular Filter Structure and Function
		6.2.2	 Podocyte Response to Damage. Podocyturia
		6.2.3	 Nephrinuria
	6.3	 Heat Shock Protein 27
	6.4	 Factors of Apoptosis and Survival of Podocytes in Urine from CGN Patients
		6.4.1	 Vascular Endothelial Growth Factor (VEGF) in CGN
	6.5	 Mechanisms of Podocytopenia Are the Main Determinants of Glomerulosclerosis
	6.6	 Immunohistochemical Evaluation of Podocytopenia in Patients with Chronic Glomerulonephritis
	6.7	 Matrix Metalloproteinases and Their Inhibitor Disturbance
	6.8	 Prognostic Value of the Studied Parameters in CGN Patients
	6.9	 Summary
	References
7: On Research and Translation of Urinary Biomarkers
	References
8: A Mechanistic-Based and Non-invasive Approach to Quantify the Capability of Kidney to Detoxify Cysteine-Disulfides
	8.1	 Introduction
	8.2	 Experimental
		8.2.1	 Method Development
		8.2.2	 Method Description
			8.2.2.1	 Chemicals
			8.2.2.2	 Stock and Calibration Solutions
			8.2.2.3	 Reduction and Derivatization
			8.2.2.4	 Chromatographic Conditions
		8.2.3	 Method Validation
			8.2.3.1	 Selectivity and Carry-over Effect
			8.2.3.2	 Linearity
			8.2.3.3	 Lower and Higher Limits of Quantification
			8.2.3.4	 Accuracy
			8.2.3.5	 Intra- and Inter-assay Precision
			8.2.3.6	 Stability and Storage Conditions
			8.2.3.7	 Quantification of uNAC vs. Free NAC
		8.2.4	 Method Applicability
			8.2.4.1	 uNAC in Urine of Rats and Mice
			8.2.4.2	 uNAC in Patients with Kidney Disease
		8.2.5	 Statistical Analysis
	8.3	 Results and Discussion
		8.3.1	 Method Development
		8.3.2	 Method Description
			8.3.2.1	 Optimization of Reduction and Derivatization Steps
			8.3.2.2	 Optimization of Chromatographic Conditions
		8.3.3	 Method Validation
			8.3.3.1	 Selectivity and Carry-over Effect
			8.3.3.2	 Linearity
			8.3.3.3	 Lower and Higher Limits of Quantification
			8.3.3.4	 Accuracy
			8.3.3.5	 Intra- and Inter-assay Precision
			8.3.3.6	 Stability and Storage Conditions
			8.3.3.7	 Quantification of uNAC vs. Free NAC
		8.3.4	 Method Applicability
			8.3.4.1	 uNAC in Urine of Rats and Mice
			8.3.4.2	 uNAC in Patients with Kidney Disease
	8.4	 Conclusions
	References
9: Diagnosis of Fluorosis by Analysis of Fluoride Content in Body Fluids Using Ion Selective Electrode Method
	9.1	 Introduction
	9.2	 Materials and Method
		9.2.1	 First Method: Estimation of SA/GAG Ratio
		9.2.2	 Second Method: Estimation of F Levels in Body Fluids (Urine and Serum)
		9.2.3	 Details of ISE Method
			9.2.3.1	 Apparatus
	9.3	 Results
	9.4	 Discussion
	References
10: Dioctophimosis: A Parasitic Zoonosis of Public Health Importance
	10.1	 Introduction
	10.2	 Dioctophimosis in Domestic Animals
	10.3	 Dioctophimosis in Wild Animals
	10.4	 Dioctophimosis in Humans
	10.5	 Diagnostic
	10.6	 Conclusion
	References
Index