Table 2.
Table presenting data for exosomes.
| Biomarker | Purpose | Number of Patients | Method | Diagnostic Value | Prognostic Value | Predictive Capacity | Type of Study | Reference | |
|---|---|---|---|---|---|---|---|---|---|
| Exosome 2 (CD248, MT-ATP) | Diagnostic | n = 116 | Urine samples were collected from 116 patients and then expression of genes and functionality of exosomal RNAs were investigates by using single-cell mapper (scMappR). Data analysis performed with R package (version 3.0.2, R-project). | BCa detection | AUC = 0.898 | Retrospective | [24] | ||
| KLHDC7B | Diagnostic and prognostic | n = 180 (group 1 = 10 BCa, LG = 4, HG = 6; 10 HCs, group 2 = 80 BCa, LG = 35, HG = 45; 80 HCs) | Urine samples collected from 90 patients. Extraction of exosomes was conducted using a commercial kit (Norgen Biotek Corp., Thorold, Canada). Nanoparticle Tracking Analysis (NTA) was used to examine the size distribution and concentration of exosomes (ZetaView particle tracker, ZetaVIEW S/N 17-310, Particle Metrix, Germany). Extracted exosomes were imaged using a JEM-1400 transmission electron microscope (JEOL Inc., Peabody, MA, USA). Western Blot was performed using Western Chemiluminescent HRP Substrate (WBKLS0100). Urine Exosome RNA Isolation Kit (Norgen Biotek Corp, Product No. 47200, Thorold, Canada) was used to extract total exosome RNA, and then evaluated by a NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). RT-qPCR was performed using SYBR Premix Ex-Taq II (RR820A, Takara, Dalian, China). Data analysis performed using SPSS 24.0 software (IBM Corp., Armonk, NY, USA). | BCa detection | BCa progression | AUC = 0.842, PPV = 68.5%, NPV = 86.7%, Se. = 68.5%, Sp. = 88.3% | Retrospective | [25] | |
| CASP14 | AUC = 0.765, PPV = 80.3%, NPV = 64.7%, Se. = 77.5%, Sp. = 70.6% | ||||||||
| PRSS1 | AUC = 0.823, PPV = 60.3%, NPV = 87.5%, Se. = 78.1%, Sp. = 75.0% | ||||||||
| MIR205HG | AUC = 0.843, PPV = 56%, NPV = 88.7%, Se. = 77.3%, Sp. = 83.1% | ||||||||
| GAS5 | AUC = 0.729, PPV = 74.7%, NPV = 64.1%, Se. = 78.7%, Sp. = 60.3% | ||||||||
| A2M | Diagnostic and surveillance | n = 156 (discovery = 12; n = 24, LG = 3, HG = 3; verification = 24, LG = 0, HG = 18; validation = 120, LG = 20, HG = 75) | Urine protein and exosome was extracted from 156 participants urine. Prepared urinary peptides were analyzed using liquid chromatography-tandem mass spectrometry LC-MS/MS. MS raw files were processed in MaxQuant (v.1.5.3.1). Data-dependent acquisition (DDA) and data-independent acquisition (DIA) methods were conducted with an Ultimate 3000 UHPLC system (Dionex, Sunnyvale, CA, USA) coupled to a Q-Exactive Plus mass spectrometer (Thermo Fisher Scientific Inc., Waltham, MA, USA). | BCa detection | n/a | A2M AUC = 0.658 CFL1 AUC = 0.629 ITIH2 AUC = 0.759 Model 1(3 biomarkers) AUC = 0.845, PPV = 48.5%, NPV = 94.9%, Se. = 88.0%, Sp. = 81.3% |
Model 2 (All biomarkers) AUC = 0.842, PPV = 42.5%, NPV = 95.8%, Se. = 85.0%, Sp. = 74.7% |
Retrospective | [26] |
| CFL1 | |||||||||
| ITIH2 | |||||||||
| APOA1 | AUC = 0.702 | ||||||||
| AFM | AUC = 0.687 | ||||||||
| FGA | AUC = 0.612 | ||||||||
| CDC5L | AUC = 0.659 | ||||||||
| CD5L | AUC = 0.658 | ||||||||
| miRNA-96 | Diagnostic | n = 100 (study group = 72, NMIBC = 22, MIBC = 29; control group = 28) | Exosomes were isolated from urine of 100 patients before treatment using miRCURY Exosome Isolation Kit (Qiagen, Hilden, Germany). Extraction of total miRNA was performed with miRcute miRNA isolation kits (Tiangen biotech, Beijing, China). miScript Reverse Transcription Kit (Qiagen GmbH, Hilden, Germany) was used for reverse transcription and polyadenylation of the miRNA to complementary DNA (cDNA). Quantification of exosomal miRNA was performed with a Stratagene Mx3005P. Statistical analysis was performed using SPSS software (IBM Corp., Armonk, NY, USA). | BCa detection | AUC = 0.85, PPV = 91.1%, NPV = 81.8%, Se. = 80.4%, Sp. = 91.8% | Prospective | [27] | ||
| miRNA-183 | AUC = 0.83, PPV = 81.6%, NPV = 78.4%, Se. = 78.4%, Sp. = 81.6% | ||||||||
| miR-93-5p | Diagnostic | n = 120 (BCa = 12, NMIBC = 6, MIBC = 6; control group = 4; validation = 104, BCa = 53, control group = 51) | Exosomes were isolated from urine collected from 120 patients before treatment in an ultracentrifuge (Beckman Coulter, Miami, FL, USA). Exosomes were processed for nanoparticle tracking analysis (NTA) with NanoSight NS300 instrument (Malvern, UK). Total protein was extracted in RIPA lysis buffer (89,900, Thermo Fisher Scientific, Waltham, MA, USA). Total RNA was extracted with the Trizol Reagent (15,596,026, Invitrogen, Carlsbad, CA, USA). RNA was quantified and assessed by NanoDrop ND-2000 (Thermo Fisher Scientific, Waltham, MA, USA). miRNA expression was quantified using TaqMan single® microRNA assays (442,975, Applied Biosystems®, Foster City, CA, USA). qRT-PCR was performed with ABI 7300 Real-Time PCR System (Applied Biosystems, Foster City, CA, USA). Data analysis was peformed using R 3.5.1 (R Foundation for Statistical Computing, Vienna, Austria). |
BCa detection | AUC = 0.838, Se. = 74.1%, Sp. = 90.2% | retrospective | [28] | ||
| miR-516a-5p | AUC = 0.790, Se. = 72.9%, Sp. = 89.9% | ||||||||
| HSP90 | diagnostic | n = 81 (discovery phase: BCa = 7, NMIBC = 3, MIBC = 4; control group= 4; validation phase: BCa = 40, NMIBC = 20, MIBC = 20, control group = 30) | Urine samples were collected from 77 and BCa tissue samples from 47 patients. Proteis concentration of Te-EVs was measured using a Micro BCa protein assay kit (Thermo Fisher Scientific, Waltham, MA, USA). Proteins in urinary and tissue samples were separated using SDS-PAGE and transferred on to a polyvinylidene difluoride (Thermo Fisher Scientific, Waltham, MA, USA). The size and concentration of EVs were analyzed using NTA system (NanoSight). TEM was used to inspect the samples with JEM-1400Plus transmission electron microscope (JEOL Ltd., Tokyo, Japan). EVs were lysed using a MPEX PTS reagent kit (GL Science). TMT 10-plex system (Thermo Fisher Scientific, Waltham, MA, USA) was used for TMT-labeling. TMT-labeled peptides were alanyzed using a Q-Exactive Plus mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA) with an UltiMate 3000 Nano-flow high-performance LC system (Dionex, Sunnyvale, CA, USA) and an HTC-PAL autosampler (CTC Analytics, Zwingen, Switzerland). Data analysis was performed using JMP Pro software (v.14.0.0, SAS Institute, CARY, N.C, USA), and visualization quantification was performed using GraphPad Prism software (v.7.05; GraphPad Software, San Diego, CA, USA). | BCa detection | AUC = 0.813, Se. = 82.5%, Sp. = 70.0% | retrospective | [29] | ||
| SDC1 | AUC = 0.785, Se. = 82.5%, Sp. = 63.3% | ||||||||
| MARCKS | AUC = 0.772, Se. = 65%, Sp. = 80% | ||||||||
| MARCKSL | AUC = 0.757, | ||||||||
| TJP2 | AUC = 0.748 | ||||||||
| CD55 | AUC = 0.706 | ||||||||
| TERC | Diagnostic and prognostic | n = 128 (LG = 20, HG = 108) | Exosomes used for sequencing were isolated from urine using differential centrifugation. Exosomes used for validation were isolated from urine using exosome extraction kit (BestBio, Shanghai, China). TEM was performed to view and capture images (Thermo Fisher Scientific, Waltham, MA, USA). NanoSight LM10 system (Malvern Instruments LTD., Malvern, UK) was used to detect the concetration and size distribution of particles. Western blot was performed using anti-TSG101 (Abcam, Cambridge, UK), anti-HSP70, antiAnnexin V, and anti-CD9 (Cell Signaling Technology, Danvers, MA, USA). Second antibody antirabbiy IgG (Millipore, Burlington, MA, USA). RNA sequencing was performed using an Illumina Novaseq 6000 system (San Diego, CA, USA). qPCR was performed using TB Green Premix Ex Taq II (Tli RNaseH Plus, Takara, Dalian, Japan) on an Applied Biosystems 7300 real-time PCR system (Waltham, MA, USA). Data analysis perfomed with Graphpad Prism 8 (GraphPad Software Inc., Sand Diego, CA, USA) and MedCalc v.15.2.2 (MedCalc software Ltd., Ostend, Belgium). |
BCa detection | AUC = 0.836, Se. = 78.65%, Sp. = 77.78% | retrospective | [30] | ||
Abbreviations: AUC—Area under the ROC Curve, n—number of patients participating in study, HG—high grade, LG—low grade, BCa—bladder cancer, PCR—polymerase chain reaction, PPV—positive predictive value, qPCR—quantitative polymerase chain reaction, RT-qPCR—Real-time quantitative polymerase chain reaction NPV—negative predictive value, Se.—sensitivity, Sp.—specificity, CD248—Tumour Endothelial Marker 1, MT-ATP—Mitochondrially Encoded ATP Synthase Membrane Subunit 6, KLHDC7B—Kelch Domain-Containing Protein 7B, CASP14—Caspase 14, PRSS1—Serine Protease 1, MIR205HG—MIR205 Host Gene, GAS5—Growth Arrest Specific 5, A2M—Alpha-2-Macroglobulin, CFL1—Cofilin 1, APOA1—Apolipoprotein A1, ITIH2—Inter-Alpha-Trypsin Inhibitor Heavy Chain 2, AFM—Afamin, FGA—Fibrinogen Alpha Chain, CDC5L—Cell Division Cycle 5 Like, CD5L—CD5 Molecule Like, miR—microRNA, HSP90—Heat Shock Protein 90, SDC1—Syndecan 1, MARCKS—Myristoylated Alanine Rich Protein Kinase C Substrate, MARCKSL—MARCKS-related Protein, TJP2—Tight Junction Protein 2, CD55—Complement Decay-accelerating Factor, TERC—Telomerase RNA Component.