Differential protein profiling of renal cell carcinoma urinary exosomes

Application of exosomes as liquid biopsy in clinical diagnosis

Liquid biopsy refers to the sampling and molecular analysis of the biofluids of circulating tumor cells, extracellular vesicles, nucleic acids, and so forth. Exosomes are small extracellular vesicles with sizes between 30–150 nm. They are secreted by multivesicular bodies through exocytosis in live cells and can participate in intercellular communication due to their contents, including nucleic acids, proteins, and lipids. Herein, we investigate publication frequencies on exosomes over the past 10 years, and review recent clinical studies on liquid biopsy of exosomes in the fields of oncology, pregnancy disorders, cardiovascular diseases, and organ transplantation. We also describe the advantages of exosomes as an effective liquid biopsy tool and the progression of exosome extraction methods. Finally, we depict the commercial development of exosome research and discuss the future role of exosomes in liquid biopsy.

Proteomic approaches for characterizing renal cell carcinoma

Renal cell carcinoma is among the top 15 most commonly diagnosed cancers worldwide, comprising multiple sub-histologies with distinct genomic, proteomic, and clinicopathological features. Proteomic methodologies enable the detection and quantitation of protein profiles associated with the disease state and have been explored to delineate the dysregulated cellular processes associated with renal cell carcinoma. In this review we highlight the reports that employed proteomic technologies to characterize tissue, blood, and urine samples obtained from renal cell carcinoma patients. We describe the proteomic approaches utilized and relate the results of studies in the larger context of renal cell carcinoma biology. Moreover, we discuss some unmet clinical needs and how emerging proteomic approaches can seek to address them. There has been significant progress to characterize the molecular features of renal cell carcinoma; however, despite the large-scale studies that have characterized the genomic and transcriptomic profiles, curative treatments are still elusive. Proteomics facilitates a direct evaluation of the functional modules that drive pathobiology, and the resulting protein profiles would have applications in diagnostics, patient stratification, and identification of novel therapeutic interventions.

Urine biopsy technologies: Cancer and beyond

Since the discovery of circulating tumor cells in 1869, technological advances in the study of biomarkers from liquid biopsy have made it possible to diagnose disease in a less invasive way. Although blood-based liquid biopsy has been used extensively for the detection of solid tumors and immune diseases, the potential of urine-based liquid biopsy has not been fully explored. Advancements in technologies for the harvesting and analysis of biomarkers are providing new opportunities for the characterization of other disease types. Liquid biopsy markers such as exfoliated bladder cancer cells, cell-free DNA (cfDNA), and exosomes have the potential to change the nature of disease management and care, as they allow a cost-effective and convenient mode of patient monitoring throughout treatment. In this review, we addressed the advancement of research in the field of disease detection for the key liquid biopsy markers such as cancer cells, cfDNA, and exosomes, with an emphasis on urine-based liquid biopsy. First, we highlighted key technologies that were widely available and used extensively for clinical urine sample analysis. Next, we presented recent technological developments in cell and genetic research, with implications for the detection of other types of diseases, besides cancer. We then concluded with some discussions on these areas, emphasizing the role of microfluidics and artificial intelligence in advancing point-of-care applications. We believe that the benefits of urine biopsy provide diagnostic development potential, which will pave opportunities for new ways to guide treatment selections and facilitate precision disease therapies.

Prognostic significance of proteomics and multi-omics studies in renal carcinoma

INTRODUCTION

Renal carcinoma, and in particular its most common variant, the clear cell subtype, is often diagnosed incidentally through abdominal imaging and frequently, the tumor is discovered at an early stage. However, 20% to 40% of patients undergoing nephrectomy for clinically localized renal cancer, even after accurate histological and clinical classification, will develop metastasis or recurrence, justifying the associated mortality rate. Therefore, even if renal carcinoma is not among the most frequent nor deadly cancers, a better prognostication is needed.

AREAS COVERED

Recently proteomics or other omics combinations have been applied to both cancer tissues, on the neoplasia itself and surrounding microenvironment, cultured cells, and biological fluids (so-called liquid biopsy) generating a list of prognostic molecular tools that will be reviewed in the present paper.

EXPERT OPINION

Although promising, none of the approaches listed above has been yet translated in clinics. This is likely due to the peculiar genetic and phenotypic heterogeneity of this cancer, which makes nearly each tumor different from all the others. Attempts to overcome this issue will be also revised. In particular, we will discuss how the application of omics-integrated approaches could provide the determinants of response to the different targeted drugs.

Urinary Extracellular Vesicles and Salt-Losing Tubulopathies: A Proteomic Approach

Renal tubular cells release urinary extracellular vesicles (uEV) that are considered a promising source of molecular markers for renal dysfunction and injury. We investigated uEV proteomes of patients with hereditary salt-losing tubulopathies (SLTs), focusing on those caused by Gitelman and Bartter (BS) syndromes, to provide potential markers for differential diagnosis. Second morning urine was collected from patients with genetically proven SLTs and uEV were isolated by the ultracentrifugation-based protocol. The uEV proteome was run through a diagonal bidimensional electrophoresis (16BAC/SDS-PAGE), to improve hydrophobic protein resolution. Sixteen differential spots from the proteome of two variants (BS2 and BS3) were analysed by nLC-ESI-MS/MS after in-gel tryptic digestion. A total of 167 protein species were identified from 7 BS2 spots and 9 BS3 spot. Most of these proteins were membrane-associated proteins, in particular transmembrane proteins, and were related to typical renal functions. The differential content of some uEV was then validated by immunoblotting. Our work suggests that uEV proteomics represents a promising strategy for the identification of differential SLT proteins. This could play a role in understanding the pathophysiological disease mechanisms and may support the recognition of different syndromes.

Extracellular Vesicles in Renal Cell Carcinoma: Multifaceted Roles and Potential Applications Identified by Experimental and Computational Methods

Renal cell carcinoma (RCC) is the most common type of kidney cancer. Increasingly evidences indicate that extracellular vesicles (EVs) orchestrate multiple processes in tumorigenesis, metastasis, immune evasion, and drug response of RCC. EVs are lipid membrane-bound vesicles in nanometer size and secreted by almost all cell types into the extracellular milieu. A myriad of bioactive molecules such as RNA, DNA, protein, and lipid are able to be delivered via EVs for the intercellular communication. Hence, the abundant content of EVs is appealing reservoir for biomarker identification through computational analysis and experimental validation. EVs with excellent biocompatibility and biodistribution are natural platforms that can be engineered to offer achievable drug delivery strategies for RCC therapies. Moreover, the multifaceted roles of EVs in RCC progression also provide substantial targets and facilitate EVs-based drug discovery, which will be accelerated by using artificial intelligence approaches. In this review, we summarized the vital roles of EVs in occurrence, metastasis, immune evasion, and drug resistance of RCC. Furthermore, we also recapitulated and prospected the EVs-based potential applications in RCC, including biomarker identification, drug vehicle development as well as drug target discovery.

Oncogenic effects of RAB27B through exosome independent function in renal cell carcinoma including sunitinib-resistant

Exosomes are 40–100 nm nano-sized extracellular vesicles. They are released from many cell types and move into the extracellular space, thereby transferring their components to recipient cells. Exosomes are receiving increasing attention as novel structures participating in intracellular communication. RAB27B is one of the leading proteins involved in exosome secretion, and oncogenic effects have been reported in several cancers. In recent years, molecularly targeted agents typified by sunitinib are widely used for the treatment of metastatic or recurrent renal cell carcinoma (RCC). However, intrinsic or acquired resistance to sunitinib has become a major issue. The present study aimed to elucidate the role of RAB27B in RCC including sunitinib-resistant and its role in exosomes. Bioinformatic analyses revealed that high expression of RAB27B correlates with progression of RCC. The expression of RAB27B protein in RCC cell lines was significantly enhanced compared with that in normal kidney cell lines. Furthermore, RAB27B protein expression was enhanced in all of the tested sunitinib-resistant RCC cell lines compared to parental cells. Although no specific effect of RAB27B on exosomes was identified in RCC cells, loss-of-function studies demonstrated that knockdown of RAB27B suppressed cell proliferation, migration and invasive activities. Moreover, anti-tumor effects of RAB27B downregulation were also observed in sunitinib-resistant RCC cells. RNA sequence and pathway analysis suggested that the oncogenic effects of RAB27B might be associated with MAPK and VEGF signaling pathways. These results showed that RAB27B is a prognostic marker and a novel therapeutic target in sunitinib-sensitive and -resistant RCCs. Further analyses should improve our understanding of sunitinib resistance in RCC.

Extracellular vesicle-associated proteins as potential biomarkers

Every cell in the body secretes extracellular vesicles (EVs) possibly as cellular signaling components and these cell-derivatives can be found in multiple numbers in biological fluids. EVs have in the scientific field received great attention in relation to pathophysiology and disease diagnostics. Altered protein expressions associated with circulating EVs in diseased individuals can serve as biomarkers for different disease states. This capacity paves the way for non-invasive screening tools and early diagnostic markers. However, no isolation method of EVs has been acknowledged as the "golden standard," thus reproducibility of the studies remains inadequate. Increasing interest in EV proteins as disease biomarkers could give rise to more scientific knowledge with diagnostic applicability. In this chapter, studies of proteins believed to be associated with EVs within cancer, autoimmunity, metabolic and neurodegenerative diseases have been outlined.

Unravelling the proteomic landscape of extracellular vesicles in prostate cancer by density-based fractionation of urine

Extracellular vesicles (EV) are increasingly being recognized as important vehicles of intercellular communication and promising diagnostic and prognostic biomarkers in cancer. Despite this enormous clinical potential, the plethora of methods to separate EV from biofluids, providing material of highly variable purity, and lacking knowledge regarding methodological repeatability pose a barrier to clinical translation. Urine is considered an ideal proximal fluid for the study of EV in urological cancers due to its direct contact with the urogenital system. We demonstrate that density-based fractionation of urine by bottom-up Optiprep density gradient centrifugation separates EV and soluble proteins with high specificity and repeatability. Mass spectrometry-based proteomic analysis of urinary EV (uEV) in men with benign and malignant prostate disease allowed us to significantly expand the known human uEV proteome with high specificity and identifies a unique biological profile in prostate cancer not uncovered by the analysis of soluble proteins. In addition, profiling the proteome of EV separated from prostate tumour conditioned medium and matched uEV confirms the specificity of the identified uEV proteome for prostate cancer. Finally, a comparative proteomic analysis with uEV from patients with bladder and renal cancer provided additional evidence of the selective enrichment of protein signatures in uEV reflecting their respective cancer tissues of origin. In conclusion, this study identifies hundreds of previously undetected proteins in uEV of prostate cancer patients and provides a powerful toolbox to map uEV content and contaminants ultimately allowing biomarker discovery in urological cancers.

Roles for Exosome in Various Kidney Diseases and Disorders

Exosome is a nanoscale vesicle with a size range of 30–100 nm. It is secreted from cell to extracellular space by exocytosis after fusion of multivesicular body (MVB) (formed by endocytic vesicles) with plasma membrane. Exosome plays several important roles in cellular homeostasis and intercellular communications. During the last two decades, exosome has acquired a wide attention to explore its additional roles in various aspects of cell biology and function in several organ systems. For the kidney, several lines of evidence have demonstrated 1that exosome is involved in the renal physiology and pathogenic mechanisms of various kidney diseases/disorders. This article summarizes roles of the exosome as the potential source of biomarkers, pathogenic molecules, and therapeutic biologics that have been extensively investigated in many kidney diseases/disorders, including lupus nephritis (LN), other glomerular diseases, acute kidney injury (AKI), diabetic nephropathy (DN), as well as in the process of renal fibrosis and chronic kidney disease (CKD) progression, in addition to polycystic kidney disease (PKD), kidney transplantation, and renal cell carcinoma (RCC). Moreover, the most recent evidence has shown its emerging role in kidney stone disease (or nephrolithiasis), involving inflammasome activation and inflammatory cascade frequently found in kidney stone pathogenesis.

In-Depth Mapping of the Urinary N-Glycoproteome: Distinct Signatures of ccRCC-related Progression

Protein N-glycosylation is one of the most important post-translational modifications and is involved in many biological processes, with aberrant changes in protein N-glycosylation patterns being closely associated with several diseases, including the progression and spreading of tumours. In light of this, identifying these aberrant protein glycoforms in tumours could be useful for understanding the molecular mechanism of this multifactorial disease, developing specific biomarkers and finding novel therapeutic targets. We investigated the urinary N-glycoproteome of clear cell renal cell carcinoma (ccRCC) patients at different stages (n = 15 at pT1 and n = 15 at pT3), and of non-ccRCC subjects (n = 15), using an N-glyco-FASP-based method. Using label-free nLC-ESI MS/MS, we identified and quantified several N-glycoproteins with altered expression and abnormal changes affecting the occupancy of the glycosylation site in the urine of RCC patients compared to control. In particular, nine of them had a specific trend that was directly related to the stage progression: CD97, COCH and P3IP1 were up-expressed whilst APOB, FINC, CERU, CFAH, HPT and PLTP were down-expressed in ccRCC patients. Overall, these results expand our knowledge related to the role of this post-translational modification in ccRCC and translation of this information into pre-clinical studies could have a significant impact on the discovery of novel biomarkers and therapeutic target in kidney cancer.

Extracellular vesicles in urological malignancies: an update

Extracellular vesicles (EVs) have an essential functional role in local tumour progression, metastatic spread and the emergence of drug resistance in bladder, kidney and prostate cancer. Thus, EVs could be diagnostic, prognostic and predictive biomarkers for these malignancies. Virtually all biomolecules (including DNA, mRNA, microRNA, long non-coding RNA, proteins and lipids) packaged into EVs have been tested as biomarkers in blood and urine samples. The results are very heterogeneous, but promising biomarker candidates have been identified. Differing methods of EV isolation, characterization and analysis of their content have been used owing to a lack of international consensus; hence, comparing study results is challenging. Furthermore, validation of potential biomarkers in independent cohorts or prospective trials has rarely been performed. Future efforts to establish EV-derived biomarkers need to adequately address these points. In addition, emerging technologies such as mass spectroscopy and chip-based approaches can identify surface markers specific for cancer-associated EVs and will enable specific separation from blood and urine EVs, which probably will improve their performance as biomarkers. Moreover, EVs could be harnessed as therapeutic drug delivery vehicles for precise and effective anticancer therapy.

Extracellular vesicles in urologic malignancies-Implementations for future cancer care

Extracellular vesicles (EVs), a heterogeneous group of vesicles differing in size and shape, cargo content and function, are membrane-bound and nano-sized vesicles that could be released by nearly all variations of cells. EVs have gained considerable attention in the past decades for their functions in modulating intercellular signalling and roles as potential pools for the novel diagnostic and prognostic biomarkers, as well as therapeutic targets in several cancers including urological neoplasms. In general, human and animal cells both can release distinct types of EVs, including exosomes, microvesicles, oncosomes and large oncosomes, and apoptotic bodies, while the content of EVs can be divided into proteins, lipids and nucleic acids. However, the lack of standard methods for isolation and detection platforms rein the widespread usage in clinical applications warranted furthermore investigations in the development of reliable, specific and sensitive isolation techniques. Whether and how the EVs work has become pertinent issues. With the aid of high-throughput proteomics or genomics methods, a fully understanding of contents contained in EVs from urogenital tumours, beyond all doubt, will improve our ability to identify the complex genomic alterations in the process of cancer and, in turn, contribute to detect potential therapeutic target and then provide personalization strategy for patient.

Exploring the key communicator role of exosomes in cancer microenvironment through proteomics

There have been many attempts to fully understand the mechanism of cancer behavior. Yet, how cancers develop and metastasize still remain elusive. Emerging concepts of cancer biology in recent years have focused on the communication of cancer with its microenvironment, since cancer cannot grow and live alone. Cancer needs to communicate with other cells for survival, and thus they secrete various messengers, including exosomes that contain many proteins, miRNAs, mRNAs, etc., for construction of the tumor microenvironment. Moreover, these intercellular communications between cancer and its microenvironment, including stromal cells or distant cells, can promote tumor growth, metastasis, and escape from immune surveillance. In this review, we summarized the role of proteins in the exosome as communicators between cancer and its microenvironment. Consequently, we present cancer specific exosome proteins and their unique roles in the interaction between cancer and its microenvironment. Clinically, these exosomes might provide useful biomarkers for cancer diagnosis and therapeutic tools for cancer treatment.

The SOD Mimic MnTnHex-2-PyP5+ Reduces the Viability and Migration of 786-O Human Renal Cancer Cells

Clear-cell renal carcinoma (ccRCC) is the most common type of renal cancer. The importance of oxidative stress in the context of this disease has been described, although there is only little information concerning the role of superoxide dismutase (SOD) enzymes. The importance of SOD in different pathological conditions promoted the development of SOD mimics (SODm). As such, manganese(III) porphyrins can mimic the natural SOD enzymes and scavenge different reactive oxygen species (ROS), thus modulating the cellular redox status. In this study, the exposure of 786-O human renal cancer cells to MnTnHex-2-PyP⁵⁺ (MnP), a very promising SODm, led to a concentration and time-dependent decrease in cell viability and in the cell proliferation indices, as well as to an increase in apoptosis. No relevant effects in terms of micronuclei formation were observed. Moreover, the exposure to MnP resulted in a concentration-dependent increase in intracellular ROS, presumably due to the generation of H₂O₂ by the inherent redox mechanisms of MnP, along with the limited ability of cancer cells to detoxify this species. Although the MnP treatment did not result in a reduction in the collective cell migration, a significant decrease in chemotactic migration was observed. Overall, these results suggest that MnP has a beneficial impact on reducing renal cancer cell viability and migration and warrant further studies regarding SODm-based therapeutic strategies against human renal cancer.

Emerging role of exosomes as promising diagnostic tool for cancer

The incidence of cancer is experiencing a steep rise in recent times. A survey report produced by GLOBOCAN 2018 estimates about 18.1 million new cases of cancer across 20 regions of the world. The bewildering number of people afflicted with cancer demands rapid diagnosis and treatment strategy. The current methods used for diagnosis of cancer are expensive, invasive, and time consuming. Hence, a new diagnostic panel has to be laid down to make the process less invasive, cost-effective, and rapid. A venture into identifying potential diagnostic targets introduced exosomes to the scientific community. A plethora of roles being packed into these biological cargoes makes them attractive targets for both therapeutic and diagnostic applications. Exosomes are membrane-bound extracellular vesicles packed with DNA, RNA, and proteins. Their presence in a wide array of body fluids such as breast milk, blood plasma, saliva, urine, serum, and cerebrospinal fluid makes them an excellent source of potential biomarkers. These nano-scale structures are capable of crossing hypoxic regions, systemic circulation and the territories of blood vessel barriers. In line with the above facts, the present review focuses on the therapeutic and diagnostic applications of exosomes in cancer.

In human nephrectomy specimens, the kidney level of tubular transport proteins does not correlate with their abundance in urinary extracellular vesicles

Human urinary extracellular vesicles (uEVs) contain proteins from all nephron segments. An assumption for years has been that uEVs might provide a noninvasive liquid biopsy that reflect physiological regulation of transporter protein expression in humans. We hypothesized that protein abundance in human kidney tissue and uEVs are directly related and tested this in paired collections of nephrectomy tissue and urine sample from 12 patients. Kidney tissue was fractioned into total kidney protein, crude membrane (plasma membrane and large intracellular vesicles)-enriched, and intracellular vesicle-enriched fractions as well as sections for immunolabeling. uEVs were isolated from spot urine samples. Antibodies were used to quantify six segment-specific proteins [proximal tubule-expressed Na+-phosphate cotransporters (NaPi-2a), thick ascending limb-expressed Tamm-Horsfall protein and renal outer medullary K+ channels, distal convoluted tubule-expressed NaCl cotransporters, intercalated cell-expressed V-type H+-ATPase subunit G3 (ATP6V1G3), and principal cell-expressed aquaporin 2] and three uEV markers (exosomal CD63, microvesicle marker vesicle‐associated membrane protein 3, and β-actin) in each fraction. By Western blot analysis and immunofluorescence labeling, we found significant positive correlations between the abundance of CD63, NaCl cotransporters, aquaporin 2, and ATP6V1G3, respectively, within the different kidney-derived fractions. We detected all nine proteins in uEVs, but their level did not correlate with kidney tissue protein abundance. uEV protein levels showed higher interpatient variability than kidney-derived fractions, indicating that factors, besides kidney protein abundance, contribute to the uEV protein level. Our data suggest that, in a random sample of nephrectomy patients, uEV protein level is not a predictor of kidney protein abundance.

A review on protein markers of exosome from different bio-resources and the antibodies used for characterization

Exosomes are small membrane vesicles (ranging from 30 nm to 150 nm), secreted by different cell types upon fusion of multivesicular bodies (MVB) to the cell plasma membrane under a variety of normal and pathological conditions. Through transferring their cargos such as proteins, lipids and nucleic acids from donor cells to recipient cells, exosomes play a crucial role in cell-to-cell communication. Due to their presence in most body fluids (such as blood, breast milk, saliva, urine, bile, pancreatic juice, cerebrospinal and peritoneal fluids), and their role in carrying bioactive molecules from the cells of origin, exosomes have attracted great interest in their diagnostic and prognostic value for various diseases and therapeutic approaches. Although a large body of literature has documented the importance of exosomes over the past decade, there is no article systematically summarizing protein markers of exosome from different resources and the antibodies that are suited to characterize exosomes. In this review, we briefly summarize the exosome marker proteins, exosomal biomarkers for different diseases, and the antibodies suitable for different bio-resources exosomes characterization.

Exosomes on the border of species and kingdom intercommunication

Over the last decades exosomes have become increasingly popular in the field of medicine. While until recently they were believed to be involved in the removal of obsolete particles from the cell, it is now known that exosomes are key players in cellular communication, carrying source-specific molecules such as proteins, growth factors, miRNA/mRNA, among others. The discovery that exosomes are not bound to intraspecies interactions, but are also capable of interkingdom communication, has once again revolutionized the field of exosomes research. A rapidly growing body of literature is shedding light at novel sources and participation of exosomes in physiological or regenerative processes, infection and disease. For the purpose of this review we have categorized 6 sources of interest (animal products, body fluids, plants, bacteria, fungus and parasites) and linked their innate roles to the clinics and potential medical applications, such as cell-based therapy, diagnostics or drug delivery.

Proteomic analysis of urinary extracellular vesicles reveal biomarkers for neurologic disease

Background

Extracellular vesicles (EVs) harbor thousands of proteins that hold promise for biomarker development. Usually difficult to purify, EVs in urine are relatively easily obtained and have demonstrated efficacy for kidney disease prediction. Herein, we further characterize the proteome of urinary EVs to explore the potential for biomarkers unrelated to kidney dysfunction, focusing on Parkinson's disease (PD).

Methods

Using a quantitative mass spectrometry approach, we measured urinary EV proteins from a discovery cohort of 50 subjects. EVs in urine were classified into subgroups and EV proteins were ranked by abundance and variability over time. Enriched pathways and ontologies in stable EV proteins were identified and proteins that predict PD were further measured in a cohort of 108 subjects.

Findings

Hundreds of commonly expressed urinary EV proteins with stable expression over time were distinguished from proteins with high variability. Bioinformatic analyses reveal a striking enrichment of endolysosomal proteins linked to Parkinson's, Alzheimer's, and Huntington's disease. Tissue and biofluid enrichment analyses show broad representation of EVs from across the body without bias towards kidney or urine proteins. Among the proteins linked to neurological diseases, SNAP23 and calbindin were the most elevated in PD cases with 86% prediction success for disease diagnosis in the discovery cohort and 76% prediction success in the replication cohort.

Interpretation

Urinary EVs are an underutilized but highly accessible resource for biomarker discovery with particular promise for neurological diseases like PD.

Extracellular Vesicles and Their Potential Use in Monitoring Cancer Progression and Therapy: The Contribution of Proteomics

Extracellular Vesicles (EVs) are small membrane-enclosed particles released by cells and able to vehiculate information between them. The term EVs categorizes many and different vesicles based on their biogenesis and release pathway, such as exosomes (Exo), ectosomes, or shedding microvesicles (SMVs), apoptotic blebs (ABs), and other EVs subsets, generating a heterogeneous group of components able to redistribute their cargo into the entire organism. Moreover EVs are becoming increasingly important in monitoring cancer progression and therapy, since they are able to carry specific disease biomarkers such as Glypican-1, colon cancer-associated transcript 2, CD63, CD24, and many others. The importance of their biological role together with their heterogeneity prompted researchers to adopt and standardize purification methods able to isolate EVs for characterizing their cargo. In this way, mass spectrometry (MS)-based proteomics approaches are emerging as promising tool for the identification and quantification of EVs protein cargoes, but this technique resulted to be deeply influenced by the low quality of the isolation techniques. This review presents the state-of-the-art of EVs isolation, purification, and characterization for omics studies, with a particular focus to their potential use in monitoring cancer progression and therapy.

Extracellular vesicles in renal physiology and clinical applications for renal disease

Many cells in the nephron release extracellular vesicles (EVs). EVs envelop nucleic acids, proteins, and lipids. The surfaces of EVs express donor cell-specific markers, ligands, and major histocompatibility complex molecules. They are involved in cell-to-cell communication, immune modulation, and the removal of unwanted materials from cells. EVs have been studied as biomarkers of specific diseases and have potential therapeutic applications. Recent research has emphasized the functions of EVs in the kidney. This review provides an overview of recent findings related to the roles of EVs in the nephron, and their utility as biomarkers and therapeutic factors in renal disease.

Urinary exosomal shuttle RNA: Promising cancer diagnosis biomarkers of lower urinary tract

BACKGROUND

Prostate and bladder cancers continue to be the first and fourth most common cancers in men worldwide; thus there is an urgent need for more accurate biomarkers that can detect these types of cancer in a non-invasive way. Liquid biopsy is a new non-invasive tool for diagnosis and with a virtually unlimited supply urine is even more attractive resource since urinary exosomes have been discovered to contain RNAs that are hallmarks of cancer. It is challenging to assay those secreting lower amounts of molecules.

METHODS

This review, based on articles identified through a PubMed/MEDLINE search, comprehensively summarizes state of the art approaches used in the discovery and validation of exosomal RNA biomarkers purified from the urine for lower urinary tract cancer.

RESULTS

The combination of PCA3 and ERG has shown a relatively good improvement in diagnostic performance; examples of other potential biomarkers and the methods utilized in their discovery are also discussed in this review.

CONCLUSIONS

Of these last markers, to date there are still few data to implement these for routine diagnosis.

Extracellular Vesicles: Mechanisms in Human Health and Disease

SIGNIFICANCE

Secreted extracellular vesicles (EVs) are now considered veritable entities for diagnosis, prognosis, and therapeutics. These structures are able to interact with target cells and modify their phenotype and function. Recent Advances: Since composition of EVs depends on the cell type of origin and the stimulation that leads to their release, the analysis of EV content remains an important input to understand the potential effects of EVs on target cells.

CRITICAL ISSUES

Here, we review recent data related to the mechanisms involved in the formation of EVs and the methods allowing specific EV isolation and identification. Also, we analyze the potential use of EVs as biomarkers in different pathologies such as diabetes, obesity, atherosclerosis, neurodegenerative diseases, and cancer. Besides, their role in these diseases is discussed. Finally, we consider EVs enriched in microRNA or drugs as potential therapeutic cargo able to deliver desirable information to target cells/tissues.

FUTURE DIRECTIONS

We underline the importance of the homogenization of the parameters of isolation of EVs and their characterization, which allow considering EVs as excellent biomarkers for diagnosis and prognosis.

Proteomic Analysis of Extracellular Vesicles for Cancer Diagnostics

Extracellular vesicles (EVs) including exosomes and microvesicles are lipid bilayer-encapsulated nanoparticles released by cells, ranging from 40 nm to several microns in diameter. Biological cargoes including proteins, RNAs, and DNAs can be ferried by EVs to neighboring and distant cells via biofluids, serving as a means of cell-to-cell communication under normal and pathological conditions, especially cancers. On the other hand, EVs have been investigated as a novel "information capsule" for early disease detection and monitoring via liquid biopsy. This review summarizes current advancements in EV subtype characterization, cancer EV capture, proteomic analysis technologies, as well as possible EV-based multiomics for cancer diagnostics.

Tumor-Derived Extracellular Vesicles as a Novel Source of Protein Biomarkers for Cancer Diagnosis and Monitoring

"Liquid biopsies" have received attention as a complementary tool for traditional tissue biopsies that may enhance the spectrum of analysis for tumor-derived factors. One such factor gaining prominence in the liquid biopsy field is extracellular vesicles (EVs), membrane-bound nanovesicles which are secreted by cells into biofluids such as blood, urine, and saliva. EVs are released in both physiological and pathological conditions and can transport a variety of molecules, including proteins, metabolites, RNA, microRNAs, and DNA, to distant sites throughout the body. As such, they are emerging as a promising source of tumor biomarkers for the noninvasive diagnosis, prognosis, and monitoring of cancer patients. In particular, the wealth of tumor-related information that can be gleaned from the EV proteomic cargo has become apparent through mass spectrometric analysis, which has provided new benchmarks for clinically focused biomarker research. In this review, the current achievements in the use of MS for identifying potential EV-derived protein biomarkers of cancer are explored, and the techniques and challenges involved in this pursuit are summarized.

Exosomes for Non-Invasive Cancer Monitoring

Exosomes, membrane-bound phospholipid vesicles having diameters of 50-200 nm, are secreted by all cell types and circulate in human body fluids. These vesicles are known to carry cellular constituents that are specific to the originating cells (e.g., cytoplasmic/membrane proteins, RNA, and DNA). Thus, exosomes, which are both structurally stable and abundant, are robust indicators of cancers and, as a result, they have been utilized to monitor this disease in a manner that is less invasive than gold standard tissue biopsies. In this review, the history of exosomes and the specific biomarkers present in exosomes that enable accurate monitoring of various diseases are described. In addition, methods for analysis of exosomes and identification of biomarkers are presented with special emphasis being given to isolation and signaling strategies. Lastly, integrated, microfluidic systems developed for exosome-based cancer diagnosis are described and future directions that research in this area will likely take are presented.

Urinary proteomic biomarkers in oncology: ready for implementation?

Introduction: Biomarkers are expected to improve the management of cancer patients by enabling early detection and prediction of therapeutic response. Proteins reflect a molecular phenotype, have high potential as biomarkers, and also are key targets for intervention. Given the ease of collection and proximity to certain tumors, the urinary proteome is a rich source of biomarkers and several proteins have been already implemented. Areas covered: We examined the literature on urine proteins and proteome analysis in oncology from reports published during the last 5 years to generate an overview on the status of urine protein and peptide biomarkers, with emphasis on their actual clinical value. Expert commentary: A few studies report on biomarkers that are ready to be implemented in patient management, among others in bladder cancer and cholangiocarcinoma. These reports are based on multi-marker approaches. A high number of biomarkers, though, has been described in studies with low statistical power. In fact, several of them have been consistently reported across different studies. The latter should be the focus of attention and be tested in properly designed confirmatory and ultimately, prospective investigations. It is expected that multi-marker classifiers for a specific context-of-use, will be the preferred path toward clinical implementation.

Recent Progress in Isolation and Detection of Extracellular Vesicles for Cancer Diagnostics

Extracellular vesicles (EVs) are emerging as one of the many new and promising biomarkers for liquid biopsy of cancer due to their loading capability of some specific proteins and nucleic acids that are closely associated with cancer states. As such, the isolation and detection of cancer-derived EVs offer important information in noninvasive diagnosis of early-stage cancer and real-time monitoring of cancer development. In light of the importance of EVs, over the last decade, researchers have made remarkable innovations to advance the development of EV isolation and detection methods by taking advantage of microfluidics, biomolecule probes, nanomaterials, surface plasmon, optics, and so on. This review introduces the basic properties of EVs and common cancer-derived EV ingredients, and provides a comprehensive overview of EV isolation and detection strategies, with emphasis on liquid biopsies of EVs for cancer diagnostics.

Circulating Tumor Cells for the Management of Renal Cell Carcinoma

Renal cell carcinoma is a highly malignant cancer that would benefit from non-invasive innovative markers providing early diagnosis and recurrence detection. Circulating tumor cells are a particularly promising marker of tumor invasion that could be used to improve the management of patients with RCC. However, the extensive genetic and immunophenotypic heterogeneity of cells from RCC and their trend to transition to the mesenchymal phenotype when they circulate in blood constitute a challenge for their sensitive and specific detection. This review analyzes published studies targeting CTC in patients with RCC, in the context of the biological, pathological, and molecular complexity of this particular cancer. Although further analytical and clinical studies are needed to pinpoint the most suitable approach for highly sensitive CTC detection in RCC patients, it is clear that this field can bring a relevant guide to clinicians and help to RCC patients. Furthermore, as described, a particular subtype of RCC-the ccRCC-can be used as a model to study the relationship between cytomorphological and genetic cellular markers of malignancy, an important issue for the study of CTC from any type of solid cancer.

Immune Modulation by Human Secreted RNases at the Extracellular Space

The ribonuclease A superfamily is a vertebrate-specific family of proteins that encompasses eight functional members in humans. The proteins are secreted by diverse innate immune cells, from blood cells to epithelial cells and their levels in our body fluids correlate with infection and inflammation processes. Recent studies ascribe a prominent role to secretory RNases in the extracellular space. Extracellular RNases endowed with immuno-modulatory and antimicrobial properties can participate in a wide variety of host defense tasks, from performing cellular housekeeping to maintaining body fluid sterility. Their expression and secretion are induced in response to a variety of injury stimuli. The secreted proteins can target damaged cells and facilitate their removal from the focus of infection or inflammation. Following tissue damage, RNases can participate in clearing RNA from cellular debris or work as signaling molecules to regulate the host response and contribute to tissue remodeling and repair. We provide here an overall perspective on the current knowledge of human RNases’ biological properties and their role in health and disease. The review also includes a brief description of other vertebrate family members and unrelated extracellular RNases that share common mechanisms of action. A better knowledge of RNase mechanism of actions and an understanding of their physiological roles should facilitate the development of novel therapeutics.

Extracellular vesicles: Toward a clinical application in urological cancer treatment

Extracellular vesicles are nanometer-sized lipid membranous vesicles that are released from almost all types of cells into the extracellular space. Extracellular vesicles have gained considerable attention in the past decade, and emerging evidence suggests that they play novel roles in mediating cancer biology. Extracellular vesicles contain pathogenic components, such as proteins, DNA fragments, messenger ribonucleic acids, non-coding ribonucleic acids and lipids, all of which mediate paracrine signaling in the tumor microenvironment. Extracellular vesicles impact the multistep process of cancer progression through modulation of the immune system, angiogenesis and pre-metastatic niche formation through transfer of their contents. Therefore, a better understanding of their roles in urological cancers will provide opportunities for novel therapeutic strategies. In addition, the contents of extracellular vesicles hold promise for the discovery of liquid-based biomarkers for prostate, kidney and bladder cancers. Here, we summarize the current research regarding extracellular vesicles in urological cancer and discuss potential clinical applications for extracellular vesicles in urological cancer.

Urinary extracellular vesicle biomarkers in urological cancers: From discovery towards clinical implementation

Urine contains cellular elements, biochemicals, and proteins derived from glomerular filtration of plasma, renal tubule excretion, and urogenital tract secretions that reflect an individual's metabolic and pathophysiologic state. Despite intensive research into the discovery of urinary biomarkers to facilitate early diagnosis, accurate prognosis and prediction of therapy response in urological cancers, none of these markers has reached widespread use. Their implementation into daily clinical practice is hampered by a substantial degree of heterogeneity in performance characteristics and uncertainty about reliability, clinical utility and cost-effectiveness, in addition to several technical limitations. Extracellular vesicles (EV) have raised interest as a potential source of biomarker discovery because of their role in intercellular communication and the resemblance of their molecular content to that of the releasing cells. We review currently used urinary biomarkers in the clinic and attempts that have been made to identify EV-derived biomarkers for urological cancers. In addition, we discuss technical and methodological considerations towards their clinical implementation.

Urine Proteome Profiling Predicts Lung Cancer from Control Cases and Other Tumors

Development of noninvasive, reliable biomarkers for lung cancer diagnosis has many clinical benefits knowing that most of lung cancer patients are diagnosed at the late stage. For this purpose, we conducted proteomic analyses of 231 human urine samples in healthy individuals (n = 33), benign pulmonary diseases (n = 40), lung cancer (n = 33), bladder cancer (n = 17), cervical cancer (n = 25), colorectal cancer (n = 22), esophageal cancer (n = 14), and gastric cancer (n = 47) patients collected from multiple medical centers. By random forest modeling, we nominated a list of urine proteins that could separate lung cancers from other cases. With a feature selection algorithm, we selected a panel of five urinary biomarkers (FTL: Ferritin light chain; MAPK1IP1L: Mitogen-Activated Protein Kinase 1 Interacting Protein 1 Like; FGB: Fibrinogen Beta Chain; RAB33B: RAB33B, Member RAS Oncogene Family; RAB15: RAB15, Member RAS Oncogene Family) and established a combinatorial model that can correctly classify the majority of lung cancer cases both in the training set (n = 46) and the test sets (n = 14–47 per set) with an AUC ranging from 0.8747 to 0.9853. A combination of five urinary biomarkers not only discriminates lung cancer patients from control groups but also differentiates lung cancer from other common tumors. The biomarker panel and the predictive model, when validated by more samples in a multi-center setting, may be used as an auxiliary diagnostic tool along with imaging technology for lung cancer detection.

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A case-control study of biomarker discovery for lung cancer diagnosis was conducted.

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Human urine profiles in control cases and cancers were characterized.

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A list of candidate biomarkers was nominated and evaluated.

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A panel of urinary biomarkers was established and tumor-specificity was evaluated.

Cancer diagnosis with a noninvasive method at the early stage of the disease is highly desirable. Here, we analyzed hundreds of human urine samples from healthy individuals, patients with benign pulmonary diseases, and 6 types of cancers by proteomics and developed a panel of five urinary proteins that can separate the lung cancer from benign pulmonary diseases as well as the other 5 cancers (bladder, cervical, colorectal, esophageal and gastric) with a good sensitivity and disease specificity. Further validation experiments with expanded sample numbers are required to investigate whether this method can be applied in a clinical setting for the diagnosis of lung cancer.

Liquid Biopsy: From Basic Research to Clinical Practice

Liquid biopsy refers to the molecular analysis in biological fluids of nucleic acids, subcellular structures, especially exosomes, and, in the context of cancer, circulating tumor cells. In the last 10 years, there has been an intensive research in liquid biopsy to achieve a less invasive and more precise personalized medicine. Molecular assessment of these circulating biomarkers can complement or even surrogate tissue biopsy. Because of this research, liquid biopsy has been introduced in clinical practice, especially in oncology, prenatal screening, and transplantation. Here we review the biology, methodological approaches, and clinical applications of the main biomarkers involved in liquid biopsy.

Role of exosomal proteins in cancer diagnosis

Exosomes are emerging as a new type of cancer biomarkers. Exosome is a bilayered nano-sized vesicle secreted by various living cells in all body fluids. Based on the expanding albeit incomplete knowledge of their biogenesis, secretion by cells and cancer cell-specific molecular and genetic contents, exosomes are viewed as promising, clinically-relevant surrogates of cancer progression and response to therapy. Preliminary proteomic, genetic and functional profiling of cancer cell-derived or cancer plasma-derived exosomes confirms their unique characteristics. Alterations in protein or nucleic acid profiles of exosomes in plasma correlate with pathological processes of many diseases including cancer. However, previous studies on exosome application in cancer diagnosis and treatment mainly focussed on miRNAs. With the development of rapid large-scale production, purification, extraction and screening of exosomal contents, exosomal protein application can be explored for early stage cancer diagnosis, monitoring and prognosis evaluation. Here, we summarized the recent developments in application of exosomal proteins for cancer diagnosis.

Emerging MS-based platforms for the characterization of tumor-derived exosomes isolated from human biofluids: challenges and promises of MudPIT

INTRODUCTION

Exosomes are small extracellular vesicles of endosomal origin that are produced and released by several type of cells. These vesicles contain different macromolecules: proteins, mRNA, miRNA, mitochondrial DNA, and lipids. Exosomes play an important role in cell-to-cell communication, also promoting cancer progression. Areas covered: Various proteomic approaches have been applied to study exosomes isolated from different human biofluids in search of possible cancer biomarkers. The results of these studies are reported, and pros and cons of each employed technique are described. Gel-free and gel-based mass spectrometry systems are discussed, giving particular emphasis on the innovative multidimensional protein identification technology (MudPIT). Expert commentary: Proteomic studies on exosomes as candidate cancer biomarkers from urine and other body fluids in cancer have shown the potential of MS-based techniques. In particular, MudPIT is a promising tool to be applied in clinical proteomics of cancer.

Proteomic analysis of exosomal cargo: the challenge of high purity vesicle isolation

The re-discovery of exosomes as intercellular messengers with high potential for diagnostic and therapeutic utility has led to them becoming a popular topic of research in recent years. One of the essential research areas in this field is the characterization of exosomal cargo, which includes numerous non-randomly packed proteins and nucleic acids. Unexpectedly, a very challenging aspect of exploration of extracellular vesicles has turned out to be their effective and selective isolation. The plurality of developed protocols leads to qualitative and quantitative variability in terms of the obtained exosomes, which significantly affects the results of downstream analyses and makes them difficult to compare, reproduce and interpret between research groups. Currently, there is a general consensus among the exosome-oriented community concerning the urgent need for the optimization and standardization of methods employed for the purification of these vesicles. Hence, we review here several strategies for exosome preparation including ultracentrifugation, chemical precipitation, affinity capturing and filtration techniques. The advantages and disadvantages of different approaches are discussed with special emphasis being placed on their adequacy for proteomics applications, which are particularly sensitive to sample quality. We conclude that certain methods, exemplified by ultracentrifugation combined with iodixanol density gradient centrifugation or gel filtration, although labor-intensive, provide superior quality exosome preparations suitable for reliable analysis by mass spectrometry.

Extracellular Vesicles in Renal Pathophysiology

Extracellular vesicles are a heterogeneous population of microparticles released by virtually all living cells which have been recently widely investigated in different biological fields. They are typically composed of two primary types (exosomes and microvesicles) and are recently commanding increasing attention as mediators of cellular signaling. Indeed, these vesicles can affect recipient cells by carrying and delivering complex cargos of biomolecules (including proteins, lipids and nucleic acids), protected from enzymatic degradation in the environment. Their importance has been demonstrated in the pathophysiology of several organs, in particular in kidney, where different cell types secrete extracellular vesicles that mediate their communication with downstream urinary tract cells. Over the past few years, evidence has been shown that vesicles participate in kidney development and normal physiology. Moreover, EVs are widely demonstrated to be implicated in cellular signaling during renal regenerative and pathological processes. Although many EV mechanisms are still poorly understood, in particular in kidney, the discovery of their role could help to shed light on renal biological processes which are so far elusive. Lastly, extracellular vesicles secreted by renal cells gather in urine, thus becoming a great resource for disease or recovery markers and a promising non-invasive diagnostic instrument for renal disease. In the present review, we discuss the most recent findings on the role of extracellular vesicles in renal physiopathology and their potential implication in diagnosis and therapy.

Confounding factors of ultrafiltration and protein analysis in extracellular vesicle research

Identification and validation of extracellular vesicle (EV)-associated biomarkers requires robust isolation and characterization protocols. We assessed the impact of some commonly implemented pre-analytical, analytical and post-analytical variables in EV research. Centrifugal filters with different membrane types and pore sizes are used to reduce large volume biofluids prior to EV isolation or to concentrate EVs. We compared five commonly reported filters for their efficiency when using plasma, urine and EV-spiked PBS. Regenerated cellulose membranes with pore size of 10 kDa recovered EVs the most efficient. Less than 40% recovery was achieved with other filters. Next, we analyzed the effect of the type of protein assays to measure EV protein in colorimetric and fluorometric kits. The fluorometric assay Qubit measured low concentration EV and BSA samples the most accurately with the lowest variation among technical and biological replicates. Lastly, we quantified Optiprep remnants in EV samples from density gradient ultracentrifugation and demonstrate that size-exclusion chromatography efficiently removes Optiprep from EVs. In conclusion, choice of centrifugal filters and protein assays confound EV analysis and should be carefully considered to increase efficiency towards biomarker discovery. SEC-based removal of Optiprep remnants from EVs can be considered for downstream applications.

Proof-of-Concept Workflow for Establishing Reference Intervals of Human Urine Proteome for Monitoring Physiological and Pathological Changes

Urine as a true non-invasive sampling source holds great potential for biomarker discovery. While approximately 2000 proteins can be detected by mass spectrometry in urine from healthy people, the amount of these proteins vary considerably. A systematic evaluation of a large number of samples is needed to determine the range of the variations. Current biomarker studies often measure limited number of urine samples in the discovery phase, which makes it difficult to determine whether proteins differentially expressed between control and disease groups represent actual difference, or are just physiological variations among the individuals, leads to failures in the validation phase with the increased sample numbers. Here, we report a streamlined workflow with capacity of measuring 8 urine proteomes per day at the coverage of >1500 proteins. With this workflow, we evaluated variations in 497 urine proteomes from 167 healthy donors, establishing reference intervals (RIs) that covered urine protein variations. We demonstrated that RIs could be used to monitor physiological changes by detecting transient outlier proteins. Furthermore, we provided a RIs-based algorithm for biomarker discovery and validation to screen for diseases such as cancer. This study provided a proof-of-principle workflow for the use of urine proteome for health monitoring and disease screening.

Urine Exosomes: An Emerging Trove of Biomarkers

Exosomes are released by most cells and can be isolated from all biofluids including urine. Exosomes are small vesicles formed as part of the endosomal pathway that contain cellular material surrounded by a lipid bilayer that can be traced to the plasma membrane. Exosomes are potentially a more targeted source of material for biomarker discovery than unfractionated urine, and provide diagnostic and pathophysiological information without an invasive tissue biopsy. Cytoplasmic contents including protein, mRNA, miRNA, and lipids have all been studied within the exosomal fraction. Many prospective urinary exosomal biomarkers have been successfully identified for a variety of kidney or genitourinary tract conditions; detection of systemic conditions may also be possible. Isolation and analysis of exosomes can be achieved by several approaches, although many require specialized equipment or involve lengthy protocols. The need for timely analysis in the clinical setting has driven considerable innovation with several promising options recently emerging. Consensus on exosome isolation, characterization, and normalization procedures would resolve critical clinical translational bottlenecks for existing candidate exosomal biomarkers and provide a template for additional discovery studies.

Extracellular vesicles in blood, milk and body fluids of the female and male urogenital tract and with special regard to reproduction

Extracellular vesicles (EVs) are released from almost all cells and tissues. They are able to transport substances (e.g. proteins, RNA or DNA) at higher concentrations than in their environment and may adhere in a receptor-controlled manner to specific cells or tissues in order to release their content into the respective target structure. Blood contains high concentrations of EVs mainly derived from platelets, and, at a smaller amount, from erythrocytes. The female and male reproductive tracts produce EVs which may be associated with fertility or infertility and are released into body fluids and mucosas of the urogenital organs. In this review, the currently relevant detection methods are presented and critically compared. During pregnancy, placenta-derived EVs are dynamically detectable in peripheral blood with changing profiles depending upon progress of pregnancy and different pregnancy-associated pathologies, such as preeclampsia. EVs offer novel non-invasive diagnostic tools which may reflect the situation of the placenta and the foetus. EVs in urine have the potential of reflecting urogenital diseases including cancers of the neighbouring organs. Several methods for detection, quantification and phenotyping of EVs have been established, which include electron microscopy, flow cytometry, ELISA-like methods, Western blotting and analyses based on Brownian motion. This review article summarises the current knowledge about EVs in blood and cord blood, in the different compartments of the male and female reproductive tracts, in trophoblast cells from normal and pre-eclamptic pregnancies, in placenta ex vivo perfusate, in the amniotic fluid, and in breast milk, as well as their potential effects on natural killer cells as possible targets.

The proteomic landscape of renal tumors

INTRODUCTION

Renal cell carcinoma (RCC) is the most fatal of the common urologic cancers, with approximately 35% of patients dying within 5 years following diagnosis. Therefore, there is a need for non-invasive markers that are capable of detecting and determining the severity of small renal masses at an early stage in order to tailor treatment and follow-up. Proteomic studies have proved to be very useful in the study of tumors. Areas covered: In this review, we will detail the current knowledge obtained by the different proteomic approaches, focusing on MS-based strategies, used to investigate RCC biology in order to identify diagnostic, prognostic and predictive biomarkers on tissue, cultured cells and biological fluids. Expert commentary: Currently, no reliable biomarkers or targets for RCC have been translated into the clinical setting. Moreover, despite the efforts of proteomics and other -omics disciplines, only a small number of them have been observed as shared targets between the different analytical platforms and biological specimens. The difficulty to define a specific molecular pattern for RCC and its subtypes highlights a peculiar profile and a heterogeneity that must be taken into account in future studies.