Proteomic analysis of urinary extracellular vesicles from high Gleason score prostate cancer

Charged multivesicular body protein 4C promotes the progression of cervical cancer through the HPV E6/miR‑543 axis

Charged multivesicular body protein 4C (CHMP4C), as a subunit of endosomal sorting complex required for transport-III, is important for the abscission checkpoint in cell division, preventing premature cell division and genetic damage. The present study aimed to assess the role of CHMP4C in cervical cancer and the associated mechanisms. The levels of CHMP4C in normal and cervical cancer tissues were detected by immunohistochemistry. The MTT assay, apoptosis, wound-healing assay, and cell invasion assay were performed. Western blotting was performed to analyze the level of cancer-related proteins following CHMP4C downregulation and the CHMP4C expression following E6 downregulation and miR-543 upregulation. The transfection effectiveness of siRNA, plasmid, and miRNA mimic as well as the expression of miR-543 after silencing E6 were assessed by RT-PCR. The dual-luciferase reporter assay was used to demonstrate a connection site between CHMP4C and miR-543. The results demonstrated that CHMP4C expression in cervical cancer tissues was significantly higher than that in normal tissues. Furthermore, downregulation of CHMP4C expression significantly reduced the proliferation, migration and invasion of cervical cancer cells and significantly increased the rate of apoptosis compared to the si-scramble group. Comparison with the si-scramble group, silencing CHMP4C expression also significantly reduced the expression of Bcl2, Bcl-xL and Survivin, and was associated with a significant increase in Caspase-7 expression. After the knockdown of human papillomavirus (HPV)-encoded E6, in comparison to the si-scramble group, microRNA (miR)-543 expression was significantly elevated and CHMP4C expression significantly decreased. Moreover, a connection site was detected between miR-543 and CHMP4C. These findings indicate that CHMP4C accelerates the tumorigenesis and progression of cervical cancer through the HPV E6/miR-543 axis.

Astrocytic FABP5 mediates retrograde endocannabinoid transport at central synapses

Endocannabinoids (eCBs) regulate synaptic function via cannabinoid receptors. While eCB signaling is well understood, the mechanisms underlying eCB synaptic transport are poorly characterized. Using 2-arachidonoylglycerol (2-AG)-mediated depolarization-induced suppression of inhibition (DSI) in the hippocampus as a readout of retrograde eCB signaling, we demonstrate that the deletion of fatty acid binding protein 5 (FABP5) impairs DSI. In FABP5 KO mice, DSI was rescued by re-expressing wild-type FABP5 but not an FABP5 mutant that does not bind 2-AG. Importantly, the deletion of astrocytic FABP5 blunted DSI, which was rescued by its re-expression in the astrocytes of FABP5 KO mice. Neuronal FABP5 was dispensable for 2-AG signaling. DSI was also rescued by expressing a secreted FABP5 variant but not by FABP7, an astrocytic FABP that does not undergo secretion. Our results demonstrate that extracellular FABP5 of astrocytic origin controls 2-AG transport and that FABP5 is adapted to coordinate intracellular and synaptic eCB transport.

Fatty acid binding protein 5 inhibitors as novel anticancer agents against metastatic castration-resistant prostate cancer

Prostate cancer (PCa) is one of the most common malignancies diagnosed among men and is the second leading cause of cancer-related death. Despite recent advancements in early diagnosis of PCa, androgen deprivation therapy (ADT) remains the most common treatment of PCa. Docetaxel (DTX) and Cabazitaxel (CTX) are two of the most extensively used drugs for metastatic castration-resistant prostate cancer (mCRPC). However, there is a clear medical need for newer and more efficacious therapies for CRPC. FABP5 is overexpressed in prostate cancer cells and chaperones fatty acids to PPARs, which leads to the upregulation of proangiogenic factors, resulting in cell survival and metastasis. The critical role and upregulation of FABP5 in PCa make FABP5 an excellent druggable target for CRPC. We reported a promising anti-PCa activity of truxillic acid monoester (TAME)-based FABP5 inhibitors (SB-FIs) and their synergy with DTX and CTX in vitro and in vivo against PC-3 cells and PC-3 tumor xenografts. In the present work, we performed an extensive SAR study on the potencies of 2nd- and 3rd-generation SB-FIs against PC-3 and RCaP cell lines. RCaP is a mouse PCa cell line, resistant to anti-androgen and first-line taxane chemotherapies, and shows a high level of the Fabp5-gene. This SAR study led to the identification of a number of 3rd-generation SB-FIs with strong cytotoxicity against these two PCa cell lines. Cell cycle analysis of selected SB-FIs revealed a clear evolution of apoptotic potency in the 1st-, 2nd- and 3rd-generation SB-FIs. Since taxanes, DTX and CTX, are ineffective against RCaP cell line, we selected a topoisomerase I inhibitor, topotecan (TPT) as a replacement for taxanes. We screened the library of SB-FIs for synergy with TPT and identified 3 SB-FIs (L3, α-11 and α-4), exhibiting strong synergy, which could remarkably expand the therapeutic window of TPT.

[Efficient capture and proteomics analysis of urinary extracellular vesicles by affinity purification]

Liquid biopsy is a promising alternative to traditional tissue biopsies for diagnosing cancer because it offers advantages such as minimal invasiveness, accessibility, and ease of operation. Extracellular vesicles (EVs) are lipid bilayer vesicles that contain proteins, DNA, and RNA and are secreted by cells. Indeed, urinary EVs are important sources of cancer biomarkers. The lipid bilayer protects EV proteins from degradation by enzymes present in bodily fluids. Prostate cancer (PCa) is among the most prevalent malignancies in developed countries and is the second-leading cause of cancer-related mortality in men. Current screening methods commonly used to initially evaluate patients with suspected PCa include serum prostate-specific antigen (PSA) testing and digital rectal examination (DRE), with magnetic resonance imaging (MRI) and transrectal ultrasound often recommended for further assessment. However, both PSA testing and DRE have limited specificities, which results in a substantial number of unnecessary prostate biopsies. Consequently, additional reliable biomarkers need to be urgently discovered for rapidly diagnosing PCa more accurately. Prostate-derived secretions, including those associated with malignancies, are detectable in urine owing to the anatomical proximity of the prostate to the urethra; hence urine is a promising liquid-biopsy medium for discovering PCa biomarkers, which is a topic that has been the focus of extensive research efforts in recent years. However, isolating EVs from biofluids in sufficient yields for proteomics analysis remains challenging. In this study, functional magnetic beads EVlent (extracellular vesicles isoLated efficiently, naturally, and totally) with high-affinity capabilities were developed for selectively enriching EVs from biological fluids.The surfaces of the beads were modified with three antibodies that target CD9, CD63, and CD81, which enables the specific recognition of EV surface proteins. The isolation performance of EVlent was validated by comprehensively characterizing urinary EVs using Western blotting (WB), nanoparticle tracking analysis (NTA), and transmission electron microscopy (TEM). WB revealed prominent bands for EV markers (CD9, TSG101, and HSP70) in EVlent-enriched samples, whereas weaker bands were observed following ultracentrifugation (UC). NTA revealed that the EVs isolated by EVlent are predominantly in the 50-400 nm size range, with a content of 4.1×109 particles/mL, which is significantly higher than the value of 1.8×109 particles/mL obtained by UC. TEM confirmed that the isolated EVs have characteristic elliptical or cup-shaped vesicular structures. These findings demonstrate that EVlent outperforms UC in terms of enrichment efficiency and purity, delivering a separation efficiency of 87.2% compared to the value of 30.3% obtained by UC. We used proteomics to analyze urinary EVs isolated from 15 healthy volunteers and 15 patients with prostate cancer using EVlent affinity magnetic beads with the aim of identifying potential biomarkers for prostate cancer. On average, 2039 proteins and 14490 peptides were identified in the control group, while 1982 proteins and 13100 peptides were identified in the patient group. Further analysis revealed 91 proteins commonly found in the Vesiclepedia database (Top 100). Compared with the healthy volunteers, 88 proteins were upregulated and 90 proteins were downregulated in patients with prostate cancer. Gene ontology (GO) analysis showed that these upregulated proteins are enriched in extracellular exosomes, extracellular space, extracellular region, collagen-containing extracellular matrix, proteolysis and protein-binding. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) highlighted associations between ribosomes, protein digestion and absorption, complement and coagulation cascades, prostate cancer, transcriptional misregulation in cancer, aldosterone-regulated sodium reabsorption, endocrine and other factor-regulated calcium reabsorption, and pancreatic secretion. Notably, four proteins including plasminogen activator urokinase (PLAU), platelet-derived growth factor subunit A (PDGFA), matrix metalloproteinase 3 (MMP3), and neuroblastoma RAS viral oncogene homolog (NRAS) were identified within the prostate cancer pathway, highlighting their potential as biomarkers for the early diagnosis and prognosis of prostate cancer. In conclusion, this study introduced EVlent as a robust platform for the efficient isolation and proteomics analysis of EVs, providing valuable insight into urinary EV biomarkers and their clinical prostate-cancer applications.

Chemical Affinity Capture of Plasma Extracellular Vesicles Enables Efficient and Large-Scale Proteomic Identification of Prostate Cancer Biomarkers

The serum prostate-specific antigen (PSA) testing is widely used for prostate cancer (PCa) screening but suffers from poor specificity, leading to unnecessary biopsies and overtreatment. The significant potential of extracellular vesicles (EVs) in cancer diagnosis has driven the development of efficient methods to isolate and identify EV biomarkers from large-scale clinical samples. Here, we systematically evaluate five commonly used EV isolation techniques through proteomic profiling of plasma-derived EVs, endorsing TiO2-based chemical affinity capture as a superior approach for analyzing EVs from complex clinical samples. This method demonstrates exceptional advantages in speed, throughput, reproducibility, and protein coverage. Using this optimized workflow, we analyzed plasma EVs from 80 patients with PCa and benign prostatic hyperplasia (BPH), identifying growth differentiation factor 15 (GDF15) as a compelling biomarker with a predictive power (AUC) of 0.908 for PCa. Extensive validation across independent cohorts comprising 457 samples, including plasma EVs and prostate tissues, confirmed GDF15's ability to distinguish PCa from BPH and stratify PCa stages. Notably, the combination of GDF15 with PSA further enhanced diagnostic efficiency, particularly for patients in the PSA diagnostic gray zone. This study establishes a robust workflow for EV protein analysis in large clinical cohorts and highlights EV-GDF15 as a promising biomarker for noninvasive PCa diagnosis.

Insights into tumor-derived exosome inhibition in cancer therapy

Exosomes are critical mediators of cell-to-cell communication in physiological and pathological processes, due to their ability to deliver a variety of bioactive molecules. Tumor-derived exosomes (TDEs), in particular, carry carcinogenic molecules that contribute to tumor progression, metastasis, immune escape, and drug resistance. Thus, TDE inhibition has emerged as a promising strategy to combat cancer. In this review, we discuss the key mechanisms of TDE biogenesis and secretion, emphasizing their implications in tumorigenesis and cancer progression. Moreover, we provide an overview of small-molecule TDE inhibitors that target specific biogenesis and/or secretion pathways, highlighting their potential use in cancer treatment. Lastly, we present the existing obstacles and propose corresponding remedies for the future development of TDE inhibitors.

Uncovering New Biomarkers for Prostate Cancer Through Proteomic and Network Analysis

BACKGROUND

Prostate cancer (PCa), is the second most prevalent solid tumor among men worldwide (7.3%), and the leading non-skin cancer in USA where it represents 14.9% of all new cancer cases diagnosed in 2024. This multifactorial disease exhibits substantial variation in incidence and mortality across different ethnic groups and geographic regions. Although prostate-specific antigen (PSA) remains widely used as a biomarker for PCa, its limitations reduce its effectiveness for accurate detection. Consequently, finding molecules that can either complement PSA and other biomarkers is a major goal in PCa research.

METHODS

Urine samples were collected from healthy donors (n = 5) and patients with low- and high-risk PCa (4 and 7 subjects, respectively) and were analyzed using proteomic data-derived systems and biology approaches. The most promising proteins were further investigated by means of The Cancer Genome Atlas (TCGA) database to assess their associations with clinical and histopathological characteristics in a larger in silico patient population.

RESULTS

By evaluating the variations in the urinary proteome as a mirror of the changes occurring in prostate tumor tissue, components of complement and coagulation cascades and glutathione metabolism emerged as hallmarks of low- and high-risk PCa patients, respectively. Moreover, our integrated approach highlighted new potential biomarkers, including CPM, KRT8, ITIH2, and RCN1.

CONCLUSIONS

The good overlap of our results with what is already reported in the literature supports the new findings in the perspective of improving the knowledge on PCa. Furthermore, they increase the panel of biomarkers that could enhance PCa management. Of course, further investigations on larger patient cohorts are required.

Size-Dependent Separation of Extracellular Vesicle Subtypes with Exodisc Enabling Proteomic Analysis in Prostate Cancer

Extracellular vesicles (EVs) are emerging as crucial biomarkers in cancer diagnostics and therapeutics with their heterogeneity presenting both challenges and opportunities in prostate cancer research. However, existing methods for isolating and characterizing EV subtypes have been limited by inefficient separation and inadequate proteomic analysis. Here we show an optimized centrifugal microfluidic device, Exodisc, that efficiently isolates large quantities of EV subtypes from particle-enriched medium, enabling comprehensive proteomic analysis of small (EV-S, 20-200 nm) and large (EV-L, >200 nm) EVs. Using this device, we successfully separated EV-S and EV-L from prostate cancer cell lines LNCaP and PC3. Mass spectrometry-based proteomics revealed that EV proteins reflect parental cell characteristics more than EV size, with EV-L demonstrating increased expression of PSMA-correlated proteins. Our optimized protocol addresses challenges in EV isolation and characterization, providing a more effective method for studying cellular and molecular mechanisms of specific EV subtypes. This study extends the potential use of EVs as a liquid biopsy for cancer theranostics, paving the way for more precise isolation of EV subtypes and potentially leading to improved biomarker discovery and the development of personalized treatments.

Fatty acid binding protein as a new age biomarker

Small lipid-binding proteins known as fatty acid-binding proteins (FABPs) are extensively expressed in cells having elevated levels of fatty acid (FA) metabolism. There are ten known FABPs in mammals that exhibit expression patterns specific to tissues and tertiary structures that are substantially preserved. FABPs were first investigated as FA transport proteins inside cells. Subsequent research has shown that they are involved in signalling within their expression cells and in metabolism of lipid, directly and through the control of expression of gene. Additionally, there is evidence that they might be released and influence circulatory function. It has been observed that some tissues and organs linked to inflammatory, metabolic illnesses and also infectious disease have markedly elevated expression levels of FABPs. Thus, in addition to previously identified markers, FABPs represent a promising new biomarker that require additional investigation to optimise illness detection and prognosis techniques.

Challenges of MS-based small extracellular vesicles proteomics

Proteomic profiling of small extracellular vesicles (sEV) is a powerful tool for discovering biomarkers of various diseases. This process most often assisted by mass spectrometry (MS) usually lacks standardization and recognition of challenges which may lead to unreliable results. General recommendations for sEV MS analyses have been briefly given in the MISEV2023 guidelines. The present work goes into detail for every step of sEV protein profiling with an overview of factors influencing such analyses. This includes reporting and defining the sEV source and vesicle isolation, protein solubilization and digestion, 'offline' and 'online' sample complexity reduction, the analysis type itself, and subsequent data analysis. Every stage in this process affects the others, which could result in different outcomes. Although characterization and comparisons of different sEV isolation methods are known and accessible and MS-based profiling details are provided for cell or tissue samples, no consensus work has been ever published to describe the whole process of sEV proteomic analysis. Reliable results can be obtained from sEV profiling provided that the analysis is well planned, prepared for, and backed by pilot studies or appropriate research.

The emerging role of extracellular vesicles and particles in prostate cancer diagnosis, and risk stratification

Current approaches for prostate cancer (PCa) diagnosis and risk stratification require greater accuracy. Extracellular vesicles and particles (EVPs) containing diverse cargos from parent cells are released into the extracellular microenvironment and play a critical role in intercellular communication. Accumulating evidence demonstrates that EVPs are emerging as a promising focus for the exploration of cancer biomarkers and therapeutic targets. However, the precise categorisation and nomenclature of EVP subpopulations remains challenging due to their compositional complexity, inherent heterogeneity in molecular composition, and structure. The recent identification of two novel non-vesicular extracellular particle subtypes, exomeres and supermeres, has altered our understanding of the distinct subpopulations of EVPs and their roles in biological and physiological processes. Here, we discuss recent advances in the field of EVPs, describe characteristics of EVP subpopulations, focus on the application and potential of EVPs in PCa diagnosis and risk stratification by liquid biopsy, and highlight the major challenges and prospects of EVP research in PCa area.

Profiling of urinary extracellular vesicle protein signatures from patients with cribriform and intraductal prostate carcinoma in a cross-sectional study

Prognostic tests and treatment approaches for optimized clinical care of prostatic neoplasms are an unmet need. Prostate cancer (PCa) and derived extracellular vesicles (EVs) proteome changes occur during initiation and progression of the disease. PCa tissue proteome has been previously characterized, but screening of tissue samples constitutes an invasive procedure. Consequently, we focused this study on liquid biopsies, such as urine samples. More specifically, urinary small extracellular vesicle and particles proteome profiles of 100 subjects were analyzed using liquid chromatography coupled to high-resolution mass spectrometry (LC-MS/MS). We identified 171 proteins that were differentially expressed between intraductal prostate cancer/cribriform (IDC/Crib) and non-IDC/non-Crib after correction for multiple testing. However, the strong correlation between IDC/Crib and Gleason Grade complicates the disentanglement of the underlying factors driving this association. Nevertheless, even after accounting for multiple testing and adjusting for ISUP (International Society of Urological Pathology) grading, two proteins continued to exhibit significant differential expression between IDC/Crib and non-IDC/non-Crib. Functional enrichment analysis based on cancer hallmark proteins disclosed a clear pattern of androgen response down-regulation in urinary EVs from IDC/Crib compared to non-IDC/non-Crib. Interestingly, proteome differences between IDC and cribriform were more subtle, suggesting high proteome heterogeneity. Overall, the urinary EV proteome reflected partly the prostate pathology.

Exploring the clinical and biological significance of the cell cycle-related gene CHMP4C in prostate cancer

BACKGROUND

Prostate cancer (PCa) stands as the second most prevalent malignancy impacting male health, and the disease's evolutionary course presents formidable challenges in the context of patient treatment and prognostic management. Charged multivesicular body protein 4 C (CHMP4C) participates in the development of several cancers by regulating cell cycle functions. However, the role of CHMP4C in prostate cancer remains unclear.

METHODS

In terms of bioinformatics, multiple PCa datasets were employed to scrutinize the expression of CHMP4C. Survival analysis coupled with a nomogram approach was employed to probe into the prognostic significance of CHMP4C. Gene set enrichment analysis (GSEA) was conducted to interrogate the functional implications of CHMP4C. In terms of cellular experimentation, the verification of RNA and protein expression levels was executed through the utilization of qRT-PCR and Western blotting. Upon the establishment of a cell line featuring stable CHMP4C knockdown, a battery of assays, including Cell Counting Kit-8 (CCK-8), wound healing, Transwell, and flow cytometry, were employed to discern the impact of CHMP4C on the proliferation, migration, invasion, and cell cycle function of PCa cells.

RESULTS

The expression of CHMP4C exhibited upregulation in both PCa cells and tissues, and patients demonstrating elevated CHMP4C expression levels experienced a notably inferior prognosis. The nomogram, constructed using CHMP4C along with clinicopathological features, demonstrated a commendable capacity for prognostic prediction. CHMP4C knockdown significantly inhibited the proliferation, migration, and invasion of PCa cells (LNcaP and PC3). CHMP4C could impact the advancement of the PCa cell cycle, and its expression might be regulated by berberine. Divergent CHMP4C expression among PCa patients could induce alterations in immune cell infiltration and gene mutation frequency.

CONCLUSIONS

Our findings suggest that CHMP4C might be a prognostic biomarker in PCa, potentially offering novel perspectives for the advancement of precision therapy for PCa.

Urine biomarkers can predict prostate cancer and PI-RADS score prior to biopsy

Prostate-Specific Antigen (PSA) based screening of prostate cancer (PCa) needs refinement. The aim of this study was the identification of urinary biomarkers to predict the Prostate Imaging-Reporting and Data System (PI-RADS) score and the presence of PCa prior to prostate biopsy. Urine samples from patients with elevated PSA were collected prior to prostate biopsy (cohort = 99). The re-analysis of mass spectrometry data from 45 samples was performed to identify urinary biomarkers to predict the PI-RADS score and the presence of PCa. The most promising candidates, i.e. SPARC-like protein 1 (SPARCL1), Lymphatic vessel endothelial hyaluronan receptor 1 (LYVE1), Alpha-1-microglobulin/bikunin precursor (AMBP), keratin 13 (KRT13), cluster of differentiation 99 (CD99) and hornerin (HRNR), were quantified by ELISA and validated in an independent cohort of 54 samples. Various biomarker combinations showed the ability to predict the PI-RADS score (AUC = 0.79). In combination with the PI-RADS score, the biomarkers improve the detection of prostate carcinoma-free men (AUC = 0.89) and of those with clinically significant PCa (AUC = 0.93). We have uncovered the potential of urinary biomarkers for a test that allows a more stringent prioritization of mpMRI use and improves the decision criteria for prostate biopsy, minimizing patient burden by decreasing the number of unnecessary prostate biopsies.

Mass spectrometry for metabolomics analysis: Applications in neonatal and cancer screening

Chemical analysis by analytical instrumentation has played a major role in disease diagnosis, which is a necessary step for disease treatment. While the treatment process often targets specific organs or compounds, the diagnostic step can occur through various means, including physical or chemical examination. Chemically, the genome may be evaluated to give information about potential genetic outcomes, the transcriptome to provide information about expression actively occurring, the proteome to offer insight on functions causing metabolite expression, or the metabolome to provide a picture of both past and ongoing physiological function in the body. Mass spectrometry (MS) has been elevated among other analytical instrumentation because it can be used to evaluate all four biological machineries of the body. In addition, MS provides enhanced sensitivity, selectivity, versatility, and speed for rapid turnaround time, qualities that are important for instance in clinical procedures involving the diagnosis of a pediatric patient in intensive care or a cancer patient undergoing surgery. In this review, we provide a summary of the use of MS to evaluate biomarkers for newborn screening and cancer diagnosis. As many reviews have recently appeared focusing on MS methods and instrumentation for metabolite analysis, we sought to describe the biological basis for many metabolomic and additional omics biomarkers used in newborn screening and how tandem MS methods have recently been applied, in comparison to traditional methods. Similar comparison is done for cancer screening, with emphasis on emerging MS approaches that allow biological fluids, tissues, and breath to be analyzed for the presence of diagnostic metabolites yielding insight for treatment options based on the understanding of prior and current physiological functions of the body.

Advances in Prostate Cancer Biomarkers and Probes

Prostate cancer is one of the most prevalent malignant tumors in men worldwide, and early diagnosis is essential to improve patient survival. This review provides a comprehensive discussion of recent advances in prostate cancer biomarkers, including molecular, cellular, and exosomal biomarkers. The potential of various biomarkers such as gene fusions (TMPRSS2-ERG), noncoding RNAs (SNHG12), proteins (PSA, PSMA, AR), and circulating tumor cells (CTCs) in the diagnosis, prognosis, and targeted therapies of prostate cancer is emphasized. In addition, this review systematically explores how multi-omics data and artificial intelligence technologies can be used for biomarker discovery and personalized medicine applications. In addition, this review provides insights into the development of specific probes, including fluorescent, electrochemical, and radionuclide probes, for sensitive and accurate detection of prostate cancer biomarkers. In conclusion, this review provides a comprehensive overview of the status and future directions of prostate cancer biomarker research, emphasizing the potential for precision diagnosis and targeted therapy.

Small extracellular vesicles: Roles and clinical application in prostate cancer

Prostate cancer is a significant health problem in the United States. It is remarkably heterogenous, ranging from slow growing disease amenable to active surveillance to highly aggressive forms requiring active treatments. Therefore, being able to precisely determine the nature of disease and appropriately match patients to available and/or novel therapeutics is crucial to improve patients' overall outcome and quality of life. Recently small extracellular vesicles (sEVs), a subset of nanoscale membranous vesicles secreted by various cells, have emerged as important analytes for liquid biopsy and promising vehicles for drug delivery. sEVs contain various biomolecules such as genetic material, proteins, and lipids that recapitulate the characteristics and state of their donor cells. The application of existing and newly developed technologies has resulted in an increased depth of knowledge about biophysical structures, biogenesis, and functions of sEVs. In prostate cancer patients, tumor-derived sEVs can be isolated from biofluids, commonly urine and blood. They mediate intercellular signaling within the tumor microenvironment and distal organ-specific sites, supporting cancer initiation, progression, and metastasis. A mounting body of evidence suggests that sEV components can be potent biomarkers for prostate cancer diagnosis, prognosis, and prediction of disease progression and treatment response. Due to enhanced circulation stability and bio-barrier permeability, sEVs can be also used as effective drug delivery carriers to improve the efficacy and specificity of anti-tumor therapies. This review discusses recent studies on sEVs in prostate cancer and is focused on their role as biomarkers and drug delivery vehicles in the clinical management of prostate cancer.

Assessment of urine sample collection and processing variables for extracellular vesicle-based proteomics

Extracellular vesicles (EVs) in urine are a promising source for developing non-invasive biomarkers. However, urine concentration and content are highly variable and dynamic, and actual urine collection and handling often is nonideal. Furthermore, patients such as those with prostate diseases have challenges in sample collection due to difficulties in holding urine at designated time points. Here, we simulated the actual situation of clinical sample collection to examine the stability of EVs in urine under different circumstances, including urine collection time and temporary storage temperature, as well as daily urine sampling under different diet conditions. EVs were isolated using functionalized EVtrap magnetic beads and characterized by nanoparticle tracking analysis (NTA), western blotting, electron microscopy, and mass spectrometry (MS). EVs in urine remained relatively stable during temporary storage for 6 hours at room temperature and for 12 hours at 4 °C, while significant fluctuations were observed in EV amounts from urine samples collected at different time points from the same individuals, especially under certain diets. Sample normalization with creatinine reduced the coefficient of variation (CV) values among EV samples from 17% to approximately 6% and facilitated downstream MS analyses. Finally, based on the results, we applied them to evaluate potential biomarker panels in prostate cancer by data-independent acquisition (DIA) MS, presenting the recommendation that can facilitate biomarker discovery with nonideal handling conditions.

Immune capture and protein profiling of small extracellular vesicles from human plasma

Extracellular vesicles (EVs), the key players in inter-cellular communication, are produced by all cell types and are present in all body fluids. Analysis of the proteome content is an important approach in structural and functional studies of these vesicles. EVs circulating in human plasma are heterogeneous in size, cellular origin, and functions. This heterogeneity and the potential presence of contamination with plasma components such as lipoprotein particles and soluble plasma proteins represent a challenge in profiling the proteome of EV subsets by mass spectrometry. An immunocapture strategy prior to mass spectrometry may be used to isolate a homogeneous subpopulation of small EVs (sEV) with a specific endocytic origin from plasma or other biofluids. Immunocapture selectively separates EV subpopulations in biofluids based on the presence of a unique protein carried on the vesicle surface. The advantages and disadvantages of EV immune capture as a preparative step for mass spectrometry are discussed.

Advances in sequencing and omics studies in prostate cancer: unveiling molecular pathogenesis and clinical applications

Background

Prostate cancer (PCa) is one of the most threatening health problems for the elderly males. However, our understanding of the disease has been limited by the research technology for a long time. Recently, the maturity of sequencing technology and omics studies has been accelerating the studies of PCa, establishing themselves as an essential impetus in this field.

Methods

We assessed Web of Science (WoS) database for publications of sequencing and omics studies in PCa on July 3rd, 2023. Bibliometrix was used to conduct ulterior bibliometric analysis of countries/affiliations, authors, sources, publications, and keywords. Subsequently, purposeful large amounts of literature reading were proceeded to analyze research hotspots in this field.

Results

3325 publications were included in the study. Research associated with sequencing and omics studies in PCa had shown an obvious increase recently. The USA and China were the most productive countries, and harbored close collaboration. CHINNAIYAN AM was identified as the most influential author, and CANCER RESEARCH exhibited huge impact in this field. Highly cited publications and their co-citation relationships were used to filtrate literatures for subsequent literature reading. Based on keyword analysis and large amounts of literature reading, 'the molecular pathogenesis of PCa' and 'the clinical application of sequencing and omics studies in PCa' were summarized as two research hotspots in the field.

Conclusion

Sequencing technology had a deep impact on the studies of PCa. Sequencing and omics studies in PCa helped researchers reveal the molecular pathogenesis, and provided new possibilities for the clinical practice of PCa.

Applications of Urinary Extracellular Vesicles in the Diagnosis and Active Surveillance of Prostate Cancer

Prostate cancer is the most common non-cutaneous cancer among men in the UK, causing significant health and economic burdens. Diagnosis and risk prognostication can be challenging due to the genetic and clinical heterogeneity of prostate cancer as well as uncertainties in our knowledge of the underlying biology and natural history of disease development. Urinary extracellular vesicles (EVs) are microscopic, lipid bilayer defined particles released by cells that carry a variety of molecular cargoes including nucleic acids, proteins and other molecules. Urine is a plentiful source of prostate-derived EVs. In this narrative review, we summarise the evidence on the function of urinary EVs and their applications in the evolving field of prostate cancer diagnostics and active surveillance. EVs are implicated in the development of all hallmarks of prostate cancer, and this knowledge has been applied to the development of multiple diagnostic tests, which are largely based on RNA and miRNA. Common gene probes included in multi-probe tests include PCA3 and ERG, and the miRNAs miR-21 and miR-141. The next decade will likely bring further improvements in the diagnostic accuracy of biomarkers as well as insights into molecular biological mechanisms of action that can be translated into opportunities in precision uro-oncology.

Multiplexed quantitative proteomics in prostate cancer biomarker development

Prostate cancer (PCa) is the most common non-skin cancer among men in the United States. However, the widely used protein biomarker in PCa, prostate-specific antigen (PSA), while useful for initial detection, its use alone cannot detect aggressive PCa and can lead to overtreatment. This chapter provides an overview of PCa protein biomarker development. It reviews the state-of-the-art liquid chromatography-mass spectrometry-based proteomics technologies for PCa biomarker development, such as enhancing the detection sensitivity of low-abundance proteins through antibody-based or antibody-independent protein/peptide enrichment, enriching post-translational modifications such as glycosylation as well as information-rich extracellular vesicles, and increasing accuracy and throughput using advanced data acquisition methodologies. This chapter also summarizes recent PCa biomarker validation studies that applied those techniques in diverse specimen types, including cell lines, tissues, proximal fluids, urine, and blood, developing novel protein biomarkers for various clinical applications, including early detection and diagnosis, prognosis, and therapeutic intervention of PCa.

Fatty acid-binding protein 5 is a functional biomarker and indicator of ferroptosis in cerebral hypoxia

The progression of human degenerative and hypoxic/ischemic diseases is accompanied by widespread cell death. One death process linking iron-catalyzed reactive species with lipid peroxidation is ferroptosis, which shows hallmarks of both programmed and necrotic death in vitro. While evidence of ferroptosis in neurodegenerative disease is indicated by iron accumulation and involvement of lipids, a stable marker for ferroptosis has not been identified. Its prevalence is thus undetermined in human pathophysiology, impeding recognition of disease areas and clinical investigations with candidate drugs. Here, we identified ferroptosis marker antigens by analyzing surface protein dynamics and discovered a single protein, Fatty Acid-Binding Protein 5 (FABP5), which was stabilized at the cell surface and specifically elevated in ferroptotic cell death. Ectopic expression and lipidomics assays demonstrated that FABP5 drives redistribution of redox-sensitive lipids and ferroptosis sensitivity in a positive-feedback loop, indicating a role as a functional biomarker. Notably, immunodetection of FABP5 in mouse stroke penumbra and in hypoxic postmortem patients was distinctly associated with hypoxically damaged neurons. Retrospective cell death characterized here by the novel ferroptosis biomarker FABP5 thus provides first evidence for a long-hypothesized intrinsic ferroptosis in hypoxia and inaugurates a means for pathological detection of ferroptosis in tissue.

Recent progress in mass spectrometry-based urinary proteomics

Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.

Experimental treatment efficacy of dmrFABP5 on prostate cancer singly or in combination with drugs in use

Enzalutamide is a drug used to treat prostate cancer (PC) and docetaxel is a drug for chemotherapeutic treatment of diverse cancer types, including PC. The effectiveness of these drugs in treating castration-resistant prostate cancer (CRPC) is poor and therefore CRPC is still largely incurable. However, the bio-inhibitor of fatty acid-binding protein 5 (FABP5), dmrFABP5, which is a mutant form of FABP5 incapable of binding to fatty acids, has been shown recently to be able to suppress the tumorigenicity and metastasis of cultured CRPC cells. The present study investigated the possible synergistic effect of dmrFABP5 combined with either enzalutamide or docetaxel on suppressing the tumorigenic properties of PC cells, including cell viability, migration, invasion and colony proliferation in soft agar. A highly significant synergistic inhibitory effect on these properties was observed when dmrFABP5 was used in combination with enzalutamide on androgen-responsive PC 22RV1 cells. Moreover, a highly significant synergistic inhibitory effect was also observed when dmrFABP5 was combined with docetaxel, and added to 22RV1 cells and to the highly malignant, androgen-receptor (AR)-negative Du145 cells. DmrFABP5 alone failed to produce any suppressive effect when added to the FABP5-negative cell line LNCaP, although enzalutamide could significantly suppress LNCaP cells when used as a single agent. These synergistic inhibitory effects of dmrFABP5 were produced by interrupting the FABP5-related signal transduction pathway in PC cells. Thus, dmrFABP5 appears to be not only a potential single therapeutic agent, but it may also be used in combination with existing drugs to suppress both AR-positive and AR-negative PC.

Deciphering Urogenital Cancers through Proteomic Biomarkers: A Systematic Review and Meta-Analysis

Urogenital cancers, which include prostate, bladder, and kidney malignancies, exert a substantial impact on global cancer-related morbidity and mortality. Proteomic biomarkers, emerging as valuable tools, aim to enhance early detection, prognostic accuracy, and the development of personalized therapeutic strategies. This study undertook a comprehensive systematic review and meta-analysis of the existing literature investigating the role and potential of proteomic biomarkers in plasma, tissue, and urine samples in urogenital cancers. Our extensive search across several databases identified 1879 differentially expressed proteins from 37 studies, signifying their potential as unique biomarkers for these cancers. A meta-analysis of the significantly differentially expressed proteins was executed, accentuating the findings through visually intuitive volcano plots. A functional enrichment analysis unveiled their significant involvement in diverse biological processes, including signal transduction, immune response, cell communication, and cell growth. A pathway analysis highlighted the participation of key pathways such as the nectin adhesion pathway, TRAIL signaling pathway, and integrin signaling pathways. These findings not only pave the way for future investigations into early detection and targeted therapeutic approaches but also underscore the fundamental role of proteomics in advancing our understanding of the molecular mechanisms underpinning urogenital cancer pathogenesis. Ultimately, these findings hold remarkable potential to significantly enhance patient care and improve clinical outcomes.

Prostate cancer-derived small extracellular vesicle proteins: the hope in diagnosis, prognosis, and therapeutics

Current diagnostic tools for prostate cancer (PCa) diagnosis and risk stratification are insufficient. The hidden onset and poor efficacy of traditional therapies against metastatic PCa make this disease a heavy burden in global men's health. Prostate cancer-derived extracellular vesicles (PCDEVs) have garnered attention in recent years due to their important role in communications in tumor microenvironment. Recent advancements have demonstrated PCDEVs proteins play an important role in PCa invasion, progression, metastasis, therapeutic resistance, and immune escape. In this review, we briefly discuss the applications of sEV proteins in PCa diagnosis and prognosis in liquid biopsy, focus on the roles of the PCa-derived small EVs (sEVs) proteins in tumor microenvironment associated with cancer progression, and explore the therapeutic potential of sEV proteins applied for future metastatic PCa therapy.

Fatty-Acid-Binding Proteins: From Lipid Transporters to Disease Biomarkers

Fatty-acid-binding proteins (FABPs) serve a crucial role in the metabolism and transport of fatty acids and other hydrophobic ligands as an intracellular protein family. They are also recognized as a critical mediator in the inflammatory and ischemic pathways. FABPs are found in a wide range of tissues and organs, allowing them to contribute to various disease/injury developments that have not been widely discussed. We have collected and analyzed research journals that have investigated the role of FABPs in various diseases. Through this review, we discuss the findings on the potential of FABPs as biomarkers for various diseases in different tissues and organs, looking at their expression levels and their roles in related diseases according to available literature data. FABPs have been reported to show significantly increased expression levels in various tissues and organs associated with metabolic and inflammatory diseases. Therefore, FABPs are a promising novel biomarker that needs further development to optimize disease diagnosis and prognosis methods along with previously discovered markers.

Fatty acid binding protein 5 regulates docetaxel sensitivity in taxane-resistant prostate cancer cells

Prostate cancer is a leading cause of cancer-related deaths in men in the United States. Although treatable when detected early, prostate cancer commonly transitions to an aggressive castration-resistant metastatic state. While taxane chemotherapeutics such as docetaxel are mainstay treatment options for prostate cancer, taxane resistance often develops. Fatty acid binding protein 5 (FABP5) is an intracellular lipid chaperone that is upregulated in advanced prostate cancer and is implicated as a key driver of its progression. The recent demonstration that FABP5 inhibitors produce synergistic inhibition of tumor growth when combined with taxane chemotherapeutics highlights the possibility that FABP5 may regulate other features of taxane function, including resistance. Employing taxane-resistant DU145-TXR cells and a combination of cytotoxicity, apoptosis, and cell cycle assays, our findings demonstrate that FABP5 knockdown sensitizes the cells to docetaxel. In contrast, docetaxel potency was unaffected by FABP5 knockdown in taxane-sensitive DU145 cells. Taxane-resistance in DU145-TXR cells stems from upregulation of the P-glycoprotein ATP binding cassette subfamily B member 1 (ABCB1). Expression analyses and functional assays confirmed that FABP5 knockdown in DU145-TXR cells markedly reduced ABCB1 expression and activity, respectively. Our study demonstrates a potential new function for FABP5 in regulating taxane sensitivity and the expression of a major P-glycoprotein efflux pump in prostate cancer cells.

Clinical Significance of Extracellular Vesicles in Prostate and Renal Cancer

Extracellular vesicles (EVs)-including apoptotic bodies, microvesicles, and exosomes-are released by almost all cell types and contain molecular footprints from their cell of origin, including lipids, proteins, metabolites, RNA, and DNA. They have been successfully isolated from blood, urine, semen, and other body fluids. In this review, we discuss the current understanding of the predictive value of EVs in prostate and renal cancer. We also describe the findings supporting the use of EVs from liquid biopsies in stratifying high-risk prostate/kidney cancer and advanced disease, such as castration-resistant (CRPC) and neuroendocrine prostate cancer (NEPC) as well as metastatic renal cell carcinoma (RCC). Assays based on EVs isolated from urine and blood have the potential to serve as highly sensitive diagnostic studies as well as predictive measures of tumor recurrence in patients with prostate and renal cancers. Overall, we discuss the biogenesis, isolation, liquid-biopsy, and therapeutic applications of EVs in CRPC, NEPC, and RCC.

Current advances of liquid biopsies in prostate cancer: Molecular biomarkers

Prostate cancer (PCa) incidence is increasing and endangers men's lives. Early detection of PCa could improve overall survival (OS) by preventing metastasis. The prostate-specific antigen (PSA) test is a popular screening method. Several advisory groups, however, warn against using the PSA test due to its high false positive rate, unsupported outcome, and limited benefit. The number of disease-related biopsies performed annually far outweighs the number of diagnoses. Thus, there is an urgent need to develop accurate diagnostic biomarkers to detect PCa and distinguish between aggressive and indolent cancers. Recently, non-coding RNA (ncRNA), circulating tumor DNA (ctDNA)/ctRNA, exosomes, and metabolomic biomarkers in the liquid biopsies (LBs) of patients with PCa showed significant differences and clinical benefits in diagnosis, prognosis, and monitoring response to therapy. The analysis of urinary exosomal ncRNA presented a substantial correlation among Exos-miR-375 downregulation, clinical T stage, and bone metastases of PCa. Furthermore, the expression of miR-532-5p in urine samples was a vital predictive biomarker of PCa progression. Thus, this review focuses on promising molecular and metabolomic biomarkers in LBs from patients with PCa. We thoroughly addressed the most recent clinical findings of LB biomarker use in diagnosing and monitoring PCa in early and advanced stages.

Pre-analytical handling conditions and protein marker recovery from urine extracellular vesicles for bladder cancer diagnosis

Extracellular vesicles (EVs) contain a variety of biomolecules and provide information about the cells that produce them. EVs from cancer cells found in urine can be used as biomarkers to detect cancer, enabling early diagnosis and treatment. The potential of alpha-2-macroglobulin (A2M) and clusterin (CLU) as novel diagnostic urinary EV (uEV) biomarkers for bladder cancer (BC) was demonstrated previously. To validate the diagnostic value of these proteins in uEVs in a large BC cohort, urine handling conditions before uEV isolation should be optimized during sample transportation from medical centers. In this study, we analyzed the uEV protein quantity, EV particle number, and uEV-A2M/CLU after urine storage at 20°C and 4°C for 0-6 days, each. A2M and CLU levels in uEVs were relatively stable when stored at 4°C for a maximum of three days and at 20°C for up to 24 h, with minimal impact on analysis results. Interestingly, pre-processing to remove debris and cells by centrifugation and filtration of urine did not show any beneficial effects on the preservation of protein biomarkers of uEVs during storage. Here, the importance of optimizing shipping conditions to minimize the impact of pre-analytical handling on the uEVs protein biomarkers was emphasized. These findings provide insights for the development of clinical protocols that use uEVs for diagnostic purposes.

Extracellular vesicles from biological fluids as potential markers in castration resistant prostate cancer

PURPOSE

Extracellular vesicles (EV) secreted from cancer cells are present in various biological fluids, carrying distinctly different cellular components compared to normal cells, and have great potential to be used as markers for disease initiation, progression, and response to treatment. This under-utilised tool provides insights into a better understanding of prostate cancer.

METHODS

EV from serum and urine of healthy men and castration-resistant prostate cancer (CRPC) patients were isolated and characterised by transmission electron microscopy, particle size analysis, and western blot. Proteomic and cholesterol liquid chromatography-mass spectrometry (LC-MS) analyses were conducted.

RESULTS

There was a successful enrichment of small EV/exosomes isolated from serum and urine. EV derived from biological fluids of CRPC patients had significant differences in composition when compared with those from healthy controls. Analysis of matched serum and urine samples from six prostate cancer patients revealed specific EV proteins common in both types of biological fluid for each patient.

CONCLUSION

Some of the EV proteins identified from our analyses have potential to be used as CRPC markers. These markers may depict a pattern in cancer progression through non-invasive sample collection.

CHMP4C as a novel marker regulates prostate cancer progression through cycle pathways and contributes to immunotherapy

Background

CHMP4C is one of the charged multivesicular protein (CHMP), and is involved in the composition of the endosomal sorting complex required for transport III (ESCRT-III), facilitating the necessary separation of daughter cells. CHMP4C has been proposed to be involved in the progression of different carcinomas. However, the value of CHMP4C in prostate cancer has not yet been explored. Prostate cancer is the most frequently occurring malignancy among male and remains a leading cause of deaths in cancers. So far, clinical therapy of prostate cancer is more inclined to molecular classification and specific clinical treatment and research. Our study investigated the expression and clinical prognosis of CHMP4C and explored its potential regulatory mechanism in prostate cancer. The immune status of CHMP4C in prostate cancer and relative immunotherapy were then analyzed in our study. Based on CHMP4C expression, a new subtype of prostate cancer was established for precision treatment.

Methods

We studied the expression of CHMP4C and relative clinical outcome using the online databases TIMER, GEPIA2, UALCAN, and multiple R packages. Meanwhile, the biological function, immune microenvironment and immunotherapy value of CHMP4C in prostate cancer were further explored on the R software platform with different R packages. Then we performed qRT-PCR, Western Blotting, transwell, CCK8, wound healing assay, colony formation assay and immunohistochemistry to verify the expression of CHMP4C, carcinogenesis and potential regulatory mechanisms in prostate cancer.

Results

We found that the expression of CHMP4C is significant in prostate cancer and the high expression of CHMP4C represents a poor clinical prognosis and malignant progression of prostate cancer. In subsequent vitro validation, CHMP4C promoted the malignant biological behavior of prostate cancer cell lines by adjusting the cell cycle. Based on CHMP4C expression, we established two new subtypes of prostate cancer and found that low CHMP4C expression has a better immune response while high CHMP4C expression was more sensitive to paclitaxel and 5-fluorouracil. Above findings revealed a new diagnostic marker for prostate cancer and facilitated the subsequent precise treatment of prostate cancer.

Tumor Cell-derived Extracellular Vesicles in Modulating Phenotypes and Immune Functions of Macrophages: Mechanisms and Therapeutic Applications

Tumor tissues consist of tumor cells and tumor stroma, which is structured by non-tumor cells and the extracellular matrix. Macrophages are the predominant immune cells in the tumor microenvironment (TME). Based on the intimate interaction between macrophages and tumor cells, macrophages are closely involved in tumor initiation and progression, playing a key role in tumor formation, angiogenesis, metastasis, and immune escape. Extracellular vesicles (EVs) are a group of membrane-enclosed structures secreted by almost all cell types. As crucial mediators of cell-to-cell communication, EVs play a role in various physiological processes and the development of diseases including cancer. According to numerous studies, tumor cell-derived extracellular vesicles (T-EVs) could highly modulate the phenotypes and functions of macrophages, thus promoting tumor development. Herein, we comprehensively introduce the role of T-EVs in regulating the M1/M2 phenotypes and immune functions of macrophages, including cytokine secretion, expression of immune regulatory molecules on the membrane, phagocytosis, and antigen presentation. More importantly, based on the regulatory effects of T-EVs on macrophages, we propose several potential therapeutic approaches that may guide future attempts to increase the effectiveness of cancer therapy.

Updates on the study of lysosomal protein dynamics: possibilities for the clinic

INTRODUCTION

The lysosome is the main degradative organelle of almost all mammalian cells, fulfilling important functions in macromolecule recycling, metabolism, and signaling. Lysosomal dysfunction is connected to a continuously growing number of pathologic conditions, and lysosomal proteins present potential biomarkers for a variety of diseases. Therefore, there is an increasing interest in their analysis in patient samples.

AREAS COVERED

We provide an overview of OMICs studies which identified lysosomal proteins as potential biomarkers for pathological conditions, covering proteomics, genomics, and transcriptomics approaches, identified through PubMed searches. With respect to discovery proteomics analyses, mainly lysosomal luminal and associated proteins were detected, while membrane proteins were found less frequently. Comprehensive coverage of the lysosomal proteome was only achieved by ultra-deep-coverage studies, but targeted approaches allowed for the reproducible quantification of lysosomal proteins in diverse sample types.

EXPERT OPINION

The low abundance of lysosomal proteins complicates their reproducible analysis in patient samples. Whole proteome shotgun analyses fail in many instances to cover the lysosomal proteome, which is due to under-sampling and/or a lack of sensitivity. With the current state of the art, targeted proteomics assays provide the best performance for the characterization of lysosomal proteins in patient samples.

A guide to mass spectrometric analysis of extracellular vesicle proteins for biomarker discovery

Exosomes (small extracellular vesicles) in living organisms play an important role in processes such as cell proliferation or intercellular communication. Recently, exosomes have been extensively investigated for biomarker discoveries for various diseases. An important aspect of exosome analysis involves the development of enrichment methods that have been introduced for successful isolation of exosomes. These methods include ultracentrifugation, size exclusion chromatography, polyethylene glycol-based precipitation, immunoaffinity-based enrichment, ultrafiltration, and asymmetric flow field-flow fractionation among others. To confirm the presence of exosomes, various characterization methods have been utilized such as Western blot analysis, atomic force microscopy, electron microscopy, optical methods, zeta potential, visual inspection, and mass spectrometry. Recent advances in high-resolution separations, high-performance mass spectrometry and comprehensive proteome databases have all contributed to the successful analysis of exosomes from patient samples. Herein we review various exosome enrichment methods, characterization methods, and recent trends of exosome investigations using mass spectrometry-based approaches for biomarker discovery.

The Roles of Exosomal Proteins: Classification, Function, and Applications

Exosome, a subpopulation of extracellular vesicles, plays diverse roles in various biological processes. As one of the most abundant components of exosomes, exosomal proteins have been revealed to participate in the development of many diseases, such as carcinoma, sarcoma, melanoma, neurological disorders, immune responses, cardiovascular diseases, and infection. Thus, understanding the functions and mechanisms of exosomal proteins potentially assists clinical diagnosis and targeted delivery of therapies. However, current knowledge about the function and application of exosomal proteins is still limited. In this review, we summarize the classification of exosomal proteins, and the roles of exosomal proteins in exosome biogenesis and disease development, as well as in the clinical applications.

Nurturing the marriages of urinary liquid biopsies and nano-diagnostics for precision urinalysis of prostate cancer

Prostate cancer remains the second-most common cancer diagnosed in men, despite the increasingly widespread use of serum prostate-specific antigen (PSA) screening. The controversial clinical implications and cost benefits of PSA screening have been highlighted due to its poor specificity, resulting in a high rate of overdiagnosis and underdiagnosis. Thus, the development of novel biomarkers for prostate cancer detection remains an intriguing challenge. Urine is emerging as a source for prostate cancer biomarker discovery. Currently, new urine biomarkers already outperform serum PSA in clinical diagnosis. Meanwhile, the advances in nanotechnology have provided a suite of diagnostic tools to study prostate cancer in more detail, sparking a new era of biomarker discoveries. In this review, we envision that future prostate cancer diagnosis will probably integrate multiplex nano-diagnostic approaches to detect novel urinary biomarkers. However, challenges remain in differentiating indolent from aggressive cancers to better inform treatment decisions, and clinical translation still needs to be overcome.

Extracellular vesicles for precision medicine in prostate cancer - Is it ready for clinical translation?

Biofluid-based biomarker tests hold great promise for precision medicine in prostate cancer (PCa) clinical practice. Extracellular vesicles (EV) are established as intercellular messengers in cancer development with EV cargos, including protein and nucleic acids, having the potential to serve as biofluid-based biomarkers. Recent clinical studies have begun to evaluate EV-based biomarkers for PCa diagnosis, prognosis, and disease/therapy resistance monitoring. Promising results have led to PCa EV biomarker validation studies which are currently underway with the next challenge being translation to robust clinical assays. However, EV research studies generally use low throughput EV isolation methods and costly molecular profiling technologies that are not suitable for clinical assays. Here, we consider the technical hurdles in translating EV biomarker research findings into precise and cost-effective clinical biomarker assays. Novel microfluidic devices coupling EV extraction with sensitive antibody-based biomarker detection are already being explored for point-of-care applications for rapid provision in personalised medicine approaches.

Potential Role of Seven Proteomics Tissue Biomarkers for Diagnosis and Prognosis of Prostate Cancer in Urine

As the currently available tests for the clinical management of prostate cancer (PCa) are still far from providing precise diagnosis and risk stratification, the identification of new molecular marker(s) remains a pertinent clinical need. Candidate PCa biomarkers from the published proteomic comparative studies of prostate tissue (2002-2020) were collected and systematically evaluated. AZGP1, MDH2, FABP5, ENO1, GSTP1, GSTM2, and EZR were chosen for further evaluation in the urine of 85 PCa patients and controls using ELISA. Statistically significant differences in protein levels between PCa and BPH showed FABP5 (p = 0.019) and ENO1 (p = 0.015). A biomarker panel based on the combination of FABP5, ENO1, and PSA provided the highest accuracy (AUC = 0.795) for PCa detection. The combination of FABP5, EZR, AZGP1, and MDH2 showed AUC = 0.889 in PCa prognosis, with 85.29% of the samples correctly classified into low and high Gleason score (GS) groups. The addition of PSA to the panel slightly increased the AUC to 0.914. AZGP1, FABP5, and EZR showed significant correlation with GS, stage, and percentage of positive biopsy cores. Although validation using larger patient cohorts will be necessary to establish the credibility of the proposed biomarker panels in a clinical context, this study opens a way for the further testing of more high-quality proteomics biomarkers, which could ultimately add value to the clinical management of PCa.

A novel signature based on pyroptosis-related genes for predicting prognosis and treatment response in prostate cancer patients

Background: Pyroptosis is a form of programmed cell death accompanied by specific inflammatory and immune responses, and it is closely related to the occurrence and progression of various cancers. However, the roles of pyroptosis-related genes (PRGs) in the prognosis, treatment response, and tumor microenvironment (TME) of prostate cancer (PCa) remain to be investigated. Methods: The mRNA expression data and clinical information of PCa patients were obtained from the Cancer Genome Atlas database (TCGA) and the cBioPortal for Cancer Genomics website, and the 52 PRGs were obtained from the published papers. The univariate, multivariate, and LASSO Cox regression algorithms were used to obtain prognostic hub PRGs. Meanwhile, qRT-PCR was used to validate the expression of hub genes between PCa lines and normal prostate epithelial cell lines. We then constructed and validated a risk model associated with the patient's disease-free survival (DFS). Finally, the relationships between risk score and clinicopathological characteristics, tumor immune microenvironment, and drug treatment response of PCa were systematically analyzed. Results: A prognostic risk model was constructed with 6 hub PRGs (CHMP4C, GSDMB, NOD2, PLCG1, CYCS, GPX4), and patients were divided into high and low-risk groups by median risk score. The risk score was confirmed to be an independent prognostic factor for PCa in both the training and external validation sets. Patients in the high-risk group had a worse prognosis than those in the low-risk group, and they had more increased somatic mutations, higher immune cell infiltration and higher expression of immune checkpoint-related genes. Moreover, they were more sensitive to cell cycle-related chemotherapeutic drugs and might be more responsive to immunotherapy. Conclusion: In our study, pyroptosis played a significant role in the management of the prognosis and tumor microenvironment of PCa. Meanwhile, the established model might help to develop more effective individual treatment strategies.

Urine stabilization and normalization strategies favor unbiased analysis of urinary EV content

Urine features an ideal source of non-invasive diagnostic markers. Some intrinsic and methodological issues still pose barriers to its full potential as liquid biopsy substrate. Unlike blood, urine concentration varies with nutrition, hydration and environmental factors. Urine is enriched with EVs from urinary-genital tract, while its conservation, purification and normalization can introduce bias in analysis of EV subsets in inter-and intra-individual comparisons. The present study evaluated the methods that decrease such biases such as appropriate and feasible urine storage, optimal single-step EV purification method for recovery of proteins and RNAs from small urine volumes and a normalization method for quantitative analysis of urine EV RNAs. Ultracentrifugation, chemical precipitation and immuno-affinity were used to isolate EVs from healthy donors' urine that was stored frozen or at room temperature for up to 6 months. Multiple urine biochemical and EV parameters, including particle count and protein content, were compared across urine samples. To this purpose nanoparticle tracking analysis (NTA) and protein assessment by BCA, ELISA and WB assays were performed. These measurements were correlated with relative abundances of selected EV mRNAs and miRNAs assessed by RT-PCR and ranked for the ability to reflect and correct for EV content variations in longitudinal urine samples. All purification methods enabled recovery and downstream analysis of EVs from as few as 1 ml of urine. Our findings highlight long term stability of EV RNAs upon urine storage at RT as well as excellent correlation of EV content in urine with some routinely measured biochemical features, such as total urine protein and albumin, but not creatinine most conventionally used for urine normalization. Comparative evaluation of mRNA and miRNAs in EV isolates revealed specific RNAs, in particular RNY4 and small miRNA panel, levels of which well reflected the inter-sample EV variation and therefore useful as possible post-analytical normalizers of EV RNA content. We describe some realistic urine processing and normalization solutions for unbiased readout of EV biomarker studies and routine clinical sampling and diagnostics providing the input for design of larger validation studies employing urine EVs as biomarkers for particular conditions and diseases.

A Breast Cancer Prediction Model Based on a Panel from Circulating Exosomal miRNAs

Breast cancer (BC) has been a serious threat to women's health. Exosomes contain a variety of biomolecules, which is an excellent choice as disease diagnostic markers, but whether it could be applied as a noninvasive biomarker for BC diagnosis demands to be additional studied. In this study, we aimed at creating a predictive model and reveal the value of plasma exosomal miRNA (exo-miRNA) in early diagnosis of BC. Firstly, exosomes isolated from plasma were identified by Nanoparticle Tracking Analysis (NTA), Transmission Electron Microscope (TEM), and Western Blot. miRNA expression in plasma samples from 56 BC patients and 40 normal controls was analyzed by high-throughput sequencing. miRNAs with strong correlation characteristics were selected by Lasso logistic regression. Then, we built the training set and test set, evaluated the Lasso regression accuracy, and evaluated the performance of different models in the training set and test set. Finally, GO analysis, KEGG, and Reactome pathway enrichment analysis were used to understand the biological significance of 16 characteristic miRNAs. The successful separation of exosomes in serum was identified by NTA, TEM, and Western Blot. The training set data matrix containing 1962 miRNAs was obtained by sequencing for model construction, and 16 strongly correlated miRNAs were selected by Lasso logistic regression. The accuracy of Lasso regression in training set and test set were 97.22% and 95.83%, respectively. We built different models and evaluated the performance of each model in the training set and test set. The results showed that the AUC values of Lasso, SVM, GBDT, and Random Forest model in the training set were 1, and the AUC values in the test set were 0.979, 0.936, 0.971, and 0.979, respectively. Bioinformatics analysis showed that 16 signature miRNAs were significantly enriched in cancer-related pathways such as herpes simplex virus 1 infection, TGF-β signaling, and Toll-like receptor family. The results of this study suggest that the 16 characteristic miRNAs screened from plasma exosomes can be used as a group of biomarkers, and the prediction model constructed based on this set of markers is expected to be used in the early diagnosis of BC.

A novel association of pyroptosis-related gene signature with the prognosis of hepatocellular carcinoma

Background

Hepatocellular carcinoma (HCC) is one of the global leading lethal tumors. Pyroptosis has recently been defined as an inflammatory programmed cell death, which is closely linked to cancer progression. However, the significance of pyroptosis-related genes (PRGs) in the prognosis of HCC remains elusive.

Methods

RNA sequencing (RNA-seq) data of HCC cases and their corresponding clinical information were collected from the Cancer Genome Atlas (TCGA) database, and differential PRGs were explored. The prognostic PRGs were analyzed with univariate COX regression and the least absolute shrinkage and selection operator (LASSO) Cox regression analysis to build a prognostic model in the TCGA training cohort. The predictive model was further validated in the TCGA test cohort and ICGC validation cohort. Differential gene function and associated pathway analysis were performed by Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genomes (KEGG). Single-sample gene set enrichment analysis (ssGSEA) was used to identify distinct immune cell infiltration. The mRNA and protein expression of prognostic PRGs was examined by quantitative RT-qPCR and immunohistochemistry.

Results

We identified 46 PRGs that were differentially expressed between normal and HCC tissues in a TCGA cohort, and HCC patients could be well categorized into two clusters associated with distinct survival rates based on expression levels of the PRGs. A three-PRG prognostic model comprising CHMP4A, HMGB1 and PLK1 was constructed in the training cohort, and HCC patients could be classified into the high- and low-risk subgroups based on the median risk score. High-risk patients exhibited shorter overall survival (OS) than low-risk ones, which was validated in the test cohort and ICGC validation cohort. The risk score of this model was confirmed as an independent prognostic factor to predict OS of HCC patients. GO, KEGG and ssGSEA demonstrated the differential immune cell infiltrations were associated with the risk scores. The higher expression of CHMP4A, HMGB1 and PLK1 were validated in HCC compared to normal in vivo and in vitro.

Conclusion

The three-PRG signature (CHMP4A, HMGB1, and PLK1) could act as an independent factor to predict the prognosis of HCC patients, which would shed light upon a potent therapeutic strategy for HCC treatment.

Targeted inhibition of tumor-derived exosomes as a novel therapeutic option for cancer

Mounting evidence indicates that tumor-derived exosomes (TDEs) play critical roles in tumor development and progression by regulating components in the tumor microenvironment (TME) in an autocrine or paracrine manner. Moreover, due to their delivery of critical molecules that react to chemotherapy and immunotherapy, TDEs also contribute to tumor drug resistance and impede the effective response of antitumor immunotherapy, thereby leading to poor clinical outcomes. There is a pressing need for the inhibition or removal of TDEs to facilitate the treatment and prognosis of cancer patients. Here, in the present review, we systematically overviewed the current strategies for TDE inhibition and clearance, providing novel insights for future tumor interventions in translational medicine. Moreover, existing challenges and potential prospects for TDE-targeted cancer therapy are also discussed to bridge the gaps between progress and promising applications.

Inhibiting or removing tumor-derived exosomes (TDEs), tiny membrane-bound packets of DNA, RNA, and proteins secreted by tumors, may improve cancer therapies. TDEs can suppress the body’s immune response, promote tumor progression and spread, and reduce efficacy of cancer drugs and immunotherapy. Gang Chen at Wuhan University, China, and co-workers have reviewed ways to remove or inhibit production of TDEs. They report that disruption of the genes for production of TDEs, drugs that inhibit TDE secretion, and removal of TDEs via plasma exchange or dialysis are all being investigated and show promise for reducing patient TDE load, thereby increasing the efficacy of anti-cancer drugs and immunotherapy. Future challenges include reducing side effects and finding less invasive ways to filter out TDEs. Gaining a better understanding of TDEs may help to improve therapies for many types of cancer.

Alpha-2-macroglobulin as a novel diagnostic biomarker for human bladder cancer in urinary extracellular vesicles

Extracellular vesicles (EVs) derived from urine are promising tools for the diagnosis of urogenital cancers. Urinary EVs (uEVs) are considered potential biomarkers for bladder cancer (BC) because urine is in direct contact with the BC tumor microenvironment and thus reflects the current state of the disease. However, challenges associated with the effective isolation and analysis of uEVs complicate the clinical detection of uEV-associated protein biomarkers. Herein, we identified uEV-derived alpha-2-macroglobulin (a2M) as a novel diagnostic biomarker for BC through comparative analysis of uEVs obtained from patients with BC pre- and post-operation using an antibody array. Furthermore, enzyme-linked immunosorbent assay of uEVs isolated from patients with BC (n=60) and non-cancer control subjects (n=23) validated the significant upregulation of a2M expression in patient uEVs (p<0.0001). There was no significant difference in whole urine a2M levels between patients with BC and controls (p=0.317). We observed that compared to classical differential centrifugation, ExoDisc, a centrifugal microfluidic tangential flow filtration device, was a significantly more effective separation method for uEV protein analysis. We expect that our approach for EV analysis will provide an efficient route for the identification of clinically meaningful uEV-based biomarkers for cancer diagnosis.

Artificially Intelligent Nanoarray Detects Various Cancers by Liquid Biopsy of Volatile Markers

Cancer is usually not symptomatic in its early stages. However, early detection can vastly improve prognosis. Liquid biopsy holds great promise for early detection, although it still suffers from many disadvantages, mainly searching for specific cancer biomarkers. Here, a new approach for liquid biopsies is proposed, based on volatile organic compound (VOC) patterns in the blood headspace. An artificial intelligence nanoarray based on a varied set of chemi-sensitive nano-based structured films is developed and used to detect and stage cancer. As a proof-of-concept, three cancer models are tested showing high incidence and mortality rates in the population: breast cancer, ovarian cancer, and pancreatic cancer. The nanoarray has >84% accuracy, >81% sensitivity, and >80% specificity for early detection and >97% accuracy, 100% sensitivity, and >88% specificity for metastasis detection. Complementary mass spectrometry analysis validates these results. The ability to analyze such a complex biological fluid as blood, while considering data of many VOCs at a time using the artificially intelligent nanoarray, increases the sensitivity of predictive models and leads to a potential efficient early diagnosis and disease-monitoring tool for cancer.

Using human urinary extracellular vesicles to study physiological and pathophysiological states and regulation of the sodium chloride cotransporter

The thiazide-sensitive sodium chloride cotransporter (NCC), expressed in the renal distal convoluted tubule, plays a major role in Na+, Cl- and K+ homeostasis and blood pressure as exemplified by the symptoms of patients with non-functional NCC and Gitelman syndrome. NCC activity is modulated by a variety of hormones, but is also influenced by the extracellular K+ concentration. The putative "renal-K+ switch" mechanism is a relatively cohesive model that links dietary K+ intake to NCC activity, and may offer new targets for blood pressure control. However, a remaining hurdle for full acceptance of this model is the lack of human data to confirm molecular findings from animal models. Extracellular vesicles (EVs) have attracted attention from the scientific community due to their potential roles in intercellular communication, disease pathogenesis, drug delivery and as possible reservoirs of biomarkers. Urinary EVs (uEVs) are an excellent sample source for the study of physiology and pathology of renal, urothelial and prostate tissues, but the diverse origins of uEVs and their dynamic molecular composition present both methodological and data interpretation challenges. This review provides a brief overview of the state-of-the-art, challenges and knowledge gaps in current uEV-based analyses, with a focus on the application of uEVs to study the "renal-K+ switch" and NCC regulation. We also provide recommendations regarding biospecimen handling, processing and reporting requirements to improve experimental reproducibility and interoperability towards the realisation of the potential of uEV-derived biomarkers in hypertension and clinical practice.