scholarly journals Liquid biopsy of extracellular vesicle biomarkers for prostate cancer personalized treatment decision

2022 ◽  
Author(s):  
Meng Han ◽  
Bairen Pang ◽  
Cheng Zhou ◽  
Xin Li ◽  
Qi Wang ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Liquid Biopsy ◽  
Treatment Decision ◽  
Extracellular Vesicle ◽  
Large Sample Size ◽  
Specific Expression ◽  
Non Invasive ◽  
Machine Learning Model ◽  
Blood And Urine Samples ◽  
Generation Sequencing

Liquid biopsy of tumor-derived extracellular vesicles (EVs) has great potential as a biomarker source for prostate cancer (CaP) early diagnosis and predicting the stages of cancer. The contents of EVs play an important role in intercellular communication and have specific expression in blood and urine samples from CaP patients. Powered by high-throughput, next-generation sequencing and proteomic technologies, novel EV biomarkers are easily detected in a non-invasive manner in different stages of CaP patients. These identified potential biomarkers can be further validated with a large sample size, machine learning model, and other different methods to improve the sensitivity and specificity of CaP diagnosis. The EV-based liquid biopsy is a novel and less-invasive alternative to surgical biopsies which would enable clinicians to potentially discover a whole picture of tumor through a simple blood or urine sample. In summary, this approach holds promise for developing personalized medicine to guide treatment decisions precisely for CaP patients.

scholarly journals Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Leyla A. Erozenci ◽  
Sander R. Piersma ◽  
Thang V. Pham ◽  
Irene V. Bijnsdorp ◽  
Connie R. Jimenez
Keyword(s):  
Expression Patterns ◽  
Interaction Network ◽  
Extracellular Vesicle ◽  
Protein Signaling ◽  
Protein Patterns ◽  
Specific Expression ◽  
Non Invasive ◽  
Data Independent Acquisition ◽  
Time Period ◽  
Using Data

AbstractThe protein content of urinary extracellular vesicles (EVs) is considered to be an attractive non-invasive biomarker source. However, little is known about the consistency and variability of urinary EV proteins within and between individuals over a longer time-period. Here, we evaluated the stability of the urinary EV proteomes of 8 healthy individuals at 9 timepoints over 6 months using data-independent-acquisition mass spectrometry. The 1802 identified proteins had a high correlation amongst all samples, with 40% of the proteome detected in every sample and 90% detected in more than 1 individual at all timepoints. Unsupervised analysis of top 10% most variable proteins yielded person-specific profiles. The core EV-protein-interaction network of 516 proteins detected in all measured samples revealed sub-clusters involved in the biological processes of G-protein signaling, cytoskeletal transport, cellular energy metabolism and immunity. Furthermore, gender-specific expression patterns were detected in the urinary EV proteome. Our findings indicate that the urinary EV proteome is stable in longitudinal samples of healthy subjects over a prolonged time-period, further underscoring its potential for reliable non-invasive diagnostic/prognostic biomarkers.

scholarly journals Prostate Cancer Liquid Biopsy Biomarkers’ Clinical Utility in Diagnosis and Prognosis

Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3373
Author(s):  
Milena Matuszczak ◽  
Jack A. Schalken ◽  
Maciej Salagierski
Keyword(s):  
Prostate Cancer ◽  
Liquid Biopsy ◽  
Current Knowledge ◽  
Prostate Gland ◽  
Specific Antigen ◽  
Transrectal Ultrasound ◽  
Digital Rectal Examination ◽  
Cost Effective ◽  
Non Invasive ◽  
Diagnosis And Prognosis

Prostate cancer (PCa) is the most common cancer in men worldwide. The current gold standard for diagnosing PCa relies on a transrectal ultrasound-guided systematic core needle biopsy indicated after detection changes in a digital rectal examination (DRE) and elevated prostate-specific antigen (PSA) level in the blood serum. PSA is a marker produced by prostate cells, not just cancer cells. Therefore, an elevated PSA level may be associated with other symptoms such as benign prostatic hyperplasia or inflammation of the prostate gland. Due to this marker’s low specificity, a common problem is overdiagnosis, which leads to unnecessary biopsies and overtreatment. This is associated with various treatment complications (such as bleeding or infection) and generates unnecessary costs. Therefore, there is no doubt that the improvement of the current procedure by applying effective, sensitive and specific markers is an urgent need. Several non-invasive, cost-effective, high-accuracy liquid biopsy diagnostic biomarkers such as Progensa PCA3, MyProstateScore ExoDx, SelectMDx, PHI, 4K, Stockholm3 and ConfirmMDx have been developed in recent years. This article compares current knowledge about them and their potential application in clinical practice.

scholarly journals Novel, non-invasive markers for detecting therapy induced neuroendocrine differentiation in castration-resistant prostate cancer patients

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Divya Bhagirath ◽  
Michael Liston ◽  
Theresa Akoto ◽  
Byron Lui ◽  
Barbara A. Bensing ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Patients ◽  
Neuroendocrine Differentiation ◽  
Extracellular Vesicle ◽  
Machine Learning Algorithms ◽  
Castration Resistant Prostate Cancer ◽  
Cellular Models ◽  
Non Invasive ◽  
Castration Resistant ◽  
Neuroendocrine Prostate Cancer

AbstractNeuroendocrine prostate cancer (NEPC), a highly aggressive variant of castration-resistant prostate cancer (CRPC), often emerges upon treatment with androgen pathway inhibitors, via neuroendocrine differentiation. Currently, NEPC diagnosis is challenging as available markers are not sufficiently specific. Our objective was to identify novel, extracellular vesicles (EV)-based biomarkers for diagnosing NEPC. Towards this, we performed small RNA next generation sequencing in serum EVs isolated from a cohort of CRPC patients with adenocarcinoma characteristics (CRPC-Adeno) vs CRPC-NE and identified significant dysregulation of 182 known and 4 novel miRNAs. We employed machine learning algorithms to develop an ‘EV-miRNA classifier’ that could robustly stratify ‘CRPC-NE’ from ‘CRPC-Adeno’. Examination of protein repertoire of exosomes from NEPC cellular models by mass spectrometry identified thrombospondin 1 (TSP1) as a specific biomarker. In view of our results, we propose that a miRNA panel and TSP1 can be used as novel, non-invasive tools to identify NEPC and guide treatment decisions. In conclusion, our study identifies for the first time, novel non-invasive exosomal/extracellular vesicle based biomarkers for detecting neuroendocrine differentiation in advanced castration resistant prostate cancer patients with important translational implications in clinical management of these patients that is currently extremely challenging.

scholarly journals Technological Approaches in the Analysis of Extracellular Vesicle Nucleotide Sequences

2021 ◽  
Vol 9 ◽  
Author(s):  
Tine Tesovnik ◽  
Barbara Jenko Bizjan ◽  
Robert Šket ◽  
Maruša Debeljak ◽  
Tadej Battelino ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nucleotide Sequence ◽  
Liquid Biopsy ◽  
Extracellular Vesicle ◽  
Nucleotide Sequences ◽  
Isolation Procedure ◽  
Transcriptomic Data ◽  
Dna And Rna ◽  
Health And Disease ◽  
Generation Sequencing

Together with metabolites, proteins, and lipid components, the EV cargo consists of DNA and RNA nucleotide sequence species, which are part of the intracellular communication network regulating specific cellular processes and provoking distinct target cell responses. The extracellular vesicle (EV) nucleotide sequence cargo molecules are often investigated in association with a particular pathology and may provide an insight into the physiological and pathological processes in hard-to-access organs and tissues. The diversity and biological function of EV nucleotide sequences are distinct regarding EV subgroups and differ in tissue- and cell-released EVs. EV DNA is present mainly in apoptotic bodies, while there are different species of EV RNAs in all subgroups of EVs. A limited sample volume of unique human liquid biopsy provides a small amount of EVs with limited isolated DNA and RNA, which can be a challenging factor for EV nucleotide sequence analysis, while the additional difficulty is technical variability of molecular nucleotide detection. Every EV study is challenged with its first step of the EV isolation procedure, which determines the EV’s purity, yield, and diameter range and has an impact on the EV’s downstream analysis with a significant impact on the final result. The gold standard EV isolation procedure with ultracentrifugation provides a low output and not highly pure isolated EVs, while modern techniques increase EV’s yield and purity. Different EV DNA and RNA detection techniques include the PCR procedure for nucleotide sequence replication of the molecules of interest, which can undergo a small-input EV DNA or RNA material. The nucleotide sequence detection approaches with their advantages and disadvantages should be considered to appropriately address the study problem and to extract specific EV nucleotide sequence information with the detection using qPCR or next-generation sequencing. Advanced next-generation sequencing techniques allow the detection of total EV genomic or transcriptomic data even at the single-molecule resolution and thus, offering a sensitive and accurate EV DNA or RNA biomarker detection. Additionally, with the processes where the EV genomic or transcriptomic data profiles are compared to identify characteristic EV differences in specific conditions, novel biomarkers could be discovered. Therefore, a suitable differential expression analysis is crucial to define the EV DNA or RNA differences between conditions under investigation. Further bioinformatics analysis can predict molecular cell targets and identify targeted and affected cellular pathways. The prediction target tools with functional studies are essential to help specify the role of the investigated EV-targeted nucleotide sequences in health and disease and support further development of EV-related therapeutics. This review will discuss the biological diversity of human liquid biopsy–obtained EV nucleotide sequences DNA and RNA species reported as potential biomarkers in health and disease and methodological principles of their detection, from human liquid biopsy EV isolation, EV nucleotide sequence extraction, techniques for their detection, and their cell target prediction.

scholarly journals Rapid and Label-Free Isolation of Tumour Cells from the Urine of Patients with Localised Prostate Cancer Using Inertial Microfluidics

Cancers ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 81 ◽  
Author(s):  
Alexey S. Rzhevskiy ◽  
Sajad Razavi Bazaz ◽  
Lin Ding ◽  
Alina Kapitannikova ◽  
Nima Sayyadi ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Liquid Biopsy ◽  
Diagnostic Value ◽  
Tumour Cells ◽  
Label Free ◽  
Non Invasive ◽  
Diagnosis And Prognosis ◽  
Potential Clinical Utility ◽  
Phosphate Buffered Saline ◽  
Microchannel Device

During the last decade, isolation of circulating tumour cells via blood liquid biopsy of prostate cancer (PCa) has attracted significant attention as an alternative, or substitute, to conventional diagnostic tests. However, it was previously determined that localised forms of PCa shed a small number of cancer cells into the bloodstream, and a large volume of blood is required just for a single test, which is impractical. To address this issue, urine has been used as an alternative to blood for liquid biopsy as a truly non-invasive, patient-friendly test. To this end, we developed a spiral microfluidic chip capable of isolating PCa cells from the urine of PCa patients. Potential clinical utility of the chip was demonstrated using anti-Glypican-1 (GPC-1) antibody as a model of the primary antibody in immunofluorescent assay for identification and detection of the collected tumour cells. The microchannel device was first evaluated using DU-145 cells in a diluted Dulbecco’s phosphate-buffered saline sample, where it demonstrated >85 (±6) % efficiency. The microchannel proved to be functional in at least 79% of cases for capturing GPC1+ putative tumour cells from the urine of patients with localised PCa. More importantly, a correlation was found between the amount of the captured GPC1+ cells and crucial diagnostic and prognostic parameter of localised PCa—Gleason score. Thus, the technique demonstrated promise for further assessment of its diagnostic value in PCa detection, diagnosis, and prognosis.

scholarly journals Non-invasive Urine Test for Molecular Classification of Clinical Significance in Newly Diagnosed Prostate Cancer Patients

2021 ◽  
Vol 8 ◽  
Author(s):  
Jinan Guo ◽  
Xuhui Zhang ◽  
Taolin Xia ◽  
Heather Johnson ◽  
Xiaoyan Feng ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Patients ◽  
Clinical Significance ◽  
Treatment Decision ◽  
Urine Test ◽  
Newly Diagnosed ◽  
Grade Group ◽  
Non Invasive ◽  
Insignificant Cancer ◽  
Clinically Significant

Objective: To avoid over-treatment of low-risk prostate cancer patients, it is important to identify clinically significant and insignificant cancer for treatment decision-making. However, no accurate test is currently available.Methods: To address this unmet medical need, we developed a novel gene classifier to distinguish clinically significant and insignificant cancer, which were classified based on the National Comprehensive Cancer Network risk stratification guidelines. A non-invasive urine test was developed using quantitative mRNA expression data of 24 genes in the classifier with an algorithm to stratify the clinical significance of the cancer. Two independent, multicenter, retrospective and prospective studies were conducted to assess the diagnostic performance of the 24-Gene Classifier and the current clinicopathological measures by univariate and multivariate logistic regression and discriminant analysis. In addition, assessments were performed in various Gleason grades/ISUP Grade Groups.Results: The results showed high diagnostic accuracy of the 24-Gene Classifier with an AUC of 0.917 (95% CI 0.892–0.942) in the retrospective cohort (n = 520), AUC of 0.959 (95% CI 0.935–0.983) in the prospective cohort (n = 207), and AUC of 0.930 (95% 0.912-CI 0.947) in the combination cohort (n = 727). Univariate and multivariate analysis showed that the 24-Gene Classifier was more accurate than cancer stage, Gleason score, and PSA, especially in the low/intermediate-grade/ISUP Grade Group 1–3 cancer subgroups.Conclusions: The 24-Gene Classifier urine test is an accurate and non-invasive liquid biopsy method for identifying clinically significant prostate cancer in newly diagnosed cancer patients. It has the potential to improve prostate cancer treatment decisions and active surveillance.

Disease Monitoring in Multiple Myeloma Patients Using Liquid Biopsy and Next Generation Sequencing of IGH Gene Rearrangements

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4430-4430
Author(s):  
Silvia Gimondi ◽  
Giulia Biancon ◽  
Antonio Vendramin ◽  
Silvia Zaninelli ◽  
Sara Rizzitano ◽  
...  
Keyword(s):  
Liquid Biopsy ◽  
Tumor Burden ◽  
Disease Monitoring ◽  
Gene Rearrangements ◽  
Plasma Samples ◽  
Time Points ◽  
Non Invasive ◽  
Generation Sequencing ◽  
Over Time

Abstract Background: Current criteria used to assess response lag behind the extraordinary evolution in the treatment of multiple myeloma (MM) patients (pts), and more sensitive techniques are being explored to detect true minimal residual disease (MRD) for new complete remission (CR) definitions. In recent years, next generation sequencing (NGS) technologies have emerged. NGS of immunoglobulin (IgH) gene rearrangements are very sensitive and also allow the identification of small subclonal population that can be monitored over time during treatment, something not possible with flow cytometry or PCR. However, the patchy pattern of bone marrow infiltration observed in MM leads to some degree of uncertainty regarding MRD-negative results, irrespectively of the technique adopted. This highlights the value of applying "liquid biopsy" as a non-invasive strategy for monitoring MRD through the analysis of circulating cell-free tumor DNA (ctDNA). The objective of the current study was to measure residual tumor burden in sequential plasma samples of a cohort of MM pts by NGS of the IgH gene rearrangements. Methods: We retrospectively analyzed 14 MM pts homogeneously treated between 2011 and 2015 with all clinical data available. We obtained serial tumor and plasma samples at diagnosis and at specified time points during treatment cycles and up to 24 months of follow-up. Genomic DNA (gDNA) was extracted from immunomagnetically selected CD138+ plasma cells at diagnosis (n=14). ctDNA was extracted from 500uL of plasma (Qiagen) at diagnosis (n=14) and at follow-up time points (n=58). IgH gene rearrangements were amplified, quality assessed (Agilent hsDNA kit) and sequenced on Ion Torrent PGM as previously described (Gimondi et al., ASH 2015). Raw reads were filtered for quality, length (>250bp) and presence of both forward and reverse primers. Reads were subsequently aligned using IgBlast against IMGT germline database and aggregated into clonotypes based on identity of CDR3, V and J segments (MigMap). Post-processing analyses were performed using VDJtools and customized R scripts. Results: PCR products quality assessment from ctDNA amplification of the entire IgH-VDJ region revealed the presence of both short (150-250bp) and long amplicons (310-360bp). Raw reads were subjected to filtering using our custom bioinformatic workflow to retain only complete IgH-VDJ gene rearrangements and discard low-quality reads. Three pts could not be evaluated due to low quality sequencing reads in all samples. At least 3 follow-up time points were available for all the remaining 11 pts whereas 6 pts had 4 time points. At diagnosis, both plasma and tumor samples revealed a high level of heterogeneity (range 1980-7753 clonotypes) with only a small fraction of shared clonotypes (346±262, mean±SD). Among the shared ones, the clonotype with the highest frequency in plasma corresponded to the tumor-associated one identified in CD138+ cells. Interestingly, in the plasma of 3 pts, additional clonotypes were detected at relatively high frequencies (range 1-16%) suggesting the presence of subclones. IgH-NGS at follow-up time points revealed that the clonotype identified at diagnosis (range 4-31% of total reads) could be easily tracked over time in plasma samples, at frequencies as low as 0.00001%. Frequencies of the tumor-associated IgH gene rearrangement in plasma showed a patient-specific modulation and reflected the tumor burden assessed according to the International Myeloma Working Group-Uniform Response Criteria. At the time of CR, the tumor-associated clonotype was undetectable in the plasma of pts who would not subsequently relapse. In patients that would lately experience progressive disease, the tumor specific clonotype was still detectable at low frequencies (range 0.00001-0.03%) in all plasma samples suggesting that liquid biopsy can be used for MRD monitoring. Conclusions: Despite the limited number of pts and follow-up samples analyzed, we demonstrate that NGS of IgH gene rearrangements from ctDNA can be used for MM disease monitoring, thus representing a non-invasive alternative strategy for clinical management. The analysis of retrospectively collected plasma samples revealed that ctDNA quality is essential for a NGS characterization of IgH gene rearrangements. Plasma samples collection and processing represent critical steps that need to be considered designing prospective liquid biopsy studies. Disclosures No relevant conflicts of interest to declare.

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