Comparative Secretome Profiling and Mutant Protein Identification in Metastatic Prostate Cancer Cells by Quantitative Mass Spectrometry-based Proteomics

Liquid biopsy to personalize treatment for metastatic prostate cancer

Liquid biopsy is an innovative approach that provides a more complete understanding of treatment response and prognosis in monitoring metastatic prostate cancer. It complements invasive tissue biopsy and involves the assessment of various biomarkers in body fluids such as blood, semen, and urine. Liquid biopsy analyzes circulating tumor cells, extracellular vesicles, circulating tumor DNA, and the secretome. This is particularly important given the heterogeneity of prostate cancer and the need for better prognostic biomarkers. Liquid biopsy can personalize the treatment of homonosensitive and castration-resistant metastatic prostate cancer by acting as a predictive and prognostic tool. This review discusses various biomarkers, assay techniques, and potential applications in daily clinical practice, highlighting the exciting possibilities that this emerging field holds for improving patient outcomes.

Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants

Proteogenomics (PG) integrates the proteome with the genome and transcriptome to refine gene models and annotation. Coupled with single-cell (SC) assays, PG effectively distinguishes heterogeneity among cell groups. Affiliating spatial information to PG reveals the high-resolution circuitry within SC atlases. Additionally, PG can investigate dynamic changes in protein-coding genes in plants across growth and development as well as stress and external stimulation, significantly contributing to the functional genome. Here we summarize existing PG research in plants and introduce the technical features of various methods. Combining PG with other omics, such as metabolomics and peptidomics, can offer even deeper insights into gene functions. We argue that the application of PG will represent an important font of foundational knowledge for plants.

Application of Proteogenomics to Urine Analysis towards the Identification of Novel Biomarkers of Prostate Cancer: An Exploratory Study

Simple Summary

Prostate cancer (PCa) is one of the most common cancers. Due to the limited and invasive approaches for PCa diagnosis, it is crucial to identify more accurate and non-invasive biomarkers for its detection. The aim of our study was to non-invasively uncover new protein targets for detecting PCa using a proteomics and proteogenomics approach. This work identified several dysregulated mutant protein isoforms in urine from PCa patients, some of them predicted to have a protective or an adverse role in these patients. These results are promising given urine’s non-invasive nature and offers an auspicious opportunity for research and development of PCa biomarkers.

Abstract

To identify new protein targets for PCa detection, first, a shotgun discovery experiment was performed to characterize the urinary proteome of PCa patients. This revealed 18 differentially abundant urinary proteins in PCa patients. Second, selected targets were clinically tested by immunoblot, and the soluble E-cadherin fragment was detected for the first time in the urine of PCa patients. Third, the proteogenome landscape of these PCa patients was characterized, revealing 1665 mutant protein isoforms. Statistical analysis revealed 6 differentially abundant mutant protein isoforms in PCa patients. Analysis of the likely effects of mutations on protein function and PPIs involving the dysregulated mutant protein isoforms suggests a protective role of mutations HSPG2*Q1062H and VASN*R161Q and an adverse role of AMBP*A286G and CD55*S162L in PCa patients. This work originally characterized the urinary proteome, focusing on the proteogenome profile of PCa patients, which is usually overlooked in the analysis of PCa and body fluids. Combined analysis of mass spectrometry data using two different software packages was performed for the first time in the context of PCa, which increased the robustness of the data analysis. The application of proteogenomics to urine proteomic analysis can be very enriching in mutation-related diseases such as cancer.

Metastatic Prostate Cancer Cells Secrete Methylglyoxal-Derived MG-H1 to Reprogram Human Osteoblasts into a Dedifferentiated, Malignant-like Phenotype: A Possible Novel Player in Prostate Cancer Bone Metastases

Bone metastases from prostate cancer (PCa) result from a complex cross-talk between PCa cells and osteoblasts (OB). Thus, targeting this interplay has become an attractive strategy to interfere with PCa bone dissemination. The agents currently used in clinical trials have proved ineffective, boosting research to identify additional mechanisms that may be involved in this two-directional talk. Here, we investigated whether and how 5-hydro-5-methylimidazolone (MG-H1), a specific methylglyoxal (MG)-derived advanced glycation end product (AGE), was a novel player in the dialogue between PCa and OB to drive PCa bone metastases. Conditioned medium from osteotropic PC3 PCa cells, pre-treated or not with a specific MG scavenger, was administrated to human primary OB and cell morphology, mesenchymal trans-differentiation, pro-osteogenic determinants, PCa-specific molecules, and migration/invasion were studied by phase-contrast microscopy, real-time PCR, western blot and specific assays, respectively. We found that PC3 cells were able to release MG-H1 that, by binding to the receptor for AGEs (RAGE) on OB, reprogrammed them into a less-differentiate phenotype, endowed with some PCa-specific molecular features and malignant properties, in a mechanism involving reactive oxidative species (ROS) production and NF-kB pathway activation. These findings provide novel insights into the mechanisms of PCa osteoblastic metastases and foster in vivo research toward new therapeutic strategies interfering with PCa/OB cross-talk.

Bioactive compounds, antioxidant activity and antiproliferative effects in prostate cancer cells of green and roasted coffee extracts obtained by microwave-assisted extraction (MAE)

Coffee consumption has been investigated as a protective factor against prostate cancer. Coffee may be related to prostate cancer risk reduction due to its phytochemical compounds, such as caffeine, chlorogenic acids, and trigonelline. The roasting process affects the content of the phytochemicals and undesired compounds can be formed. Microwave-assisted extraction is an alternative to conventional extraction techniques since it preserves more bioactive compounds. Therefore, this study aimed to evaluate the phytochemical composition and the putative preventive effects in prostate cancer development of coffee beans submitted to four different coffee-roasting degrees extracted using microwave-assisted extraction. Coffea arabica green beans (1) were roasted into light (2), medium (3) and dark (4) and these four coffee samples were submitted to microwave-assisted extraction. The antioxidant capacity of these samples was evaluated by five different methods. Caffeine, chlorogenic acid and caffeic acid were measured through HPLC. Samples were tested against PC-3 and DU-145 metastatic prostate cancer cell lines regarding their effects on cell viability, cell cycle progression and apoptotic cell death. We found that green and light roasted coffee extracts had the highest antioxidant activity. Caffeine content was not affected by roasting, chlorogenic acid was degraded due to the temperature, and caffeic acid increased in light roasted and decreased in medium and dark roasted. Green and light roasted coffee extracts promoted higher inhibition of cell viability, caused greater cell cycle arrest in S and G₂/M and induced apoptosis more compared to medium and dark roasted coffee extracts and the control samples. Coffee extracts were more effective against DU-145 than in PC-3 cells. Our data provide initial evidence that among the four tested samples, the consumption of green and light coffee extracts contributes to inhibit prostate cancer tumor progression features, potentially preventing aspects related to advanced prostate cancer subtypes.

Clinical proteomics for prostate cancer: understanding prostate cancer pathology and protein biomarkers for improved disease management

Following the introduction of routine Prostate Specific Antigen (PSA) screening in the early 1990′s, Prostate Cancer (PCa) is often detected at an early stage. There are also a growing number of treatment options available and so the associated mortality rate is generally low. However, PCa is an extremely complex and heterogenous disease and many patients suffer disease recurrence following initial therapy. Disease recurrence commonly results in metastasis and metastatic PCa has an average survival rate of just 3–5 years. A significant problem in the clinical management of PCa is being able to differentiate between patients who will respond to standard therapies and those who may benefit from more aggressive intervention at an earlier stage. It is also acknowledged that for many men the disease is not life threatenting. Hence, there is a growing desire to identify patients who can be spared the significant side effects associated with PCa treatment until such time (if ever) their disease progresses to the point where treatment is required. To these important clinical needs, current biomarkers and clinical methods for patient stratification and personlised treatment are insufficient. This review provides a comprehensive overview of the complexities of PCa pathology and disease management. In this context it is possible to review current biomarkers and proteomic technologies that will support development of biomarker-driven decision tools to meet current important clinical needs. With such an in-depth understanding of disease pathology, the development of novel clinical biomarkers can proceed in an efficient and effective manner, such that they have a better chance of improving patient outcomes.

An overview of advances in multi-omics analysis in prostate cancer

Prostate cancer (PCa) is a deadly disease for men, and studies of all types of omics data are necessary to promote precision medicine. The maturity of sequencing technology, the improvements of computer processing power, and the progress achieved in omics analysis methods have improved research efficiency and saved research costs. The occurrence and development of PCa is due to multisystem and multilevel pathological changes. Although omics research at a single level is important, this approach often has limitations. In contrast, the combined analysis of multiple types of omics data can better analyze PCa changes as a whole, thus ensuring the validity of research results to the greatest extent. This paper introduces the applications of single omics in PCa and then summarizes research progress in the combined analysis of two or more types of omics data, so as to systematically and comprehensively analyze the necessity of combined analysis of multiple omics data in PCa.

Current Challenges and Implications of Proteogenomic Approaches in Prostate Cancer

In the recent past, next-generation sequencing (NGS) approaches have heralded the omics era. With NGS data burgeoning, there arose a need to disseminate the omic data better. Proteogenomics has been vividly used for characterising the functions of candidate genes and is applied in ascertaining various diseased phenotypes, including cancers. However, not much is known about the role and application of proteogenomics, especially Prostate Cancer (PCa). In this review, we outline the need for proteogenomic approaches, their applications and their role in PCa.

Effect of the roasting levels of Coffea arabica L. extracts on their potential antioxidant capacity and antiproliferative activity in human prostate cancer cells

Coffee, besides being one of the most consumed stimulating beverages in the world, has important bioactive activities, which have been attracting increasing attention from researchers. However, the standard process of roasting causes changes in its chemical composition. In the present study, extracts obtained from green and roasted beans (light, medium and dark) of Coffea arabica Linnaeus were submitted to high-power ultrasonic extraction and atomization by spray drying. Colorimetric analysis was used to classify the roasting levels of the dried extract samples. The effects of the roasting process on the bioactivity of the dried extracts were verified through the following assays: caffeine, chlorogenic acid and caffeic acid, by HPLC-PDA; total phenolics by Folin–Ciocalteu; antioxidant activity by DPPH, FRAP, ABTS and ORAC; antiproliferative activity, using the MTT assay; and cell cycle and apoptosis by flow cytometry in metastatic prostate cancer cell lines from bone (PC-3) and brain (DU-145). The results showed that the lowest levels of caffeine, chlorogenic and caffeic acids were observed in dark roasted coffee. In comparison to medium and dark extracts in PC-3 cells, the green and light coffee extracts had higher antioxidant activities and promoted cytotoxicity followed by cell cycle arrest in phase S and apoptosis induction. Thus, the roasting level of the coffee extracts may be related to the potential chemoprotective effects of Coffea arabica L. in prostate cancer cells.

Coffee, besides being one of the most consumed stimulating beverages in the world, has important bioactive activities, which have been attracting increasing attention from researchers.

Secretome profiling of PC3/nKR cells, a novel highly migrating prostate cancer subline derived from PC3 cells

Prostate cancer (PCa) is the most common cancer among men worldwide. Most PCa cases are not fatal; however, the outlook is poor when PCa spreads to another organ. Bone is the target organ in about 80% of patients who experience metastasis from a primary PCa tumor. In the present study, we characterized the secretome of PC3/nKR cells, which are a new subline of PC3 cells that were originally isolated from nude mice that were implanted with PC3 cells without anti-natural killer (NK) cell treatment. Wound healing and Transwell assays revealed that PC3/nKR cells had increased migratory and invasive activities in addition to a higher resistance to NK cells-induced cytotoxicity as compared to PC3 cells. We quantitatively profiled the secreted proteins of PC3/nKR and PC3 cells by liquid chromatography-tandem mass spectrometry analysis coupled with 2-plex tandem mass tag labeling. In total, 598 secretory proteins were identified, and 561 proteins were quantified, among which 45 proteins were secreted more and 40 proteins were secreted less by PC3/nKR cells than by PC3 cells. For validation, the adapter molecule crk, serpin B3, and cystatin-M were analyzed by western blotting. PC3/nKR cells showed the selective secretion of NKG2D ligand 2, HLA-A, and IL-6, which may contribute to their NK cell-mediated cytotoxicity resistance, and had a high secretion of crk protein, which may contribute to their high migration and invasion properties. Based on our secretome analysis, we propose that PC3/nKR cells represent a new cell system for studying the metastasis and progression of PCa.

An Optimized Method for the Proteomic Analysis of Low Volumes of Cell Culture Media and the Secretome: The Application and the Demonstration of Altered Protein Expression in iPSC-Derived Neuronal Cell Lines from Parkinson's Disease Patients

Traditionally, cell culture medium in iPSC-derived cell work is not the main focus of the research and often is considered as just "food for cells". We demonstrate that by manipulation of the media and optimized methodology, it is possible to use this solution to study the proteins that the cell secretes (the "secretome"). This is particularly useful in the study of iPSC-derived neurons, which require long culture time. We demonstrate that media can be used to model diseases with optimized incubation and sampling times. The ability not to sacrifice cells allows significant cost and research benefits. In this manuscript we describe an optimized method for the analysis of the cell media from iPSC-derived neuronal lines from control and Parkinson's disease patients. We have evaluated the use of standard and supplement B27-free cell media as well as five different sample preparation techniques for proteomic analysis of the cell secretome. Mass spectral analysis of culture media allowed for the identification of >500 proteins, in 500 μL of media, which is less volume than reported previously (20-40 mL). Using shorter incubation times and our optimized methodology, we describe the use of this technique to study and describe potential disease mechanisms in Parkinson's disease.

Modern urology perspectives on prostate cancer biomarkers

Introduction

Prostate cancer (PCa) is the most common type of cancer among men in Europe. Current recommendations for screening and diagnosis are based on prostate-specific antigen (PSA) measurements and the digital rectal examination (DRE). Both of them are triggers for prostate biopsy. Limited specificity of the PSA test brings, however, a need to develop new, better diagnostic tools. Several commercially available variations of the PSA test including: prostate health index (PHI), 4Kscore as well as molecular PCA3 score, have already revealed its value, lowering the number of unnecessary biopsies.

Material and methods

This review summarizes published results of the current most promising, clinically proven and experimentally evaluated PCa biomarkers which have potential for creation of new diagnostic tests.

Results

In the last few years new approaches for providing significantly better biomarkers, an alternative to PSA, have been introduced. Modern biomarkers show improvement in being used as not only a diagnosis procedure, but also for staging, evaluating aggressiveness and managing the therapeutic process. The most promising group are molecular markers, among them microRNAs(miRNAs) and long noncoding RNAs (lncRNAs) are most frequent. Their superiority, over standard PSA, in predicting tumor formation in early stages, and clinically non-symptomatic metastases has been noticed. Extracellular vesicles presence in biofluids have brought focus of many research groups, indicating their potential significance. This group of nanoparticles has potential not only in diagnostic and therapy management process, but also as a potential therapeutic target.

Conclusions

Finding better PCa biomarkers, replacing the current PSA measurement, is firmly needed in modern urology practice.