Molecular markers for prostate cancer in formalin-fixed paraffin-embedded tissues

Circ_0076305 facilitates prostate cancer development via sponging miR-411-5p and regulating PGK1

Abnormal expression of circular RNA (circRNA) is tightly linked to cancer progression. In this study, we aimed to investigate the biological role of circ_0076305 in prostate cancer (PCa). RT-qPCR was utilized to examine circ_0076305, microRNA-411-5p (miR-411-5p) and phosphoglycerate kinase 1 (PGK1) expression in PCa tissues and cells. CCK-8 assay, EdU assay, wound-healing assay and flow cytometry were executed to investigate the regulatory function of circ_0076305 on the proliferation, migration and apoptosis of PCa cells. Western blot (WB) assay was applied for measuring the protein levels. The effect of circ_0076305 on cellular glycolysis was examined using commercial kits. RNA immunoprecipitation (RIP) and dual-luciferase reporter assays were conducted for confirming the association between miR-411-5p and circ_0076305 or PGK1. The role of circ_0076305 in vivo was detected via establishing mice xenograft model. Circ_0076305 was highly expressed in PCa. Circ_0076305 silencing could repress cell growth, migration and glycolysis while triggered apoptosis in PCa cells. MiR-411-5p was targeted by circ_0076305, and miR-411-5p suppression counteracted the influence of circ_0076305 silencing in PCa cells. Additionally, miR-411-5p directly targeted PGK1, and miR-411-5p upregulation restrained PCa cell malignant behaviours via reducing PGK1. Mechanically, circ_0076305 sponged miR-411-5p to affect PGK1 expression. Importantly, circ_0076305 interference inhibited tumour growth in vivo. Circ_0076305 served as a novel oncogene PCa progression through regulation of miR-411-5p/PGK1 axis.

miR-96-5p, miR-134-5p, miR-181b-5p and miR-200b-3p heterogenous expression in sites of prostate cancer versus benign prostate hyperplasia-archival samples study

MicroRNAs are involved in various pathologies including cancer. The aim of the study was to assess the level of expression of miR-96-5p, -134-5p, -181b-5p, -200b-3p in FFPE samples of prostate cancer, adjacent cancer-free tissue, and benign prostatic hyperplasia. Samples of 23 FFPE prostate cancer and 22 benign prostatic hyperplasias were dissected and HE stained. Compartments of tumor tissue and adjacent healthy glandular tissue were isolated from each sample using Laser Capture Microdissection. Total RNA was isolated from dissected tissues. Expression of miR-96-5p, miR-134-5p, 181b-5p, and miR-200b-3p was determined by real-time RT-qPCR method. The expression of miR-200b-3p was significantly higher in cancerous prostate: both in adenocarcinomatous glands and in the adjacent, apparently unaffected glands compared to BPH samples. The expression of miR-181b-5p was lower in in both prostate cancer tissues and adjacent tissue compared to BPH samples. Expression of miR-96-5p and miR-134-5p was lower in prostate cancer tissues compared to BPH. Levels of miR-96-5p, miR-134-5p, and 181b-5p negatively correlated with the Gleason score. Given further studies, miR-96-5p, miR-134-5p and especially miR-200b-3p and miR-181b-5p may differentiate BPH and PC.

YB-1: The key to personalised prostate cancer management?

Y-box-binding protein 1 (YB-1) is a DNA/RNA binding protein increasingly implicated in the regulation of cancer cell biology. Normally located in the cytoplasm, nuclear localisation in prostate cancer is associated with more aggressive, potentially treatment-resistant disease. This is attributed to the ability of YB-1 to act as a transcription factor for various target genes associated with androgen receptor signalling, survival, DNA repair, proliferation, invasion, differentiation, angiogenesis and hypoxia. This review aims to examine the clinical potential of YB-1 in the detection and therapeutic management of prostate cancer.

Platform independent protein-based cell-of-origin subtyping of diffuse large B-cell lymphoma in formalin-fixed paraffin-embedded tissue

Diffuse large B-cell lymphoma (DLBCL) is commonly classified by gene expression profiling according to its cell of origin (COO) into activated B-cell (ABC)-like and germinal center B-cell (GCB)-like subgroups. Here we report the application of label-free nano-liquid chromatography - Sequential Window Acquisition of all THeoretical fragment-ion spectra - mass spectrometry (nanoLC-SWATH-MS) to the COO classification of DLBCL in formalin-fixed paraffin-embedded (FFPE) tissue. To generate a protein signature capable of predicting Affymetrix-based GCB scores, the summed log₂-transformed fragment ion intensities of 780 proteins quantified in a training set of 42 DLBCL cases were used as independent variables in a penalized zero-sum elastic net regression model with variable selection. The eight-protein signature obtained showed an excellent correlation (r = 0.873) between predicted and true GCB scores and yielded only 9 (21.4%) minor discrepancies between the three classifications: ABC, GCB, and unclassified. The robustness of the model was validated successfully in two independent cohorts of 42 and 31 DLBCL cases, the latter cohort comprising only patients aged >75 years, with Pearson correlation coefficients of 0.846 and 0.815, respectively, between predicted and NanoString nCounter based GCB scores. We further show that the 8-protein signature is directly transferable to both a triple quadrupole and a Q Exactive quadrupole-Orbitrap mass spectrometer, thus obviating the need for proprietary instrumentation and reagents. This method may therefore be used for robust and competitive classification of DLBCLs on the protein level.

The association of let-7c, miR-21, miR-145, miR-182, and miR-221 with clinicopathologic parameters of prostate cancer in patients diagnosed with low-risk disease

BACKGROUND

The diagnostic benefit of prostate specific antigen (PSA) is limited, owing to its lack of specificity, particularly in men with PSA levels of 4.0 to 10.0 ng/mL. Therefore, there is a need for more specific and sensitive biomarkers to improve diagnostic accuracy and to predict prostate cancer (PCa) progression. Assessing the expression levels of specific microRNAs (miRNAs) in patients with PCa may be helpful in detecting cancer and predicting the cancer prognosis and its evolution, and may serve as markers to decide the treatment. We examined the expression levels of five miRNAs (let-7c, miR-21, miR-145, miR-185, and miR-221) on patients with low-risk PCa who had been eligible for active surveillance but underwent radical prostatectomy. We investigated the correlation between the relative expression of miRNAs and clinicopathologic parameters to evaluate their clinical significance.

MATERIALS AND METHODS

Total RNA was isolated from the tumor and the corresponding non-neoplastic prostate tissue of 45 patients who underwent radical prostatectomy. Quantitative reverse transcriptase-polymerase chain reaction was used to measure the levels of let-7c, miR-21, miR-145, miR-185, miR-221, and RNU6B expression, using TaqMan MicroRNA Assays. miRNA expression was examined in low-risk PCa, and miRNAs' association with Gleason upgraded (GU) and biochemical recurrent (BR) patients was evaluated.

RESULTS

We observed that miR-21 and miR-182 were overexpressed; conversely, let-7c, miR-145, and miR-221 were underexpressed in patients with low-risk PCa. GU patients (n = 16) and non-upgraded patients (n = 28) were compared. miR-145 was downregulated significantly in the GU group (P = 0.03). Similarly, miR-221 was downregulated significantly in patients with BR (n = 14) compared with non-recurrent patients (n = 30) (P = 0.04). Receiver operator characteristics (ROC) curve analysis revealed that miR-221 levels were significantly associated with BR in patients with a cut-off <-1.666, a value at which sensitivity was 70% and specificity 71% (area under curve [AUC] = 0.705, P = 0.030).

CONCLUSIONS

There is still a need for a tumor marker with higher sensitivity and specificity than that of PSA. Among the five miRNAs examined, miR-221 was most associated with biochemical recurrence in low-risk PCa.

Circulating MicroRNAs as Biomarkers in Diffuse Large B-cell Lymphoma: A Pilot Prospective Longitudinal Clinical Study

Objectives:

Diffuse large B-cell lymphoma (DLBCL) is highly heterogeneous in terms of phenotype and treatment response in patients. These characteristics make the prognosis difficult to establish and hinder the use of new personalized treatments in clinical practice. In this context, there is currently a need to define new biomarkers enabling a better definition of DLBCL subtypes, prognosis evaluation, and an overview of the resistance to chemotherapeutics. The aim of this study was to evaluate the use of microRNAs found in plasma from patients with DLBCL as biomarkers of tumor evolution in these patients.

Method:

For this purpose, a plasma biobank was created with samples from patients with DLBCL. The evolution of the level of selected microRNAs during treatment has been studied. A total of 19 patients with DLBCL were included in this pilot mono-centered study and a total of 68 samples were analyzed.

Results:

The first step of this study was the selection of the microRNAs to be quantified in all the samples of the biobank and that could potentially be used as biomarkers. To this end, quantification of 377 microRNAs was performed on the plasma samples of 2 selected patients with DLBCL and 1 healthy donor with no history of cancer. Among the 377 microRNAs evaluated, 7 were selected and analyzed in the entire biobank.

Conclusions:

This study highlighted 5 circulating microRNAs whose plasma levels would be worth further investigating for the characterization of DLBCL evolution in patients. MiR-21 and miR-197 had a significant higher plasmatic level in patients with tumors unresponsive to treatment. With a higher plasma level in patients with complete remission, miR-19b, miR-20a, and miR-451 could enable to differentiate, at the remission review, patients with residual tumor, from patients with complete remission.

Targeted proteomics in urinary extracellular vesicles identifies biomarkers for diagnosis and prognosis of prostate cancer

Rapid and reliable diagnosis of prostate cancer (PCa) is highly desirable as current used methods lack specificity. In addition, identification of PCa biomarkers that can classify patients into high- and low-risk groups for disease progression at early stage will improve treatment decision-making. Here, we describe a set of protein-combination panels in urinary extracellular vesicles (EVs), defined by targeted proteomics and immunoblotting techniques that improve early non-invasive detection and stratification of PCa patients.We report a two-protein combination in urinary EVs that classifies benign and PCa patients (ADSV-TGM4), and a combination of five proteins able to significantly distinguish between high- and low-grade PCa patients (CD63-GLPK5-SPHM-PSA-PAPP). Proteins composing the panels were validated by immunohistochemistry assays in tissue microarrays (TMAs) confirming a strong link between the urinary EVs proteome and alterations in PCa tissues. Moreover, ADSV and TGM4 abundance yielded a high diagnostic potential in tissue and promising TGM4 prognostic power. These results suggest that the proteins identified in urinary EVs distinguishing high- and low grade PCa are a reflection of histological changes that may be a consequence of their functional involvement in PCa development. In conclusion, our study resulted in the identification of protein-combination panels present in urinary EVs that exhibit high sensitivity and specificity for PCa detection and patient stratification. Moreover, our study highlights the potential of targeted proteomic approaches–such as selected reaction monitoring (SRM)–as diagnostic assay for liquid biopsies via urinary EVs to improve diagnosis and prognosis of suspected PCa patients.

Impact of RASSF1A gene methylation on the metastatic axillary nodal status in breast cancer patients

Hypermethylation of CpG islands is a hallmark of cancer and occurs at an early stage in breast tumorigenesis. To gain insight into the epigenetic switches that may promote and/or contribute to the initial neoplastic events during breast carcinogenesis, the present study focused on the DNA methylation profile of invasive breast carcinoma. The aim of the study was to evaluate the prognostic significance of Ras association domain family 1 isoform A (RASSF1A) promoter methylation status in operable breast cancer, and to analyze the utility of this biomarker regarding its association with metastatic and nonmetastatic axillary nodal status. For this purpose, formalin-fixed, paraffin-embedded tissue specimens from 116 breast cancer patients with known axillary nodal status were subjected to assessment of RASSF1A promoter methylation status by methylation-specific polymerase chain reaction (MSP) and methylation-sensitive high-resolution melting assay, and the results were subsequently validated by bisulfite sequencing. A multinomial logistic regression model was used to model the dependence of distinct levels of methylation status of the RASSF1A promoter on the nodal status. Promoter region CpG hypermethylation was identified by MSP in 97 (83.6%) of 116 primary breast tumors, while hypermethylation of RASSF1A was confirmed by MS-HRM in 107 (92.2%) of 116 cases of breast cancer. Based on the results of the multinomial logistic regression model, there was no significant difference between the frequency of RASSF1A promoter methylation and axillary lymph node status of patients in general. However, upon adjustment of pN stage, an association was identified between pN0 lymph node-negative status (without axillary metastases) and percentage of RASSF1A methylation in two groups of heterogeneous methylated alleles with ≤50% methylated (P<0.05) and >50% methylated alleles (P<0.0001). If a patients' nodal status changes from pN- to pN+ then the risk of having >50% methylated alleles increases by 7%. The present study revealed a specific phenomenon, suggesting that the presence of heterogeneous methylated alleles in the RASSF1A gene is significantly associated with lymph node-negative status in breast cancer patients. Furthermore, greater significance with negative axillary nodal status was observed with a higher level of heterogeneous methylated alleles in the RASSF1A gene.

Expression of stem cell-regulating miRNAs in oral cavity and oropharynx squamous cell carcinoma

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common tumor worldwide and is histologically heterogeneous. Studies have demonstrated the presence of stem cell markers in HNSCC, and microRNAs (miRNAs) have emerged as powerful regulators of differentiation, controlling the self-renewal of stem cells. miRNAs are non-coding RNA molecules that regulate gene expression post-transcriptionally. Many miRNAs have been described as regulators of stem cells in different types of cancer.

METHODS

We have analyzed the expression of let-7a, miR-34, miR-125b, miR-138, miR-145, miR-183, miR-200b, miR-203, and miR-205 by real-time RT-PCR (qPCR), in 35 oral cavity and oropharynx squamous cell carcinoma (SCC) samples and 10 non-neoplastic oral mucosa controls, to determine possible associations between the expression of these miRNAs and clinical and pathological features of these tumors.

RESULTS

We observed downregulation of miR-200b and miR-203 in 60.0% and 71.4% of the samples, respectively. Upregulation of miR-138 and miR-183 was observed in 50.0% of the samples. Downregulation of let-7a was associated with perineural invasion. Upregulation of miR-138, miRNA-145, and miR-205 was associated with advanced tumor stages, vascular invasion, and lymph node metastasis, respectively.

CONCLUSIONS

Our study provides evidence of the expression of miRNAs associated with stem cell regulation in oral cavity and oropharynx SCC and the association of these miRNAs with clinical and pathological features of these tumors.

Genomic and Histopathological Tissue Biomarkers That Predict Radiotherapy Response in Localised Prostate Cancer

Localised prostate cancer, in particular, intermediate risk disease, has varied survival outcomes that cannot be predicted accurately using current clinical risk factors. External beam radiotherapy (EBRT) is one of the standard curative treatment options for localised disease and its efficacy is related to wide ranging aspects of tumour biology. Histopathological techniques including immunohistochemistry and a variety of genomic assays have been used to identify biomarkers of tumour proliferation, cell cycle checkpoints, hypoxia, DNA repair, apoptosis, and androgen synthesis, which predict response to radiotherapy. Global measures of genomic instability also show exciting capacity to predict survival outcomes following EBRT. There is also an urgent clinical need for biomarkers to predict the radiotherapy fraction sensitivity of different prostate tumours and preclinical studies point to possible candidates. Finally, the increased resolution of next generation sequencing (NGS) is likely to enable yet more precise molecular predictions of radiotherapy response and fraction sensitivity.

miRNA Expression Analyses in Prostate Cancer Clinical Tissues

A critical challenge in prostate cancer (PCa) clinical management is posed by the inadequacy of currently used biomarkers for disease screening, diagnosis, prognosis and treatment. In recent years, microRNAs (miRNAs) have emerged as promising alternate biomarkers for prostate cancer diagnosis and prognosis. However, the development of miRNAs as effective biomarkers for prostate cancer heavily relies on their accurate detection in clinical tissues. miRNA analyses in prostate cancer clinical specimens is often challenging owing to tumor heterogeneity, sampling errors, stromal contamination etc. The goal of this article is to describe a simplified workflow for miRNA analyses in archived FFPE or fresh frozen prostate cancer clinical specimens using a combination of quantitative real-time PCR (RT-PCR) and in situ hybridization (ISH). Within this workflow, we optimize the existing methodologies for miRNA extraction from FFPE and frozen prostate tissues and expression analyses by Taqman-probe based miRNA RT-PCR. In addition, we describe an optimized method for ISH analyses formiRNA detection in prostate tissues using locked nucleic acid (LNA)- based probes. Our optimized miRNA ISH protocol can be applied to prostate cancer tissue slides or prostate cancer tissue microarrays (TMA).

SULF2 overexpression positively regulates tumorigenicity of human prostate cancer cells

Background

SULF2 is a 6-O-endosulfatase which removes 6-O sulfate residues from N-glucosamine present on heparan sulfate (HS). The sulfation pattern of HS influences signaling events mediated by heparan sulfate proteoglycans (HSPGs) located on cell surface, which are critical for the interactions with growth factors and their receptors. Alterations in SULF2 expression have been identified in the context of several cancer types but its function in cancer is still unclear where the precise molecular mechanism involved has not been fully deciphered. To further investigate SULF2 role in tumorigenesis, we overexpressed such gene in prostate cancer cell lines.

Methods

The normal prostate epithelial cell line RWPE-1 and the prostate cancer cells DU-145, and PC3 were transfected with SULF2-expressing plasmid pcDNA3.1/Myc-His(−)-Hsulf-2. Transfected cells were then submitted to viability, migration and colony formation assays.

Results

Transfection of DU-145 and PC3 prostate cancer cells with SULF2 resulted in increased viability, which did not occur with normal prostate cells. The effect was reverted by the knockdown of SULF2 using specific siRNAs. Furthermore, forced expression of SULF2 augmented cell migration and colony formation in both prostate cell lines. Detailed structural analysis of HS from cells overexpressing SULF2 showed a reduction of the trisulfated disaccharide UA(2S)-GlcNS(6S). There was an increase in epithelial-mesenchymal transition markers and an increase in WNT signaling pathway.

Conclusions

These results indicate that SULF2 have a pro-tumorigenic effect in DU-145 and PC3 cancer cells, suggesting an important role of this enzyme in prostatic cancer metastasis.