Proteomics and the search for biomarkers for renal cancer

Poria acid inhibit the growth and metastasis of renal cell carcinoma by inhibiting the PI3K/akt/NF-κb signaling pathway

Background

Poria acid (PAC) is a triterpene compound found in Poria cocos, a traditional Chinese medicine (TCM). The current study aims to explore the therapeutic effects and potential mechanisms of PAC on the migration and proliferation of human renal cell carcinoma (RCC) cells as well as tumor growth in animal model.

Methods

Cell viability and proliferative capacity of normal renal cells and RCC cells were investigated by MTT assay. In addition, 786-O cells were divided into four groups and treated with different concentrations of PAC (0, 20, 40, and 60 μM) for 48 h. Cell scratch test and cell invasion assay were performed to evaluate the effects of PAC on the invasion and migration of RCC cells, respectively. The effects of PAC on apoptosis of RCC cells and expression levels of PI3K/Akt/NF-kB signaling pathway-related biomarkers were investigated using TUNEL staining and Western blotting methods, respectively. Effects of PAC on the inhibitory activity of RCC tumor in mice were evaluated in a 786-O CDX model.

Results

The study found that PAC inhibited the viability of RCC cells in a dose-dependent manner, as demonstrated by in vitro cell assays (p < 0.05). However, PAC showed no significant inhibitory effect on normal renal cells (p > 0.05). PAC also significantly inhibited the migration and invasion of RCC via EMT/MMP signaling pathways (p < 0.05). Immunofluorescence and immunoblotting results showed that PAC induced the apoptosis of RCC, which was accompanied by changes in the expression levels of apoptosis-related proteins (p < 0.05). Moreover, PAC significantly downregulated the PI3K/Akt/NF-kB signaling pathway in a concentration-dependent manner (p < 0.05). The effect of PAC on RCC apoptosis was dramatically reversed by 740Y-P (PI3K agonist) (p < 0.05) but significantly enhanced in the presence of LY294002 (PI3K inhibitor) (p < 0.05). The results of in vivo experiment also demonstrated that the antitumor activity of PAC was achieved by affecting the PI3K/Akt/NF-kB signaling pathway.

Conclusions

PAC can effectively suppress the proliferation, invasion and migration of RCC cells, and exhibit anti-tumor effects in RCC model by inhibiting the PI3K/Akt/NF-kB signaling pathway.

Synergistic anti-tumour activity of sorafenib in combination with pegylated resveratrol is mediated by Akt/mTOR/p70S6k-4EBP-1 and c-Raf7MEK/ERK signaling pathways

Introduction

To investigate the inhibitory effect of sorafenib combined with PEGylated resveratrol on renal cell carcinoma (RCC) and its potential mechanism.

Methods

MTT assay was used to detect the inhibitory effects of PEGylated resveratrol and sorafenib alone or combination on proliferation of RCC cells. Scratch and transwell assays were performed to examine the effects on the in vitro migration and invasion of RCC cells, respectively. The anti-tumor activity as well as splenic lymphocyte proliferation of the combination therapy was evaluated in the RCC xenograft mouse model. Western blotting method was used to detect changes in proteins involved in the antitumor efficacy related signaling pathways.

Results

Inhibitory effects of PEGylated resveratrol combined with sorafenib incubation on the proliferation of Renca cells was synergistically enhanced compared with the mono-incubation group (both P < 0.01, CI < 1). Scratch and transwell assays revealed that combined incubation could significantly inhibit the migration and invasion of 786-O cells in vitro. Combined PEGylated resveratrol with sorafenib could significantly inhibit the growth of Renca renal carcinoma in mice with the tumor growth inhibition (TGI) of 85.5% and one achieved complete remission on D14, while the two monotherapies were both below 43% on D14, suggesting that current combination may have synergistic anti-renal carcinoma activity. Compared with the control group, PEGylated resveratrol combined with sorafenib in vivo promoted the proliferation of unactivated splenic lymphocytes and the proliferation of lymphocytes stimulated with concanavalin A and lipopolysaccharide. Western blotting results showed that combination therapy may suppress the growth of renal cell carcinoma by inhibiting AKT/mTOR/p70S6k-4EBP-1 and c-Raf7MEK/ERK signaling pathways.

Conclusion

PEGylated resveratrol combined with sorafenib can achieve synergistic anti-RCC activity, and the mechanism may be related to the inhibition of Akt/mTOR/p70S6k-4EBP-1 and c-Raf7MEK/ERK signaling pathways.

Quantitative Phosphoproteomics Analysis Uncovers PAK2- and CDK1-Mediated Malignant Signaling Pathways in Clear Cell Renal Cell Carcinoma

Clear cell Renal Cell Carcinoma (ccRCC) is among the 10 most common cancers in both men and women and causes more than 140,000 deaths worldwide every year. In order to elucidate the underlying molecular mechanisms orchestrated by phosphorylation modifications, we performed a comprehensive quantitative phosphoproteomics characterization of ccRCC tumor and normal adjacent tissues. Here, we identified 16,253 phosphopeptides, of which more than 9000 were singly quantified. Our in-depth analysis revealed 600 phosphopeptides to be significantly differentially regulated between tumor and normal tissues. Moreover, our data revealed that significantly up-regulated phosphoproteins are associated with protein synthesis and cytoskeletal re-organization which suggests proliferative and migratory behavior of renal tumors. This is supported by a mesenchymal profile of ccRCC phosphorylation events. Our rigorous characterization of the renal phosphoproteome also suggests that both epidermal growth factor receptor and vascular endothelial growth factor receptor are important mediators of phospho signaling in RCC pathogenesis. Furthermore, we determined the kinases p21-activated kinase 2, cyclin-dependent kinase 1 and c-Jun N-terminal kinase 1 to be master kinases that are responsible for phosphorylation of many substrates associated with cell proliferation, inflammation and migration. Moreover, high expression of p21-activated kinase 2 is associated with worse survival outcome of ccRCC patients. These master kinases are targetable by inhibitory drugs such as fostamatinib, minocycline, tamoxifen and bosutinib which can serve as novel therapeutic agents for ccRCC treatment.

LAMTOR3 is a prognostic biomarker in kidney renal clear cell carcinoma

Objective

The objective of the study was to investigate the expression of LAMTOR3 in kidney renal clear cell carcinoma (KIRC) and its clinical significance.

Methods

The expression of LAMTOR3 in KIRC and its relationship with clinical features were analyzed using the UALCAN online database. The results were verified using KIRC gene chip data and clinical specimens. The prognosis of KIRC patients was analyzed with the GEPIA2 database. GO, KEGG, and GSEA analyses were conducted to analyze the possible molecular mechanism of LAMTOR3 in KIRC. Immunohistochemical (IHC) and hematoxylin and eosin (H&E) staining were used for histopathological detection.

Results

UALCAN database analysis showed that LAMTOR3 expression in KIRC was significantly lower than in normal kidney tissues and correlated with the clinical stage, pathological grade, and tumor genotype (p < .05). GSE53757 dataset analysis consistently showed that the expression of LAMTOR3 in KIRC was significantly lower than in normal kidney tissues (p < .01). GEPIA2 database analysis indicated that patients with low LAMTOR3 expression had poor overall and disease‐free survival rates. GSEA analysis suggested that LAMTOR3 positively regulated the citrate cycle and drug metabolism cytochrome P450 and negatively regulated folate biosynthesis and olfactory transduction. The expression of LAMTOR3 in KIRC was also significantly correlated with immune cell infiltration. Finally, IHC showed that LAMTOR3 expression in the KIRC tissues was lower than in the adjacent normal tissues.

Conclusion

LAMTOR3 expression is significantly lower in KIRC. LAMTOR3 may be a potential marker for KIRC diagnosis and therapy.

Quantitative Proteomics Identifies Secreted Diagnostic Biomarkers as well as Tumor-Dependent Prognostic Targets for Clear Cell Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC) is the third most common and most malignant urological cancer, with a 5-year survival rate of 10% for patients with advanced tumors. Here, we identified 10,160 unique proteins by in-depth quantitative proteomics, of which 955 proteins were significantly regulated between tumor and normal adjacent tissues. We verified four putatively secreted biomarker candidates, namely, PLOD2, FERMT3, SPARC, and SIRPα, as highly expressed proteins that are not affected by intratumor and intertumor heterogeneity. Moreover, SPARC displayed a significant increase in urine samples of patients with ccRCC, making it a promising marker for the detection of the disease in body fluids. Furthermore, based on molecular expression profiles, we propose a biomarker panel for the robust classification of ccRCC tumors into two main clusters, which significantly differed in patient outcome with an almost three times higher risk of death for cluster 1 tumors compared with cluster 2 tumors. Moreover, among the most significant clustering proteins, 13 were targets of repurposed inhibitory FDA-approved drugs. Our rigorous proteomics approach identified promising diagnostic and tumor-discriminative biomarker candidates which can serve as therapeutic targets for the treatment of ccRCC. IMPLICATIONS: Our in-depth quantitative proteomics analysis of ccRCC tissues identifies the putatively secreted protein SPARC as a promising urine biomarker and reveals two molecular tumor phenotypes.

Urinary Extracellular Vesicles as Potential Biomarkers for Urologic Cancers: An Overview of Current Methods and Advances

Urologic cancers are a heterogeneous group of tumors, some of which have poor prognosis. This is partly due to the unavailability of specific and sensitive diagnostic techniques and monitoring tests, ideally non- or minimally invasive. Hence, liquid biopsies are promising tools that have been gaining significant attention over the last decade. Among the different classes of biomarkers that can be isolated from biofluids, urinary extracellular vesicles (uEVs) are a promising low-invasive source of biomarkers, with the potential to improve cancer diagnosis and disease management. Different techniques have been developed to isolate and characterize the cargo of these vesicles; however, no consensus has been reached, challenging the comparison among studies. This results in a vast number of studies portraying an extensive list of uEV-derived candidate biomarkers for urologic cancers, with the potential to improve clinical outcome; however, without significant validation. Herein, we review the current published research on miRNA and protein-derived uEV for prostate, bladder and kidney cancers, focusing on different uEV isolation methods, and its implications for biomarker studies.

Proteomic Analysis of Mouse Brain Subjected to Spaceflight

There is evidence that spaceflight poses acute and late risks to the central nervous system. To explore possible mechanisms, the proteomic changes following spaceflight in mouse brain were characterized. Space Shuttle Atlantis (STS-135) was launched from the Kennedy Space Center (KSC) on a 13-day mission. Within 3–5 h after landing, brain tissue was collected to evaluate protein expression profiles using quantitative proteomic analysis. Our results showed that there were 26 proteins that were significantly altered after spaceflight in the gray and/or white matter. While there was no overlap between the white and gray matter in terms of individual proteins, there was overlap in terms of function, synaptic plasticity, vesical activity, protein/organelle transport, and metabolism. Our data demonstrate that exposure to the spaceflight environment induces significant changes in protein expression related to neuronal structure and metabolic function. This might lead to a significant impact on brain structural and functional integrity that could affect the outcome of space missions.

PGRMC1 Is a Novel Potential Tumor Biomarker of Human Renal Cell Carcinoma Based on Quantitative Proteomic and Integrative Biological Assessments

Progesterone receptor membrane component 1 (PGRMC1) is widely observed with an elevated level in multiple human cancers. However, the roles of PGRMC1 in renal cancer are not clear and merit further study. In this report, we made a systematic, integrative biological assessment for PGRMC1 in renal cell carcinoma (RCC) by a quantitative proteomic identification, immunohistochemical detection, and its clinic pathologic significance analysis. We found that PGRMC1 abundance is increased by 3.91-fold in RCC tissues compared with its autologous para-cancerous tissues by a quantitative proteome identification. To validate the proteomic result with more confidence, 135 clinic RCC tissues were recruited to measure PGRMC1 abundance by immunohistochemical staining, and 63.7% RCC samples (n = 86) showed a higher abundance of PGRMC1 than the noncancerous counterparts. And the elevated PGRMC1 level was related to the tumor malignancy degree and overall survival of RCC patients. Meanwhile the average serum PGRMC1 concentration for RCC patients (n = 18) was significantly increased by 1.67 fold compared with healthy persons. Moreover an exogenous elevated abundance of PGRMC1 by plasmid transfections significantly enhanced cell proliferation of renal cancer cells in vitro. Our findings demonstrate PGRMC1, which promotes RCC progression phenotypes in vitro and in vivo, is a novel potential biomarker and therapeutic target for RCC.

Plasma netrin-1 levels significantly increase in smokers

OBJECTIVES

Netrin-1 is a laminin like protein that has recently been suggested to involve in the pathophysiology of atherosclerosis and treatment targets. The relationship between netrin-1 and atherosclerosis has not been evaluated in a human research previously and the effect of smoking on plasma netrin-1 levels as well. In this study, we aimed to evaluate plasma netrin-1 levels in smokers and non-smokers and the impact of smoking on netrin-1 levels. Our second aim was to evaluate the existence of peripheral artery disease in these groups by means of ankle brachial index (ABI) measurements and the relation between plasma netrin-1 levels and peripheral artery disease.

DESIGN AND METHODS

Smoker and non-smoker male patients were contributed in the study, 112 males in each group. ABI of all patients was determined with an automatic device and plasma netrin-1 levels were quantified with an enzyme-linked immunosorbent assay. Netrin-1 levels were compared between smoker and non-smoker cases, and the cases with and without peripheral arterial disease.

RESULTS

Plasma netrin-1 levels of smokers (4.54±2.87pg/mL) were significantly higher than in non-smokers (3.81±1.26pg/mL) (p=0.015). Similarly, netrin-1 levels of cases with peripheral arterial disease (6.21±2.16pg/mL) were significantly higher than the ones without peripheral arterial disease (4.07±2.16pg/mL) (p=0.002). Amount of smoking (packet⋅year) and ABI were found to be significantly related with netrin-1 levels. The relationship between PAD and netrin-1 levels remained significant after adjusting for smoking status.

CONCLUSION

We can conclude that plasma netrin-1 levels significantly increase in smokers and peripheral artery disease is significantly related with netrin-1 levels after adjusting for smoking status.

Identification of potential serum proteomic biomarkers for clear cell renal cell carcinoma

Objective

To investigate discriminating protein patterns and serum biomarkers between clear cell renal cell carcinoma (ccRCC) patients and healthy controls, as well as between paired pre- and post-operative ccRCC patients.

Methods

We used magnetic bead-based separation followed by matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) to identify patients with ccRCC. A total of 162 serum samples were analyzed in this study, among which there were 58 serum samples from ccRCC patients, 40 from additional paired pre- and post-operative ccRCC patients (n = 20), and 64 from healthy volunteers as healthy controls. ClinProTools software identified several distinct markers between ccRCC patients and healthy controls, as well as between pre- and post-operative patients.

Results

Patients with ccRCC could be identified with a mean sensitivity of 88.38% and a mean specificity of 91.67%. Of 67 m/z peaks that differed among the ccRCC, healthy controls, pre- and post-operative ccRCC patients, 24 were significantly different (P<0.05). Three candidate peaks, which were upregulated in ccRCC group and showed a tendency to return to healthy control values after surgery, were identified as peptide regions of RNA-binding protein 6 (RBP6), tubulin beta chain (TUBB), and zinc finger protein 3 (ZFP3) with the m/z values of 1466.98, 1618.22, and 5905.23, respectively.

Conclusion

MB-MALDI-TOF-MS method could generate serum peptidome profiles of ccRCC, and provide a new approach to identify potential biomarkers for diagnosis as well as prognosis of this malignancy.

Mass spectrometry based biomarker discovery, verification, and validation--quality assurance and control of protein biomarker assays

In its early years, mass spectrometry (MS)-based proteomics focused on the cataloging of proteins found in different species or different tissues. By 2005, proteomics was being used for protein quantitation, typically based on "proteotypic" peptides which act as surrogates for the parent proteins. Biomarker discovery is usually done by non-targeted "shotgun" proteomics, using relative quantitation methods to determine protein expression changes that correlate with disease (output given as "up-or-down regulation" or "fold-increases"). MS-based techniques can also perform "absolute" quantitation which is required for clinical applications (output given as protein concentrations). Here we describe the differences between these methods, factors that affect the precision and accuracy of the results, and some examples of recent studies using MS-based proteomics to verify cancer-related biomarkers.

MALDI-TOF MS as evolving cancer diagnostic tool: a review

Recent developments in mass spectrometry have introduced clinical proteomics to the forefront of diseases diagnosis, offering reliable, robust and efficient analytical method for biomarker discovery and monitoring. MALDI-TOF is a powerful tool for surveying proteins and peptides comprising the realm for clinical analysis. MALDI-TOF has the potential to revolutionize cancer diagnostics by facilitating biomarker discovery, enabling tissue imaging and quantifying biomarker levels. Healthy (control) and cancerous tissues can be analyzed on the basis of mass spectrometry (MALDI-TOF) imaging to identify cancer-specific changes that may prove to be clinically useful. We review MALDI-TOF profiling techniques as tools for detection of cancer biomarkers in various cancers. We mainly discuss recent advances including period from 2011 to 2013.

MRM for the verification of cancer biomarker proteins: recent applications to human plasma and serum

Accurate cancer biomarkers are needed for early detection, disease classification, prediction of therapeutic response and monitoring treatment. While there appears to be no shortage of candidate biomarker proteins, a major bottleneck in the biomarker pipeline continues to be their verification by enzyme linked immunosorbent assays. Multiple reaction monitoring (MRM), also known as selected reaction monitoring, is a targeted mass spectrometry approach to protein quantitation and is emerging to bridge the gap between biomarker discovery and clinical validation. Highly multiplexed MRM assays are readily configured and enable simultaneous verification of large numbers of candidates facilitating the development of biomarker panels which can increase specificity. This review focuses on recent applications of MRM to the analysis of plasma and serum from cancer patients for biomarker verification. The current status of this approach is discussed along with future directions for targeted mass spectrometry in clinical biomarker validation.

Angiogenic markers: molecular targets for personalized medicine in pituitary adenoma

AIM

Pituitary adenomas are typically slow-growing and histologically benign tumors that can occasionally behave in a malignant-like manner, invading adjacent structures or recurring after treatment. Using protein analysis methods and multiplex xMAP assays, we aimed to find out if these particular types of tumors express angiogenic markers VEGF and basic FGF (bFGF), which are associated with tumor growth and invasiveness, and quantify them in order to establish their usefulness as biomarkers.

MATERIALS & METHODS

We have analysed the expression of angiogenic markers VEGF and bFGF in serum and tissue specimens from 66 pituitary adenomas (43 invasive and 23 noninvasive). For serum analysis, we used xMAP and ELISA, and for tissue analysis, we performed histopathology and immunohistochemistry.

RESULTS & CONCLUSION

We measured the serum angiogenic factors in pituitary adenomas. The quantification methods revealed significant differences between pituitary adenoma patients and controls, for both VEGF (212.4 vs 112.5 pg/ml in controls) and bFGF (mean value of 12.6 vs 10.8 pg/ml in controls), and also differentiated between invasive and noninvasive adenomas (p < 0.05). The tissue expression of VEGF and bFGF strongly correlated with their serum level increase. Our findings can be further developed into methods for selection of patients suitable for personalized, antiangiogenic therapy.

Differential protein profiling of renal cell carcinoma urinary exosomes

Renal cell carcinoma (RCC) accounts for about 3% of all human malignancies and its incidence is increasing. There are no standard biomarkers currently used in the clinical management of patients with renal cell carcinoma. A promising strategy for new biomarker detection is comparative proteomics of urinary exosomes (UE), nanovesicles released by every epithelial cell facing the urinary space, enriched in renal proteins and excluding high-abundance plasmatic proteins, such as albumin. Aim of the work is to establish the protein profile of exosomes isolated from urines of RCC patient compared with control subjects. We enrolled 29 clear cell RCC patients and 23 control healthy subjects (CTRL), age and sex-matched, for urine collection and vesicle isolation by differential centrifugation. Such vesicles were morphologically and biochemically characterized and proved to share exosome properties. Proteomic analysis, performed on 9 urinary exosome (UE) pooled samples by gel based digestion followed by LC-MS/MS, led to the identification of 261 proteins from CTRL subject UE and 186 from RCC patient UE, and demonstrated that most of the identified proteins are membrane associated or cytoplasmic. Moreover, about a half of identified proteins are not shared between RCC and control UE. Starting from these observations, and from the literature, we selected a panel of 10 proteins, whose UE differential content was subjected to immunoblotting validation. Results show for the first time that RCC UE protein content is substantially and reproducibly different from control UE, and that these differences may provide clues for new RCC biomarker discovery.