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1.
Br J Cancer ; 123(1): 137-147, 2020 07.
Article in English | MEDLINE | ID: mdl-32390008

ABSTRACT

BACKGROUND: Indoleamine 2,3-dioxygenase (IDO), the first step in the kynurenine pathway (KP), is upregulated in some cancers and represents an attractive therapeutic target given its role in tumour immune evasion. However, the recent failure of an IDO inhibitor in a late phase trial raises questions about this strategy. METHODS: Matched renal cell carcinoma (RCC) and normal kidney tissues were subject to proteomic profiling. Tissue immunohistochemistry and gene expression data were used to validate findings. Phenotypic effects of loss/gain of expression were examined in vitro. RESULTS: Quinolate phosphoribosyltransferase (QPRT), the final and rate-limiting enzyme in the KP, was identified as being downregulated in RCC. Loss of QPRT expression led to increased potential for anchorage-independent growth. Gene expression, mass spectrometry (clear cell and chromophobe RCC) and tissue immunohistochemistry (clear cell, papillary and chromophobe), confirmed loss or decreased expression of QPRT and showed downregulation of other KP enzymes, including kynurenine 3-monoxygenase (KMO) and 3-hydroxyanthranilate-3,4-dioxygenase (HAAO), with a concomitant maintenance or upregulation of nicotinamide phosphoribosyltransferase (NAMPT), the key enzyme in the NAD+ salvage pathway. CONCLUSIONS: Widespread dysregulation of the KP is common in RCC and is likely to contribute to tumour immune evasion, carrying implications for effective therapeutic targeting of this critical pathway.


Subject(s)
3-Hydroxyanthranilate 3,4-Dioxygenase/genetics , Carcinoma, Renal Cell/genetics , Cytokines/genetics , Kynurenine 3-Monooxygenase/genetics , Kynurenine/genetics , Nicotinamide Phosphoribosyltransferase/genetics , Carcinoma, Renal Cell/immunology , Carcinoma, Renal Cell/pathology , Cell Line, Tumor , Gene Expression Profiling , Gene Expression Regulation, Neoplastic/genetics , Humans , Kynurenine/metabolism , Metabolic Networks and Pathways/genetics , Proteomics , Tumor Escape/genetics , Tumor Escape/immunology
2.
J Pathol ; 247(3): 381-391, 2019 03.
Article in English | MEDLINE | ID: mdl-30426503

ABSTRACT

Skeletal metastasis occurs in around 75% of advanced breast cancers, with the disease incurable once cancer cells disseminate to bone, but there remains an unmet need for biomarkers to identify patients at high risk of bone recurrence. This study aimed to identify such a biomarker and to assess its utility in predicting response to adjuvant zoledronic acid (zoledronate). We used quantitative proteomics (stable isotope labelling by amino acids in cell culture-mass spectrometry; SILAC-MS) to compare protein expression in a bone-homing variant (BM1) of the human breast cancer cell line MDA-MB-231 with parental non-bone-homing cells to identify novel biomarkers for risk of subsequent bone metastasis in early breast cancer. SILAC-MS showed that dedicator of cytokinesis protein 4 (DOCK4) was upregulated in bone-homing BM1 cells, confirmed by western blotting. BM1 cells also had enhanced invasive ability compared with parental cells, which could be reduced by DOCK4-shRNA. In a training tissue microarray (TMA) comprising 345 patients with early breast cancer, immunohistochemistry followed by Cox regression revealed that high DOCK4 expression correlated with histological grade (p = 0.004) but not oestrogen receptor status (p = 0.19) or lymph node involvement (p = 0.15). A clinical validation TMA used tissue samples and the clinical database from the large AZURE adjuvant study (n = 689). Adjusted Cox regression analyses showed that high DOCK4 expression in the control arm (no zoledronate) was significantly prognostic for first recurrence in bone (HR 2.13, 95%CI 1.06-4.30, p = 0.034). No corresponding association was found in patients who received zoledronate (HR 0.812, 95%CI 0.176-3.76, p = 0.790), suggesting that treatment with zoledronate may counteract the higher risk for bone relapse from high DOCK4-expressing tumours. High DOCK4 expression was not associated with metastasis to non-skeletal sites when these were assessed collectively. In conclusion, high DOCK4 in early breast cancer is significantly associated with aggressive disease and with future bone metastasis and is a potentially useful biomarker for subsequent bone metastasis risk. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


Subject(s)
Biomarkers, Tumor/metabolism , Bone Neoplasms/secondary , Breast Neoplasms/metabolism , GTPase-Activating Proteins/metabolism , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/genetics , Bone Density Conservation Agents/therapeutic use , Bone Neoplasms/diagnosis , Bone Neoplasms/drug therapy , Bone Neoplasms/metabolism , Breast Neoplasms/pathology , Cell Line, Tumor , Cell Movement/physiology , Chemotherapy, Adjuvant , Female , GTPase-Activating Proteins/genetics , Gene Knockdown Techniques/methods , Humans , Middle Aged , Neoplasm Grading , Neoplasm Proteins/metabolism , Prognosis , Proteomics/methods , Risk Assessment/methods , Tumor Cells, Cultured , Up-Regulation , Young Adult , Zoledronic Acid/therapeutic use
3.
J Gen Virol ; 96(Pt 7): 1533-50, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25711964

ABSTRACT

Hepatocellular carcinoma (HCC) carries a dismal prognosis, with advanced disease being resistant to both radiotherapy and conventional cytotoxic drugs, whilst anti-angiogenic drugs are marginally efficacious. Oncolytic viruses (OVs) offer the promise of selective cancer therapy through direct and immune-mediated mechanisms. The premise of OVs lies in their preferential genomic replication, protein expression and productive infection of malignant cells. Numerous OVs are being tested in preclinical models of HCC, with good evidence of direct and immune-mediated anti-tumour efficacy. Efforts to enhance the performance of these agents have concentrated on engineering OV cellular specificity, immune evasion, enhancing anti-tumour potency and improving delivery. The lead agent in HCC clinical trials, JX-594, a recombinant Wyeth strain vaccinia virus, has demonstrated evidence for significant benefit and earned orphan drug status. Thus, JX-594 appears to be transcending the barrier between novel laboratory science and credible clinical therapy. Relatively few other OVs have entered clinical testing, a hurdle that must be overcome if significant progress is to be made in this field. This review summarizes the preclinical and clinical experience of OV therapy in the difficult-to-treat area of HCC.


Subject(s)
Carcinoma, Hepatocellular/therapy , Liver Neoplasms/therapy , Oncolytic Virotherapy/methods , Oncolytic Virotherapy/trends , Oncolytic Viruses/growth & development , Oncolytic Viruses/immunology , Animals , Antiviral Agents/therapeutic use , Clinical Trials as Topic , Drug Evaluation, Preclinical , Humans , Oncolytic Viruses/genetics , Orphan Drug Production , Vaccinia virus/genetics , Vaccinia virus/growth & development , Vaccinia virus/immunology
4.
Proteomics ; 14(9): 1006-0, 2014 May.
Article in English | MEDLINE | ID: mdl-24678027

ABSTRACT

Despite recent developments in bottom-up proteomics, the need still exists in a fast, uncomplicated, and robust method for comprehensive sample processing especially when applied to low protein amounts. The suspension trapping method combines the advantage of efficient SDS-based protein extraction with rapid detergent removal, reactor-type protein digestion, and peptide cleanup. Proteins are solubilized in SDS. The sample is acidified and introduced into the suspension trapping tip incorporating the depth filter and hydrophobic compartments, filled with the neutral pH methanolic solution. The instantly formed fine protein suspension is trapped in the depth filter stack-this crucial step is aimed at separating the particulate matter in space. SDS and other contaminants are removed in the flow-through, and a protease is introduced. Following the digestion, the peptides are cleaned up using the tip's hydrophobic part. The methodology allows processing of protein loads down to the low microgram/submicrogram levels. The detergent removal takes about 5 min, whereas the tryptic proteolysis of a cellular lysate is complete in as little as 30 min. We have successfully utilized the method for analysis of cellular lysates, enriched membrane preparations, and immunoprecipitates. We expect that due to its robustness and simplicity, the method will become an essential proteomics tool.


Subject(s)
Peptide Fragments/analysis , Peptide Fragments/isolation & purification , Proteins/analysis , Proteins/isolation & purification , Proteomics/methods , Detergents/chemistry , HeLa Cells , Humans , Hydrophobic and Hydrophilic Interactions , Immunoprecipitation , Peptide Fragments/chemistry , Proteins/chemistry , Sodium Dodecyl Sulfate/chemistry
5.
Hum Mol Genet ; 21(2): 456-62, 2012 Jan 15.
Article in English | MEDLINE | ID: mdl-22010048

ABSTRACT

Renal cell carcinoma (RCC) is the most lethal urologic cancer. Only two common susceptibility loci for RCC have been confirmed to date. To identify additional RCC common susceptibility loci, we conducted an independent genome-wide association study (GWAS). We analyzed 533 191 single nucleotide polymorphisms (SNPs) for association with RCC in 894 cases and 1516 controls of European descent recruited from MD Anderson Cancer Center in the primary scan, and validated the top 500 SNPs in silico in 3772 cases and 8505 controls of European descent involved in the only published GWAS of RCC. We identified two common variants in linkage disequilibrium, rs718314 and rs1049380 (r(2) = 0.64, D ' = 0.84), in the inositol 1,4,5-triphosphate receptor, type 2 (ITPR2) gene on 12p11.23 as novel susceptibility loci for RCC (P = 8.89 × 10(-10) and P = 6.07 × 10(-9), respectively, in meta-analysis) with an allelic odds ratio of 1.19 [95% confidence interval (CI): 1.13-1.26] for rs718314 and 1.18 (95% CI: 1.12-1.25) for rs1049380. It has been recently identified that rs718314 in ITPR2 is associated with waist-hip ratio (WHR) phenotype. To our knowledge, this is the first genetic locus associated with both cancer risk and WHR.


Subject(s)
Carcinoma, Renal Cell/genetics , Chromosomes, Human, Pair 12 , Genetic Predisposition to Disease , Genome-Wide Association Study , Kidney Neoplasms/genetics , Humans
6.
BJU Int ; 113(3): 416-28, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24053769

ABSTRACT

OBJECTIVES: To evaluate our clinical experience with percutaneous image-guided radiofrequency ablation (RFA) of 200 renal tumours in a large tertiary referral university institution. PATIENTS AND METHODS: Image-guided RFA (ultrasonography or computed tomography [CT]) of 200 renal tumours in 165 patients from June 2004 to 2012 was prospectively evaluated. Institutional Review Board approval was granted. The treatment response and technical success were defined by absence of contrast enhancement within the tumour on contrast enhanced CT or magnetic resonance imaging. Both major and minor complications, glomerular filtration rate (GFR) before and after RFA, the management and outcomes of the complications, as well as oncological outcome were prospectively documented. Multivariate analysis was used to determine variables associated with major complications and also the percentage GFR change after RFA. The overall (OS), 5-year cancer-specific (CSS), local recurrence-free (LRFS) and metastasis-free survival (MFS) rates are presented using the Kaplan-Meier curves. RESULTS: In all, 200 tumours were RF ablated with a mean (range) tumour size of 2.9 (1-5.6) cm and the mean (range) patient age was 67.7 (21-88.6) years with a mean follow-up period of 46.1 months. The primary technical and overall technical success rate was 95.5% and 98.5%, respectively. Two independent predictors of successful RFA in a single sitting were tumour size (<3 cm) and exophytic location in multivariate logistic regression analysis. Major complications included ureteric injury (six patients), calyceal-cutaneous fistula (one), acute tubular necrosis (one) and abscess (two). Two independent predictors of ureteric injury were central location and lower pole position. Within this cohort of patients, only four patients developed significant renal function deterioration i.e. >25% decreased in GFR. In all, 161 (98%) patients of the 165 patients have preservation of renal function. Any change in renal function after RFA was not influenced by tumour factors or solitary kidney status. In our clinical series, this yielded a 5-year OS, CSS, LRFS and MFS rates of 75.8%, 97.9%, 93.5% and 87.7% respectively. CONCLUSIONS: Image-guided RFA is a safe, nephron sparing and effective treatment for small renal cell carcinoma (RCC) tumours with a low rate of recurrence and has good 5-year CSS and MFS rates.


Subject(s)
Carcinoma, Renal Cell/surgery , Catheter Ablation/methods , Kidney Neoplasms/surgery , Adult , Aged , Aged, 80 and over , Carcinoma, Renal Cell/pathology , Carcinoma, Renal Cell/physiopathology , Catheter Ablation/adverse effects , Constriction, Pathologic/etiology , Cutaneous Fistula/etiology , Dissection/methods , Female , Follow-Up Studies , Glomerular Filtration Rate/physiology , Humans , Hypothermia, Induced/methods , Kidney Neoplasms/pathology , Kidney Neoplasms/physiopathology , Magnetic Resonance Imaging , Male , Middle Aged , Neoplasm, Residual/pathology , Neoplasm, Residual/surgery , Radiography, Interventional , Tomography, X-Ray Computed , Treatment Outcome , Ultrasonography, Interventional , Ureteral Diseases/etiology , Urinary Fistula/etiology , Young Adult
7.
Kidney Int ; 84(6): 1214-25, 2013 Dec.
Article in English | MEDLINE | ID: mdl-23739232

ABSTRACT

Early identification and prognostic stratification of delayed graft function following renal transplantation has significant potential to improve outcome. Mass spectrometry analysis of serum samples, before and on day 2 post transplant from five patients with delayed graft function and five with an uncomplicated transplant, identified aminoacylase-1 (ACY-1) as a potential outcome biomarker. Following assay development, analysis of longitudinal samples from an initial validation cohort of 55 patients confirmed that the ACY-1 level on day 1 or 2 was a moderate predictor of delayed graft function, similar to serum creatinine, complementing the strongest predictor cystatin C. A further validation cohort of 194 patients confirmed this association with area under ROC curves (95% CI) for day 1 serum (138 patients) of 0.74 (0.67-0.85) for ACY-1, 0.9 (0.84-0.95) for cystatin C, and 0.93 (0.88-0.97) for both combined. Significant differences in serum ACY-1 levels were apparent between delayed, slow, and immediate graft function. Analysis of long-term follow-up for 54 patients with delayed graft function showed a highly significant association between day 1 or 3 serum ACY-1 and dialysis-free survival, mainly associated with the donor-brain-dead transplant type. Thus, proteomic analysis provides novel insights into the potential clinical utility of serum ACY-1 levels immediately post transplantation, enabling subdivision of patients with delayed graft function in terms of long-term outcome. Our study requires independent confirmation.


Subject(s)
Amidohydrolases/blood , Delayed Graft Function/etiology , Kidney Transplantation/adverse effects , Adult , Aged , Area Under Curve , Biomarkers/blood , Creatinine/blood , Cystatin C/blood , Delayed Graft Function/blood , Delayed Graft Function/enzymology , Delayed Graft Function/therapy , Disease-Free Survival , Early Diagnosis , Enzyme-Linked Immunosorbent Assay , Female , Humans , Longitudinal Studies , Male , Mass Spectrometry , Middle Aged , Predictive Value of Tests , Prospective Studies , Proteomics/methods , ROC Curve , Renal Dialysis , Reproducibility of Results , Time Factors , Treatment Outcome
8.
Clin Cancer Res ; 29(7): 1220-1231, 2023 04 03.
Article in English | MEDLINE | ID: mdl-36815791

ABSTRACT

PURPOSE: Patients with resected localized clear-cell renal cell carcinoma (ccRCC) remain at variable risk of recurrence. Incorporation of biomarkers may refine risk prediction and inform adjuvant treatment decisions. We explored the role of tumor genomics in this setting, leveraging the largest cohort to date of localized ccRCC tissues subjected to targeted gene sequencing. EXPERIMENTAL DESIGN: The somatic mutation status of 12 genes was determined in 943 ccRCC cases from a multinational cohort of patients, and associations to outcomes were examined in a Discovery (n = 469) and Validation (n = 474) framework. RESULTS: Tumors containing a von-Hippel Lindau (VHL) mutation alone were associated with significantly improved outcomes in comparison with tumors containing a VHL plus additional mutations. Within the Discovery cohort, those with VHL+0, VHL+1, VHL+2, and VHL+≥3 tumors had disease-free survival (DFS) rates of 90.8%, 80.1%, 68.2%, and 50.7% respectively, at 5 years. This trend was replicated in the Validation cohort. Notably, these genomically defined groups were independent of tumor mutational burden. Amongst patients eligible for adjuvant therapy, those with a VHL+0 tumor (29%) had a 5-year DFS rate of 79.3% and could, therefore, potentially be spared further treatment. Conversely, patients with VHL+2 and VHL+≥3 tumors (32%) had equivalent DFS rates of 45.6% and 35.3%, respectively, and should be prioritized for adjuvant therapy. CONCLUSIONS: Genomic characterization of ccRCC identified biologically distinct groups of patients with divergent relapse rates. These groups account for the ∼80% of cases with VHL mutations and could be used to personalize adjuvant treatment discussions with patients as well as inform future adjuvant trial design.


Subject(s)
Carcinoma, Renal Cell , Kidney Neoplasms , Humans , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/therapy , Carcinoma, Renal Cell/metabolism , Kidney Neoplasms/genetics , Kidney Neoplasms/therapy , Kidney Neoplasms/metabolism , Von Hippel-Lindau Tumor Suppressor Protein/genetics , Neoplasm Recurrence, Local/genetics , Mutation
9.
BMC Med ; 10: 112, 2012 Sep 27.
Article in English | MEDLINE | ID: mdl-23016578

ABSTRACT

Significant advances in our understanding of the biology of renal cell carcinoma (RCC) have been achieved in recent years. These insights have led to the introduction of novel targeted therapies, revolutionising the management of patients with advanced disease. Nevertheless, there are still no biomarkers in routine clinical use in RCC. Tools used routinely to determine prognosis have not changed over the past decade; classification remains largely morphology based; and patients continue to be exposed to potentially toxic therapy with no indication of the likelihood of response. Thus the need for biomarkers in RCC is urgent. Here, we focus on recent advances in our understanding of the genetics and epigenetics of RCC, and the potential for such knowledge to provide novel markers and therapeutic targets. We highlight on-going research that is likely to deliver further candidate markers as well as generating large, well-annotated sample banks that will facilitate future studies. It is imperative that promising candidates are validated using these resources, and in subsequent prospective clinical trials, so that future biomarkers may be used in the clinic to personalize patient care.


Subject(s)
Biomarkers/analysis , Epigenomics/methods , Genomics/methods , Kidney Neoplasms/diagnosis , Epigenomics/trends , Genomics/trends , Humans
10.
BMC Cancer ; 12: 598, 2012 Dec 14.
Article in English | MEDLINE | ID: mdl-23241439

ABSTRACT

BACKGROUND: Over recent years a number of novel therapies have shown promise in advanced renal cell carcinoma (RCC). Internationally the standard of care of first-line therapy is sunitinib™, after a clear survival benefit was demonstrated over interferon-α. Convention dictates that sunitinib is continued until evidence of disease progression, assuming tolerability, although there is no evidence that this approach is superior to intermittent periods of treatment. The purpose of the STAR trial is to compare the standard treatment strategy (conventional continuation strategy, CCS) with a novel drug free interval strategy (DFIS) which includes planned treatment breaks. METHODS/DESIGN: The STAR trial is an NIHR HTA-funded UK pragmatic randomised phase II/III clinical trial in the first-line treatment of advanced RCC. Participants will be randomised (1:1) to either a sunitinib CCS or a DFIS. The overall aim of the trial is to determine whether a DFIS is non-inferior, in terms of 2-year overall survival (OS) and quality adjusted life years (QALY) (averaged over treatment and follow up), compared to a CCS. The QALY primary endpoint was selected to assess whether any detriment in terms of OS could be balanced with improvements in quality of life (QoL). This is a complex trial with a number of design challenges, and to address these issues a feasibility stage is incorporated into the trial design. Predetermined recruitment (stage A) and efficacy (stage B) intermediary endpoints must be met to allow continuation to the overall phase III trial (stage C). An integral qualitative patient preference and understanding study will occur alongside the feasibility stage to investigate patients' feelings regarding participation or non-participation in the trial. DISCUSSION: The optimal duration of continuing sunitinib in advanced RCC is unknown. Novel targeted therapies do not always have the same constraints to treatment duration as standard chemotherapeutic agents and currently there are no randomised data comparing different treatment durations. Incorporating planned treatment breaks has the potential to improve QoL and cost effectiveness, hopefully without significant detriment on OS, as has been demonstrated in other cancer types with other treatments. TRIAL REGISTRATION: Controlled-trials.com ISRCTN 06473203.


Subject(s)
Antineoplastic Agents/therapeutic use , Carcinoma, Renal Cell/drug therapy , Indoles/therapeutic use , Kidney Neoplasms/drug therapy , Protein Kinase Inhibitors/therapeutic use , Pyrroles/therapeutic use , Adult , Aged , Antineoplastic Agents/economics , Carcinoma, Renal Cell/radiotherapy , Carcinoma, Renal Cell/secondary , Cost-Benefit Analysis , Female , Humans , Indoles/economics , Kidney Neoplasms/radiotherapy , Male , Middle Aged , Protein Kinase Inhibitors/economics , Pyrroles/economics , Quality of Life , Quality-Adjusted Life Years , Sunitinib , Survival Analysis , United Kingdom , Withholding Treatment , Young Adult
11.
Proteomics ; 11(10): 2134-8, 2011 May.
Article in English | MEDLINE | ID: mdl-21500345

ABSTRACT

The need to find biomarkers for hepatobiliary diseases including cholangiocarcinoma (CCA) has led to an interest in using bile as a proximal fluid in biomarker discovery experiments, although there are inherent challenges both in its acquisition and analysis. The study described here greatly extends previous studies that have started to characterise the bile proteome. Bile from four patients with hilar CCA was depleted of albumin and immunoglobulin G and analysed by GeLC-MS/MS. The number of proteins identified per bile sample was between 378 and 741. Overall, the products of 813 unique genes were identified, considerably extending current knowledge of the malignant bile proteome. Of these, 268 were present in at least 3 out of 4 patients. This data set represents the largest catalogue of bile proteins to date and together with other studies in the literature constitutes an important prelude to the potential promise of expression proteomics and subsequent validation studies in CCA biomarker discovery.


Subject(s)
Bile Duct Neoplasms/metabolism , Bile Ducts, Intrahepatic/pathology , Bile/chemistry , Cholangiocarcinoma/metabolism , Peptide Mapping/methods , Proteins/analysis , Bile/metabolism , Bile Duct Neoplasms/pathology , Bile Ducts, Intrahepatic/metabolism , Chromatography, Liquid , Computational Biology , Databases, Genetic , Humans , Proteins/classification , Proteome/chemistry , Proteome/metabolism , Tandem Mass Spectrometry
12.
Proteomics ; 11(11): 2222-35, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21548096

ABSTRACT

Immunodepletion of clinical fluids to overcome the dominance by a few very abundant proteins has been explored but studies are few, commonly examining only limited aspects with one analytical platform. We have systematically compared immunodepletion of 6, 14, or 20 proteins using serum from renal transplant patients, analysing reproducibility, depth of coverage, efficiency, and specificity using 2-D DIGE ('top-down') and LC-MS/MS ('bottom-up'). A progressive increase in protein number (≥2 unique peptides) was found from 159 in unfractionated serum to 301 following 20 protein depletion using a relatively high-throughput 1-D-LC-MS/MS approach, including known biomarkers and moderate-lower abundance proteins such as NGAL and cytokine/growth factor receptors. On the contrary, readout by 2-D DIGE demonstrated good reproducibility of immunodepletion, but additional proteins seen tended to be isoforms of existing proteins. Depletion of 14 or 20 proteins followed by LC-MS/MS showed excellent reproducibility of proteins detected and a significant overlap between columns. Using label-free analysis, greater run-to-run variability was seen with the Prot20 column compared with the MARS14 column (median %CVs of 30.9 versus 18.2%, respectively) and a corresponding wider precision profile for the Prot20. These results illustrate the potential of immunodepletion followed by 1-D nano-LC-LTQ Orbitrap Velos analysis in a moderate through-put biomarker discovery process.


Subject(s)
Biomarkers/analysis , Blood Proteins/chemistry , Immunosorbent Techniques , Proteomics/methods , Biomarkers/chemistry , Blood Proteins/analysis , Blood Proteins/isolation & purification , Chromatography, Liquid , Databases, Protein , Humans , Protein Isoforms , Reproducibility of Results , Tandem Mass Spectrometry
13.
J Proteome Res ; 10(2): 896-906, 2011 Feb 04.
Article in English | MEDLINE | ID: mdl-21117664

ABSTRACT

Annotated formalin-fixed, paraffin-embedded (FFPE) tissue archives constitute a valuable resource for retrospective biomarker discovery. However, proteomic exploration of archival tissue is impeded by extensive formalin-induced covalent cross-linking. Robust methodology enabling proteomic profiling of archival resources is urgently needed. Recent work is beginning to support the feasibility of biomarker discovery in archival tissues, but further developments in extraction methods which are compatible with quantitative approaches are urgently needed. We report a cost-effective extraction methodology permitting quantitative proteomic analyses of small amounts of FFPE tissue for biomarker investigation. This surfactant/heat-based approach results in effective and reproducible protein extraction in FFPE tissue blocks. In combination with a liquid chromatography-mass spectrometry-based label-free quantitative proteomics methodology, the protocol enables the robust representative and quantitative analyses of the archival proteome. Preliminary validation studies in renal cancer tissues have identified typically 250-300 proteins per 500 ng of tissue with 1D LC-MS/MS with comparable extraction in FFPE and fresh frozen tissue blocks and preservation of tumor/normal differential expression patterns (205 proteins, r = 0.682; p < 10(-15)). The initial methodology presented here provides a quantitative approach for assessing the potential suitability of the vast FFPE tissue archives as an alternate resource for biomarker discovery and will allow exploration of methods to increase depth of coverage and investigate the impact of preanalytical factors.


Subject(s)
Biomarkers/analysis , Paraffin Embedding , Proteome/analysis , Proteomics/methods , Biomarkers, Tumor/metabolism , Chemical Fractionation , Chromatography, Liquid , Formaldehyde , Histocytochemistry , Humans , Intracellular Space/chemistry , Kidney Neoplasms/metabolism , Reproducibility of Results , Statistics, Nonparametric , Tandem Mass Spectrometry
14.
Psychooncology ; 20(3): 242-51, 2011 Mar.
Article in English | MEDLINE | ID: mdl-20336633

ABSTRACT

OBJECTIVE: Following publication of national guidelines on detection and management of psychosocial problems in oncology, this study explores frequency of discussion of emotional and social issues in outpatient oncology consultations. METHODS: Analysis of baseline data from 212 outpatients participating in a randomized controlled trial. Baseline data included content analysis of audio recordings of consultations, Functional Assessment of Cancer Therapy-General (FACT-G) questionnaire subscale scores, and patient and clinician self-rated preferences and perceptions of communication. RESULTS: Fifty-nine percent patients and 75% clinicians expressed preferences to discuss emotional issues during consultations. Analysis of audio recordings showed that they were discussed in 27% of the consultations, regardless of severity of emotional problems reported by patients (FACT-G Emotional well-being subscale). Fifty percent of clinicians reported discussing emotional issues 'often' or 'almost always', compared with 18% of patients. Forty-four percent patients and 39% clinicians reported that they would discuss social activities, but they were actually discussed in 46% of consultations. Patients predominantly initiated discussion of emotional and social issues (85 and 60% consultations, respectively). CONCLUSIONS: Low prevalence of discussion of psychosocial issues cannot be accounted for by patient or clinician communication preferences. If clinicians rely on patients to initiate discussion of psychosocial issues, patients' problems may go unaddressed.


Subject(s)
Communication , Emotions , Neoplasms/psychology , Outpatient Clinics, Hospital , Physician-Patient Relations , Referral and Consultation/statistics & numerical data , Adult , Aged , Aged, 80 and over , Computers , Female , Humans , Male , Middle Aged , Pilot Projects , Quality of Life , Randomized Controlled Trials as Topic , Social Support , Surveys and Questionnaires
15.
J Immunol ; 183(7): 4312-21, 2009 Oct 01.
Article in English | MEDLINE | ID: mdl-19734207

ABSTRACT

Oncolytic virotherapy may mediate antitumor effects via direct oncolysis or immune-mediated tumor regression. Although the ability of oncolytic viruses to generate adaptive antitumor immunity has been characterized, their interactions with the innate immune system are relatively unclear. Using a human in vitro system, this study investigates the innate immunological consequences of reovirus therapy and its potential to activate NK cell-mediated antitumor activity. Dendritic cells (DC) loaded with reovirus-infected human melanoma Mel888 cells (DC-MelReo), but not reovirus-infected tumor cells alone, induced IFN-gamma production within the NK cell population upon coculture with PBMC, in a cell-to-cell contact-dependent manner. DC-MelReo secreted the chemokines CCL2, 3, 4, 5, 7, 8, 11, and CXCL10; these culture supernatants induced NK cell chemotaxis. Coculture of DC-MelReo with purified NK cells induced reciprocal contact-dependent phenotypic DC maturation, while DC-MelReo elicited up-regulation of the activation marker CD69 on NK cells, in a partially contact and partially IL-12 dependent manner. Significantly, DC-MelReo induced NK cell cytotoxicity toward tumor cells by a type I IFN dependent mechanism. These data demonstrate that tumor infection by reovirus can act via DC to induce NK cell recruitment, activation, and cytotoxicity, along with reciprocal DC maturation. These findings suggest that reciprocal DC-NK cell interactions, following reovirus therapy, may play an important role in altering the immune milieu of the tumor microenvironment and mediating tumor regression.


Subject(s)
Cell Communication/immunology , Dendritic Cells/immunology , Dendritic Cells/virology , Killer Cells, Natural/immunology , Killer Cells, Natural/virology , Melanoma, Experimental/immunology , Melanoma, Experimental/prevention & control , Reoviridae/immunology , Cell Line, Tumor , Cells, Cultured , Chemotaxis, Leukocyte/immunology , Coculture Techniques , Cytotoxicity, Immunologic , Dendritic Cells/pathology , Humans , Killer Cells, Natural/pathology , Melanoma, Experimental/virology , Oncolytic Virotherapy/methods , Reoviridae Infections/immunology , Reoviridae Infections/prevention & control , Reoviridae Infections/virology
16.
J Pathol ; 217(4): 497-506, 2009 Mar.
Article in English | MEDLINE | ID: mdl-19156775

ABSTRACT

The development of efficient formaldehyde cross-link reversal strategies will make the vast diagnostic tissue archives of pathology departments amenable to prospective and retrospective translational research, particularly in biomarker-driven proteomic investigations. Heat-induced antigen retrieval strategies (HIARs) have achieved varying degrees of cross-link reversal, potentially enabling archival tissue usage for proteomic applications outside its current remit of immunohistochemistry (IHC). While most successes achieved so far have been based on retrieving tryptic peptide fragments using shot-gun proteomic approaches, attempts at extracting full-length, non-degraded, immunoreactive proteins from archival tissue have proved challenging. We have developed a novel heat-induced antigen retrieval strategy using SDS-containing Laemmli buffer for efficient intact protein recovery from formalin-fixed tissues for subsequent analysis by western blotting. Protocol optimization and comparison of extraction efficacies with frozen tissues and current leader methodology is presented. Quantitative validation of methodology was carried out in a cohort of matched tumour/normal, frozen/FFPE renal tissue samples from 10 patients, probed by western blotting for a selected panel of seven proteins known to be differentially expressed in renal cancer. Our data show that the protocol enables efficient extraction of non-degraded, full-length, immunoreactive protein, with tumour versus normal differential expression profiles for a majority of the panel of proteins tested being comparable to matched frozen tissue controls (rank correlation, r = 0.7292, p < 1.825e-09). However, the variability observed in extraction efficacies for some membrane proteins emphasizes the need for cautious interpretation of quantitative data from this subset of proteins. The method provides a viable, cost-effective quantitative option for the validation of potential biomarker panels through a range of clinical samples from existing diagnostic archives, provided that validation of the method is first carried out for the specific proteins under study.


Subject(s)
Proteins/isolation & purification , Actins/analysis , Antibodies, Monoclonal , Biomarkers/analysis , Blotting, Western/methods , Carcinoma, Renal Cell/chemistry , Electrophoresis, Polyacrylamide Gel/methods , Humans , Kidney Neoplasms/chemistry , Mass Spectrometry , Membrane Proteins/isolation & purification , Paraffin Embedding , Proteomics , Reproducibility of Results , Tissue Fixation
17.
J Immunol ; 181(5): 3108-15, 2008 Sep 01.
Article in English | MEDLINE | ID: mdl-18713981

ABSTRACT

In vivo, dendritic cells (DC) are programmed to orchestrate innate and adaptive immunity in response to pathogen-derived "danger" signals. Under particular circumstances, DC can also be directly cytotoxic against tumor cells, potentially allowing them to release tumor associated Ags from dying cells and then prime antitumor immunity against them. In this study, we describe the innate characteristics of DC (OK-DC) generated in vitro after exposure of immature human myeloid-derived DC to OK432, a penicillin-inactivated and lyophilized preparation of Streptococcus pyrogenes. OK-DC produced proinflammatory cytokines, stimulated autologous T cell proliferation and IFN-gamma secretion, expressed CCR7, and migrated in response to MIP-3beta. Moreover, OK-DC displayed strong, specific cytotoxicity toward tumor cell targets. This cytotoxicity was associated with novel, OK432-induced up-regulation of CD40L on the cell surface of OK-DC, and was absolutely dependent on expression of CD40 on the tumor targets. These data demonstrate that maturation of human DC with OK432, an adjuvant suitable for clinical use, induces direct tumor cell killing by DC, and describes a novel CD40/CD40L-mediated mechanism for specific DC antitumor cytotoxicity.


Subject(s)
CD40 Antigens/metabolism , CD40 Ligand/metabolism , Cytotoxicity, Immunologic , Dendritic Cells/immunology , Neoplasms/immunology , Picibanil/pharmacology , CD40 Ligand/genetics , Cell Death , Dendritic Cells/drug effects , Humans , Neoplasms/pathology , Up-Regulation/drug effects
18.
Eur Urol Oncol ; 3(6): 773-779, 2020 12.
Article in English | MEDLINE | ID: mdl-31411979

ABSTRACT

BACKGROUND: Some 1.5 million people in the UK have a learning disability (LD). This vulnerable group derives less benefit from population-based education programs. They are prone to underenrolment in screening programs and may lack the ability to perform self-examination. OBJECTIVE: To identify patients with LD in England and assess their testicular cancer (TC) survival in comparison to the general population. DESIGN, SETTING, AND PARTICIPANTS: Patient records were identified from the Hospital Episode Statistics database. All patients resident in England with a diagnosis of mental debility, "developmental disorder of scholastic skills", or attending under the specialty of LD between April 1, 2001 and June 30, 2015 were included. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We measured survival outcomes according to the Kaplan-Meier method and used log-rank tests to assess survival difference between demographic groups. RESULTS AND LIMITATIONS: Of 158138 male patients with LD, 331 had TC and 32 died of cancer. LD patients had a poorer prognosis, with 10-yr TC-specific survival of 88.4% (95% confidence interval [CI] 84.5-92.4%) in the LD group versus 96.8% (95% CI 96.6-97.1%) in the non-LD group. LD patients also had lower all-cause survival rates. The 10-yr survival rate was 77.6% (95% CI 72.2-83.3%) for LD patients versus 89.9% (95% CI 89.4-90.3%) for non-LD patients, while the corresponding 5-yr rates were 84% (95% CI 79.9-88.4%) versus 92.2% (95% CI 91.8-92.5%). CONCLUSIONS: Education regarding self-examination for TC must be provided in a format suitable for those with LD. Carers for male patients with LD should be informed about testicular examination and sinister signs. PATIENT SUMMARY: Testicular cancer patients who also have a learning disability (LD) have a one in nine chance of dying, compared to a one in 36 chance for testicular cancer patients without LD. This is because patients with LD are less likely to detect the disease at an earlier stage.


Subject(s)
Learning Disabilities/complications , Patient Education as Topic , Survivorship , Testicular Neoplasms/mortality , Adult , Diagnostic Self Evaluation , England/epidemiology , Follow-Up Studies , Humans , Kaplan-Meier Estimate , Male , Middle Aged , Survival Rate , Testicular Neoplasms/complications , Testicular Neoplasms/diagnosis , Testicular Neoplasms/therapy , Young Adult
19.
BMJ Open ; 10(5): e035938, 2020 05 11.
Article in English | MEDLINE | ID: mdl-32398335

ABSTRACT

OBJECTIVES: To describe the frequency and nature of symptoms in patients presenting with suspected renal cell carcinoma (RCC) and examine their reliability in achieving early diagnosis. DESIGN: Multicentre prospective observational cohort study. SETTING AND PARTICIPANTS: Eleven UK centres recruiting patients presenting with suspected newly diagnosed RCC. Symptoms reported by patients were recorded and reviewed. Comprehensive clinico-pathological and outcome data were also collected. OUTCOMES: Type and frequency of reported symptoms, incidental diagnosis rate, metastasis-free survival and cancer-specific survival. RESULTS: Of 706 patients recruited between 2011 and 2014, 608 patients with a confirmed RCC formed the primary study population. The majority (60%) of patients were diagnosed incidentally. 87% of patients with stage Ia and 36% with stage III or IV disease presented incidentally. Visible haematuria was reported in 23% of patients and was commonly associated with advanced disease (49% had stage III or IV disease). Symptomatic presentation was associated with poorer outcomes, likely reflecting the presence of higher stage disease. Symptom patterns among the 54 patients subsequently found to have a benign renal mass were similar to those with a confirmed RCC. CONCLUSIONS: Raising public awareness of RCC-related symptoms as a strategy to improve early detection rates is limited by the fact that related symptoms are relatively uncommon and often associated with advanced disease. Greater attention must be paid to the feasibility of screening strategies and the identification of circulating diagnostic biomarkers.


Subject(s)
Carcinoma, Renal Cell/diagnosis , Early Detection of Cancer , Incidental Findings , Kidney Neoplasms/diagnosis , Symptom Assessment , Adult , Aged , Aged, 80 and over , Cohort Studies , Early Detection of Cancer/methods , Female , Hematuria/diagnosis , Hematuria/epidemiology , Hematuria/etiology , Humans , Kidney Neoplasms/mortality , Kidney Neoplasms/pathology , Male , Middle Aged , Progression-Free Survival , Prospective Studies , United Kingdom
20.
Urology ; 136: 162-168, 2020 02.
Article in English | MEDLINE | ID: mdl-31705948

ABSTRACT

OBJECTIVE: To examine changes in outcome by the Leibovich score using contemporary and historic cohorts of patients presenting with renal cell carcinoma (RCC) PATIENTS AND METHODS: Prospective observational multicenter cohort study, recruiting patients with suspected newly diagnosed RCC. A historical cohort of patients was examined for comparison. Metastasis-free survival (MFS) formed the primary outcome measure. Model discrimination and calibration were evaluated using Cox proportional hazard regression and the Kaplan-Meier method. Overall performance of the Leibovich model was assessed by estimating explained variation. RESULTS: Seven hundred and six patients were recruited between 2011 and 2014 and RCC confirmed in 608 (86%) patients. Application of the Leibovich score to patients with localized clear cell RCC in this contemporary cohort demonstrated good model discrimination (c-index = 0.77) but suboptimal calibration, with improved MFS for intermediate- and high-risk patients (5-year MFS 85% and 50%, respectively) compared to the original Leibovich cohort (74% and 31%) and a historic (1998-2006) UK cohort (76% and 37%). The proportion of variation in outcome explained by the model is low and has declined over time (28% historic vs 22% contemporary UK cohort). CONCLUSION: Prognostic models are widely employed in patients with localized RCC to guide surveillance intensity and clinical trial selection. However, the majority of the variation in outcome remains unexplained by the Leibovich model and, over time, MFS rates among intermediate- and high-risk classified patients have altered. These findings are likely to have implications for all such models used in this setting.


Subject(s)
Carcinoma, Renal Cell/surgery , Kidney Neoplasms/surgery , Nephrectomy , Adult , Aged , Aged, 80 and over , Cohort Studies , Female , Humans , Male , Middle Aged , Outcome Assessment, Health Care , Prognosis , Prospective Studies , Time Factors , United Kingdom , Young Adult
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