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  1. Article ; Online: A simple serum depletion method for proteomics analysis

    Alexandre Zougman / John P Wilson / Rosamonde E Banks

    BioTechniques, Vol 69, Iss 2, Pp 148-

    2020  Volume 151

    Abstract: Serum is the body fluid most often used in biomarker discovery. Albumin, the most abundant serum protein, contributes approximately 50% of the serum protein content, with an additional dozen abundant proteins dominating the rest of the serum proteome. To ...

    Abstract Serum is the body fluid most often used in biomarker discovery. Albumin, the most abundant serum protein, contributes approximately 50% of the serum protein content, with an additional dozen abundant proteins dominating the rest of the serum proteome. To profile this challenging protein mixture by proteomics, the abundant proteins must be depleted to allow for detection of the low-abundant proteins, the primary biomarker targets. Current serum depletion approaches for proteomics are costly and relatively complex to couple with protein digestion. We demonstrate a simple, affordable serum depletion methodology that, within a few minutes of processing, results in two captured serum fractions – albumin-depleted and albumin-rich – which are digested in situ. We believe our method is a useful addition to the biomarker sample preparation toolbox.
    Keywords albumin depletion ; serum protein fractionation ; serum proteomics ; SiTrap ; STrap ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Future Science Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: C-STrap Sample Preparation Method--In-Situ Cysteinyl Peptide Capture for Bottom-Up Proteomics Analysis in the STrap Format.

    Alexandre Zougman / Rosamonde E Banks

    PLoS ONE, Vol 10, Iss 9, p e

    2015  Volume 0138775

    Abstract: Recently we introduced the concept of Suspension Trapping (STrap) for bottom-up proteomics sample processing that is based upon SDS-mediated protein extraction, swift detergent removal and rapid reactor-type protein digestion in a quartz depth filter ... ...

    Abstract Recently we introduced the concept of Suspension Trapping (STrap) for bottom-up proteomics sample processing that is based upon SDS-mediated protein extraction, swift detergent removal and rapid reactor-type protein digestion in a quartz depth filter trap. As the depth filter surface is made of silica, it is readily modifiable with various functional groups using the silane coupling chemistries. Thus, during the digest, peptides possessing specific features could be targeted for enrichment by the functionalized depth filter material while non-targeted peptides could be collected as an unbound distinct fraction after the digest. In the example presented here the quartz depth filter surface is functionalized with the pyridyldithiol group therefore enabling reversible in-situ capture of the cysteine-containing peptides generated during the STrap-based digest. The described C-STrap method retains all advantages of the original STrap methodology and provides robust foundation for the conception of the targeted in-situ peptide fractionation in the STrap format for bottom-up proteomics. The presented data support the method's use in qualitative and semi-quantitative proteomics experiments.
    Keywords Medicine ; R ; Science ; Q
    Subject code 540
    Language English
    Publishing date 2015-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Challenges of early renal cancer detection

    Michelle Wilson / Naveen S Vasudev / Grant D Stewart / Adebanji Adeyoju / Jon Cartledge / Michael Kimuli / Shibendra Datta / Damian Hanbury / David Hrouda / Grenville Oades / Poulam Patel / Naeem Soomro / Mark Sullivan / Jeff Webster / Peter J Selby / Rosamonde E Banks

    BMJ Open, Vol 10, Iss

    symptom patterns and incidental diagnosis rate in a multicentre prospective UK cohort of patients presenting with suspected renal cancer

    2020  Volume 5

    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 ... ...

    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.
    Keywords Medicine ; R
    Language English
    Publishing date 2020-05-01T00:00:00Z
    Publisher BMJ Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Discovery and validation of urinary biomarkers for detection of renal cell carcinoma

    Frantzi, Maria / Antonia Vlahou / Axel S. Merseburger / Dan Theodorescu / Harald Mischak / Holger Husi / Jochen Metzger / Jonathan J. Cartledge / Joost P. Schanstra / Julie Klein / Korbinian Brand / Markus A. Kuczyk / Mohammed Dakna / Rosamonde E. Banks / William Mullen

    Journal of proteomics. 2014 Feb. 26, v. 98

    2014  

    Abstract: Renal cell carcinoma (RCC) is often accompanied by non-specific symptoms. The increase of incidentally discovered small renal masses also presents a diagnostic dilemma. This study investigates whether RCC-specific peptides with diagnostic potential can ... ...

    Abstract Renal cell carcinoma (RCC) is often accompanied by non-specific symptoms. The increase of incidentally discovered small renal masses also presents a diagnostic dilemma. This study investigates whether RCC-specific peptides with diagnostic potential can be detected in urine and whether a combination of such peptides could form a urinary screening tool.For the discovery of RCC-specific biomarkers, we have employed CE–MS to analyze urine samples from patients with RCC (N=40) compared to non-diseased controls (N=68).86 peptides were found to be specifically associated to RCC, of which sequence could be obtained for 40. A classifier based on these peptides was evaluated in an independent set of 76 samples, resulting in 80% sensitivity and 87% specificity. The specificity of the marker panel was further validated in a historical dataset of 1077 samples including age-matched controls (N=218), patients with related cancer types and renal diseases (N=859). In silico protease prediction based on the cleavage sites of differentially excreted peptides, suggested modified activity of certain proteases including cathepsins, ADAMTS and kallikreins some of which were previously found to be associated to RCC.RCC can be detected with high accuracy based on specific urinary peptides.Clear cell renal cell carcinoma (RCC) has the highest incidence among the renal malignancies, often presenting non-specific or no symptoms at all. Moreover, with no diagnostic marker being available so far, almost 30% of the patients are diagnosed with metastatic disease and 30–40% of the patients initially diagnosed with localized tumor relapse. These facts introduce the clinical need of early diagnosis. This study is focused on the investigation of a marker model based on urinary peptides, as a tool for the detection of RCC in selected patients at risk. Upon evaluation of the marker model in an independent blinded set of 76 samples, 80% sensitivity and 87% specificity were reported. An additional dataset of 1077 samples was subsequently employed for further evaluation of the specificity of the classifier.
    Keywords biomarkers ; capillary electrophoresis ; cathepsins ; data collection ; early diagnosis ; kallikreins ; kidney diseases ; mass spectrometry ; metastasis ; models ; neoplasm cells ; neoplasms ; patients ; peptides ; prediction ; relapse ; risk ; screening ; urine
    Language English
    Dates of publication 2014-0226
    Size p. 44-58.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2400835-7
    ISSN 1876-7737 ; 1874-3919
    ISSN (online) 1876-7737
    ISSN 1874-3919
    DOI 10.1016/j.jprot.2013.12.010
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Methods for the evaluation of biomarkers in patients with kidney and liver diseases

    Peter J Selby / Rosamonde E Banks / Walter Gregory / Jenny Hewison / William Rosenberg / Douglas G Altman / Jonathan J Deeks / Christopher McCabe / Julie Parkes / Catharine Sturgeon / Douglas Thompson / Maureen Twiddy / Janine Bestall / Joan Bedlington / Tilly Hale / Jacqueline Dinnes / Marc Jones / Andrew Lewington / Michael P Messenger /
    Vicky Napp / Alice Sitch / Sudeep Tanwar / Naveen S Vasudev / Paul Baxter / Sue Bell / David A Cairns / Nicola Calder / Neil Corrigan / Francesco Del Galdo / Peter Heudtlass / Nick Hornigold / Claire Hulme / Michelle Hutchinson / Carys Lippiatt / Tobias Livingstone / Roberta Longo / Matthew Potton / Stephanie Roberts / Sheryl Sim / Sebastian Trainor / Matthew Welberry Smith / James Neuberger / Douglas Thorburn / Paul Richardson / John Christie / Neil Sheerin / William McKane / Paul Gibbs / Anusha Edwards / Naeem Soomro

    Programme Grants for Applied Research, Vol 6, Iss

    multicentre research programme including ELUCIDATE RCT

    2018  Volume 3

    Abstract: Background: Protein biomarkers with associations with the activity and outcomes of diseases are being identified by modern proteomic technologies. They may be simple, accessible, cheap and safe tests that can inform diagnosis, prognosis, treatment ... ...

    Abstract Background: Protein biomarkers with associations with the activity and outcomes of diseases are being identified by modern proteomic technologies. They may be simple, accessible, cheap and safe tests that can inform diagnosis, prognosis, treatment selection, monitoring of disease activity and therapy and may substitute for complex, invasive and expensive tests. However, their potential is not yet being realised. Design and methods: The study consisted of three workstreams to create a framework for research: workstream 1, methodology – to define current practice and explore methodology innovations for biomarkers for monitoring disease; workstream 2, clinical translation – to create a framework of research practice, high-quality samples and related clinical data to evaluate the validity and clinical utility of protein biomarkers; and workstream 3, the ELF to Uncover Cirrhosis as an Indication for Diagnosis and Action for Treatable Event (ELUCIDATE) randomised controlled trial (RCT) – an exemplar RCT of an established test, the ADVIA Centaur® Enhanced Liver Fibrosis (ELF) test (Siemens Healthcare Diagnostics Ltd, Camberley, UK) [consisting of a panel of three markers – (1) serum hyaluronic acid, (2) amino-terminal propeptide of type III procollagen and (3) tissue inhibitor of metalloproteinase 1], for liver cirrhosis to determine its impact on diagnostic timing and the management of cirrhosis and the process of care and improving outcomes. Results: The methodology workstream evaluated the quality of recommendations for using prostate-specific antigen to monitor patients, systematically reviewed RCTs of monitoring strategies and reviewed the monitoring biomarker literature and how monitoring can have an impact on outcomes. Simulation studies were conducted to evaluate monitoring and improve the merits of health care. The monitoring biomarker literature is modest and robust conclusions are infrequent. We recommend improvements in research practice. Patients strongly endorsed the need for robust and conclusive ...
    Keywords biomarkers ; liver disease ; kidney disease ; prostate-specific antigen ; monitoring trials ; simulation of biomarker studies ; elf test ; elucidate ; renal cancer ; renal transplantation ; diagnosis of cirrhosis ; Public aspects of medicine ; RA1-1270
    Subject code 610
    Language English
    Publishing date 2018-06-01T00:00:00Z
    Publisher NIHR Journals Library
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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