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Article ; Online: AUTHOR REPLY.

Vasudev, Naveen S / Selby, Peter J / Banks, Rosamonde E

2020 Volume 136, Page(s) 168

Language	English
Publishing date	2020-02-19
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	192062-5
ISSN	1527-9995 ; 0090-4295
ISSN (online)	1527-9995
ISSN	0090-4295
DOI	10.1016/j.urology.2019.09.046
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Article ; Online: A simple serum depletion method for proteomics analysis.

Zougman, Alexandre / Wilson, John P / Banks, Rosamonde E

BioTechniques

2020 Volume 69, Issue 2, Page(s) 148–151

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
MeSH term(s)	Biomarkers/blood ; Blood Proteins/chemistry ; Blood Proteins/isolation & purification ; Chromatography, Reverse-Phase ; Humans ; Proteome/analysis ; Proteome/chemistry ; Proteome/isolation & purification ; Proteomics/methods
Chemical Substances	Biomarkers ; Blood Proteins ; Proteome
Language	English
Publishing date	2020-05-06
Publishing country	England
Document type	Journal Article
ZDB-ID	48453-2
ISSN	1940-9818 ; 0736-6205
ISSN (online)	1940-9818
ISSN	0736-6205
DOI	10.2144/btn-2020-0017
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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 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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Article ; Online: Oncogene-induced cellular senescence elicits an anti-Warburg effect.

Banks, Rosamonde E

Proteomics

2013 Volume 13, Issue 17, Page(s) 2542–2543

Abstract: ... cancer. The phenotypic consequences, i.e., the inhibition of cell proliferation, are well described ...

Abstract	Oncogene-induced senescence is now recognized as being an important mechanism in protecting against cancer. The phenotypic consequences, i.e., the inhibition of cell proliferation, are well described in model systems and specific events/key players defined. However, there is still the need to understand, at a more global level, the network of events involved both in terms of cause and consequence. This paper shows the power of systematic proteomic analyses, both targeted and global, in addressing such biological questions, highlighting the widespread nature of histone acetylation changes, and the opposite metabolic changes to those seen in the Warburg effect.
MeSH term(s)	Cellular Senescence/genetics ; Glycolysis/physiology ; Histones/metabolism ; Humans ; Mitochondrial Proteins/biosynthesis ; Neoplasms/metabolism ; Oncogenes ; Proteomics/methods ; ras Proteins/genetics
Chemical Substances	Histones ; Mitochondrial Proteins ; ras Proteins (EC 3.6.5.2)
Language	English
Publishing date	2013-09
Publishing country	Germany
Document type	Journal Article ; Comment
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.201300335
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Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article: An Exploratory Analysis of Changes in Circulating Plasma Protein Profiles Following Image-Guided Ablation of Renal Tumours Provides Evidence for Effects on Multiple Biological Processes.

Wah, Tze Min / Zhong, Jim / Wilson, Michelle / Vasudev, Naveen S / Banks, Rosamonde E

Cancers

2021 Volume 13, Issue 23

Abstract: Further biological understanding of the immune and inflammatory responses following ablation is critical to the rational development of combination ablation-immunotherapies. Our pilot exploratory study evaluated the circulating plasma protein profiles ... ...

Abstract	Further biological understanding of the immune and inflammatory responses following ablation is critical to the rational development of combination ablation-immunotherapies. Our pilot exploratory study evaluated the circulating plasma protein profiles after image-guided ablation (IGA) of small renal masses to determine the resultant systemic effects and provide insight into impact both on the tumour and immune system. Patients undergoing cryotherapy (CRYO), radiofrequency ablation (RFA) or microwave ablation (MWA) for small renal tumours were recruited. Blood samples were obtained at four timepoints; two baselines prior to IGA and at 24 h and 1-3 months post-IGA, and a panel of 164 proteins measured. Of 55 patients recruited, 35 underwent ablation (25 CRYO, 8 RFA, 2 MWA) and biomarker measurements. The most marked changes were 24 h post-CRYO, with 29 proteins increasing and 18 decreasing significantly, principally cytokines and proteins involved in regulating inflammation, danger-associated molecular patterns (DAMPs), cell proliferation, hypoxic response, apoptosis and migration. Intra-individual variation was low but inter-individual variation was apparent, for example all patients showed increases in IL-6 (1.7 to 29-fold) but only 50% in CD27. Functional annotation analysis highlighted immune/inflammation and cell proliferation/angiogenesis-related clusters, with interaction networks around IL-6, IL-10, VEGF-A and several chemokines. Increases in IL-8, IL-6, and CCL23 correlated with cryoprobe number (
Language	English
Publishing date	2021-11-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers13236037
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Article ; Online: Detergent-Free Simultaneous Sample Preparation Method for Proteomics and Metabolomics.

Zougman, Alexandre / Wilson, John P / Roberts, Lee D / Banks, Rosamonde E

Journal of proteome research

2019 Volume 19, Issue 7, Page(s) 2838–2844

Abstract: The integration of omics techniques has seen a step change in our understanding of biological systems. However, multiomics has been impaired by mutually exclusive omic separation methods and the destructive nature of the techniques when sample is limited. ...

Abstract	The integration of omics techniques has seen a step change in our understanding of biological systems. However, multiomics has been impaired by mutually exclusive omic separation methods and the destructive nature of the techniques when sample is limited. We describe Simultaneous Trapping (SiTrap), a simple and effective detergent-free method that facilitates direct measurement of the proteome and metabolome in the same sample extract. This "single-pot" multiomics processing is particularly beneficial in cases when sample amounts are limited or are heterogeneous, for example, tissue biopsies. We demonstrate the value of the SiTrap methodology as an essential multiomics tool in a proof-of-principle integrated study of renal cancer tissue biopsy samples. We believe SiTrap has the potential to become an indispensable tool in translational medical research.
MeSH term(s)	Metabolome ; Metabolomics ; Proteome ; Proteomics
Chemical Substances	Proteome
Language	English
Publishing date	2019-12-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.9b00662
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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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Article ; Online: C-STrap Sample Preparation Method--In-Situ Cysteinyl Peptide Capture for Bottom-Up Proteomics Analysis in the STrap Format.

Zougman, Alexandre / Banks, Rosamonde E

PloS one

2015 Volume 10, Issue 9, Page(s) e0138775

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.
MeSH term(s)	Chromatography, Liquid/methods ; HeLa Cells ; Humans ; Immunoprecipitation ; Mass Spectrometry/methods ; Peptides/chemistry ; Peptides/metabolism ; Protein Binding ; Proteomics/methods ; TOR Serine-Threonine Kinases/metabolism
Chemical Substances	Peptides ; TOR Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2015-09-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0138775
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Article: Preanalytical influences in clinical proteomic studies: raising awareness of fundamental issues in sample banking.

Banks, Rosamonde E

Clinical chemistry

2007 Volume 54, Issue 1, Page(s) 6–7

MeSH term(s)	Algorithms ; Bias ; Biomarkers, Tumor/blood ; Blood Specimen Collection ; Humans ; Male ; Prostatic Neoplasms/diagnosis ; Proteomics ; Reproducibility of Results ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2007-12-21
Publishing country	England
Document type	Editorial ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1373/clinchem.2007.097667
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Article ; Online: Standard Versus Modified Ipilimumab, in Combination With Nivolumab, in Advanced Renal Cell Carcinoma: A Randomized Phase II Trial (PRISM).

Vasudev, Naveen S / Ainsworth, Gemma / Brown, Sarah / Pickering, Lisa / Waddell, Tom / Fife, Kate / Griffiths, Richard / Sharma, Anand / Katona, Eszter / Howard, Helen / Velikova, Galina / Maraveyas, Anthony / Brown, Janet / Pezaro, Carmel / Tuthill, Mark / Boleti, Ekaterini / Bahl, Amit / Szabados, Bernadett / Banks, Rosamonde E /

Brown, Joanne / Venugopal, Balaji / Patel, Poulam / Jain, Ankit / Symeonides, Stefan N / Nathan, Paul / Collinson, Fiona J / Powles, Thomas

Journal of clinical oncology : official journal of the American Society of Clinical Oncology

2023 Volume 42, Issue 3, Page(s) 312–323

Abstract: Purpose: Ipilimumab (IPI), in combination with nivolumab (NIVO), is an approved frontline treatment option for patients with intermediate- or poor-risk advanced renal cell carcinoma (aRCC). We conducted a randomized phase II trial to evaluate whether ... ...

Abstract	Purpose: Ipilimumab (IPI), in combination with nivolumab (NIVO), is an approved frontline treatment option for patients with intermediate- or poor-risk advanced renal cell carcinoma (aRCC). We conducted a randomized phase II trial to evaluate whether administering IPI once every 12 weeks (modified), instead of once every 3 weeks (standard), in combination with NIVO, is associated with a favorable toxicity profile. Methods: Treatment-naïve patients with clear-cell aRCC were randomly assigned 2:1 to receive four doses of modified or standard IPI, 1 mg/kg, in combination with NIVO (3 mg/kg). The primary end point was the proportion of patients with a grade 3-5 treatment-related adverse event (trAE) among those who received at least one dose of therapy. The key secondary end point was 12-month progression-free survival (PFS) in the modified arm compared with historical sunitinib control. The study was not designed to formally compare arms for efficacy. Results: Between March 2018 and January 2020, 192 patients (69.8% intermediate/poor-risk) were randomly assigned and received at least one dose of study drug. The incidence of grade 3-5 trAEs was significantly lower among participants receiving modified versus standard IPI (32.8% Conclusion: Rates of grade 3-5 trAEs were significantly lower in patients receiving modified versus standard IPI. Although 12-month PFS did not meet the prespecified efficacy threshold compared with historical control, informal comparison of treatment groups did not suggest any reduction in efficacy with the modified schedule.
MeSH term(s)	Humans ; Nivolumab/therapeutic use ; Ipilimumab ; Carcinoma, Renal Cell/drug therapy ; Carcinoma, Renal Cell/pathology ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Kidney Neoplasms/drug therapy ; Kidney Neoplasms/pathology
Chemical Substances	Nivolumab (31YO63LBSN) ; Ipilimumab
Language	English
Publishing date	2023-11-06
Publishing country	United States
Document type	Randomized Controlled Trial ; Clinical Trial, Phase II ; Journal Article
ZDB-ID	604914-x
ISSN	1527-7755 ; 0732-183X
ISSN (online)	1527-7755
ISSN	0732-183X
DOI	10.1200/JCO.23.00236
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