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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: Cellular Barcoding Identifies Clonal Substitution as a Hallmark of Local Recurrence in a Surgical Model of Head and Neck Squamous Cell Carcinoma

    Vincent Roh / Pierre Abramowski / Agnès Hiou-Feige / Kerstin Cornils / Jean-Paul Rivals / Alexandre Zougman / Tim Aranyossy / Lars Thielecke / Zinnia Truan / Maxime Mermod / Yan Monnier / Vladimir Prassolov / Ingmar Glauche / Ali Nowrouzi / Amir Abdollahi / Boris Fehse / Christian Simon / Genrich V. Tolstonog

    Cell Reports, Vol 25, Iss 8, Pp 2208-2222.e

    2018  Volume 7

    Abstract: Summary: Local recurrence after surgery for head and neck squamous cell carcinoma (HNSCC) remains a common event associated with a dismal prognosis. Improving this outcome requires a better understanding of cancer cell populations that expand from ... ...

    Abstract Summary: Local recurrence after surgery for head and neck squamous cell carcinoma (HNSCC) remains a common event associated with a dismal prognosis. Improving this outcome requires a better understanding of cancer cell populations that expand from postsurgical minimal residual disease (MRD). Therefore, we assessed clonal dynamics in a surgical model of barcoded HNSCC growing in the submental region of immunodeficient mice. Clonal substitution and massive reduction of clonal heterogeneity emerged as hallmarks of local recurrence, as the clones dominating in less heterogeneous recurrences were scarce in their matched primary tumors. These lineages were selected by their ability to persist after surgery and competitively expand from MRD. Clones enriched in recurrences exhibited both private and shared genetic features and likely originated from ancestors shared with clones dominating in primary tumors. They demonstrated high invasiveness and epithelial-to-mesenchymal transition, eventually providing an attractive target for obtaining better local control for these tumors. : Roh et al. combine fluorescent protein marking and cellular barcoding to investigate the clonal composition of matched primary and recurrent tumors in a surgical model of HNSCC. They demonstrate that clones present in primary tumors are substituted by other initially rare clones expanding after resection. Keywords: head and neck squamous cell carcinoma, clonal heterogeneity, clonal substitution, recurrent tumor-initiating clones, epithelial-mesenchymal transition, invasion, RGB marking, DNA barcoding, LeGO vectors
    Keywords Biology (General) ; QH301-705.5
    Subject code 571
    Language English
    Publishing date 2018-11-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Immunohistochemical and Proteomic Evaluation of Nuclear Ubiquitous Casein and Cyclin-Dependent Kinases Substrate in Invasive Ductal Carcinoma of the Breast

    Piotr Ziółkowski / Elżbieta Gamian / Beata Osiecka / Alexandre Zougman / Jacek R. Wiśniewski

    BioMed Research International, Vol

    2009  Volume 2009

    Abstract: Nuclear ubiquitous casein and cyclin-dependent kinases substrate (NUCKS) is 27 kDa chromosomal protein of unknown function. Its amino acid composition as well as structure of its DNA binding domain resembles that of high-mobility group A, HMGA proteins. ... ...

    Abstract Nuclear ubiquitous casein and cyclin-dependent kinases substrate (NUCKS) is 27 kDa chromosomal protein of unknown function. Its amino acid composition as well as structure of its DNA binding domain resembles that of high-mobility group A, HMGA proteins. HMGA proteins are associated with various malignancies. Since changes in expression of HMGA are considered as marker of tumor progression, it is possible that similar changes in expression of NUCKS could be useful tool in diagnosis and prognosis of breast cancer. For identification and analysis of NUCKS we used proteomic and histochemical methods. Analysis of patient-matched samples of normal and breast cancer by mass spectrometry revealed elevated levels of NUCKS in protein extracts from ductal breast cancers. We elicited specific antibodies against NUCKS and used them for immunohistochemistry in invasive ductal carcinoma of breast. We found high expression of NUCKS in 84.3% of cancer cells. We suggest that such overexpression of NUCKS can play significant role in breast cancer biology.
    Keywords Biotechnology ; TP248.13-248.65 ; Chemical technology ; TP1-1185 ; Technology ; T ; DOAJ:Biotechnology ; DOAJ:Life Sciences ; DOAJ:Biology and Life Sciences
    Subject code 616
    Language English
    Publishing date 2009-01-01T00:00:00Z
    Publisher Hindawi Publishing Corporation
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Immunohistochemical and Proteomic Evaluation of Nuclear Ubiquitous Casein and Cyclin-Dependent Kinases Substrate in Invasive Ductal Carcinoma of the Breast

    Piotr Ziółkowski / Elżbieta Gamian / Beata Osiecka / Alexandre Zougman / Jacek R. Wiśniewski

    Journal of Biomedicine and Biotechnology, Vol

    2009  Volume 2009

    Abstract: Nuclear ubiquitous casein and cyclin-dependent kinases substrate (NUCKS) is 27 kDa chromosomal protein of unknown function. Its amino acid composition as well as structure of its DNA binding domain resembles that of high-mobility group A, HMGA proteins. ... ...

    Abstract Nuclear ubiquitous casein and cyclin-dependent kinases substrate (NUCKS) is 27 kDa chromosomal protein of unknown function. Its amino acid composition as well as structure of its DNA binding domain resembles that of high-mobility group A, HMGA proteins. HMGA proteins are associated with various malignancies. Since changes in expression of HMGA are considered as marker of tumor progression, it is possible that similar changes in expression of NUCKS could be useful tool in diagnosis and prognosis of breast cancer. For identification and analysis of NUCKS we used proteomic and histochemical methods. Analysis of patient-matched samples of normal and breast cancer by mass spectrometry revealed elevated levels of NUCKS in protein extracts from ductal breast cancers. We elicited specific antibodies against NUCKS and used them for immunohistochemistry in invasive ductal carcinoma of breast. We found high expression of NUCKS in 84.3% of cancer cells. We suggest that such overexpression of NUCKS can play significant role in breast cancer biology.
    Keywords Biotechnology ; TP248.13-248.65 ; Chemical technology ; TP1-1185 ; Technology ; T ; DOAJ:Biotechnology ; DOAJ:Life Sciences ; DOAJ:Biology and Life Sciences
    Subject code 616
    Language English
    Publishing date 2009-01-01T00:00:00Z
    Publisher Hindawi Publishing Corporation
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: Biomarkers and response to bevacizumab--response.

    Collinson, Fiona / Hutchinson, Michelle / Craven, Rachel A / Cairns, David A / Alexandre, Zougman / Wind, Tobias C / Gahir, Narinder / Messenger, Michael P / Jackson, Sharon / Thompson, Douglas / Adusei, Cybil / Ledermann, Jonathan / Hall, Geoffrey / Jayson, Gordon C / Selby, Peter J / Banks, Rosamonde E

    Clinical cancer research : an official journal of the American Association for Cancer Research

    2014  Volume 20, Issue 4, Page(s) 1058

    MeSH term(s) Angiogenesis Inhibitors/therapeutic use ; Antibodies, Monoclonal, Humanized/therapeutic use ; Biomarkers, Tumor/blood ; Fallopian Tube Neoplasms/blood ; Female ; Humans ; Ovarian Neoplasms/blood ; Patient Selection ; Peritoneal Neoplasms/blood
    Chemical Substances Angiogenesis Inhibitors ; Antibodies, Monoclonal, Humanized ; Biomarkers, Tumor
    Language English
    Publishing date 2014-02-28
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 1225457-5
    ISSN 1557-3265 ; 1078-0432
    ISSN (online) 1557-3265
    ISSN 1078-0432
    DOI 10.1158/1078-0432.CCR-13-3269
    Database MEDical Literature Analysis and Retrieval System OnLINE

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