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    Proteomic insights into non-small cell lung cancer: New ideas for cancer diagnosis and therapy from a functional viewpoint
    (Amsterdam : Elsevier, 2014) Linxweiler, Johannes; Kollipara, Laxmikanth; Zahedi, René P.; Lampel, Pavel; Zimmermann, Richard; Greiner, Markus
    We recently characterized SEC62 as an oncogene in non-small-cell lung cancer (NSCLC). Here we aimed to gain further insight into the molecular mechanisms of the cancer-related functions of this oncogene. We performed 2D-DIGE proteome analysis of tumor material from patients with NSCLC and of HEK293 cells stably overexpressing plasmid-encoded SEC62, combined with investigation of the Sec62 interactome. Furthermore, we analyzed the proteomic effects of siRNA-mediated depletion of the Sec62-interacting protein Sec63. We identified a comprehensive list of differentially regulated proteins, providing new insights into the molecular mechanisms of the cancer-related functions of Sec62 in cell migration, drug resistance, and Ca2+-homeostasis.
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    The potential of fractional diagonal chromatography strategies for the enrichment of post-translational modifications
    (Amsterdam : Elsevier, 2014) Venne, A. Saskia; Zahedi, René P.
    More than 450 post-translational modifications (PTMs) are known, however, currently only some of those can be enriched and analyzed from complex samples such as cell lysates. Therefore, we need additional methods and concepts to improve our understanding about the dynamic crosstalk of PTMs and the highly context-dependent regulation of protein function by so-called ‘PTM codes’. The mere focus on affinity-based enrichment techniques may not be sufficient to achieve this ambitious goal. However, the complementary use of two-dimensional chromatography-based strategies such as COFRADIC and ChaFRADIC might open new avenues for enriching a variety of so far inaccessible PTMs for large-scale proteome studies.