Immunophenotyping without antibodies: New perspectives for lymphoma characterization

Aims: Accurate classification of haematological malignancies is a prerequisite for their correct diagnosis, prognosis and therapy. Clear classification of lymphomas is often hindered by the limited number of available cell surface protein markers that are suitable for immunophenotyping. A systematic and quantitative analysis of cell surface proteins is thus required to identify new protein markers on lymphoma subtypes in an unbiased and discovery-driven approach. Methods: Nine Hodgkin and non-Hodgkin B cell lines of diffuse large cell type and mediastinal type were investigated by cell surface capture (CSC) technology, a mass spectrometry-based method to identify cell surface glycoproteins. Selected proteins are verified by antibody-based methods, including flow cytometry and immunohistochemistry on cell line arrays. Results: A total of 747 predicted transmembrane proteins were identified from all cell lines, including 142 CD (cluster of differentiation) annotated proteins. A group of differentially expressed cell surface glycoproteins between Hodgkin and non-Hodgkin B cell lines was revealed via quantitative CSC technology. In addition to classical and expected CD molecules such as CD20 and CD30, less frequently expressed molecules such as CD2 on Hodgkin lymphoma (HL) cell lines were identified by CSC and verified by immunohistochemistry in cell lines and primary lymphoma tissue. A panel of CSC-identified differentiation glycoprotein candidates is currently under investigation on tissue microarrays (TMAs) from patient sample

Identifizierung VHL-assoziierter Veränderungen im klarzelligen Nierenzellkarzinom: Anwendung von kombinierten Genom- und Expressionsanalysen

Zusammenfassung: Das sporadische Nierenzellkarzinom (NZK) ist ein heterogener solider Tumor, der traditionell basierend auf morphologischen Kriterien in weitere Subtypen unterteilt wird. In den letzten Jahren konnten unter Anwendung molekularer Hochdurchsatzanalysen genetische, transkriptionelle und translationale Alterationen identifiziert werden. Diese Marker eignen sich zum einen für die molekulare Klassifizierung des NZK und haben zum anderen prognostische Wertigkeit. Die isolierte Betrachtung genetischer, transkriptioneller und translationaler Veränderungen verhindert jedoch ein tieferes Verständnis für die komplexen Vorgänge der Karzinogenese. Wir fassen hier aktuelle Forschungsergebnisse zur molekularen Charakterisierung des NZK zusammen und stellen ein systembiologisches Konzept zur Identifizierung neuer Tumormarker vor. Diese könnten zukünftig Einsatz in der Diagnostik und Therapie des sporadischen NZK finde

Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins

Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins

Micro-pharmacokinetics: quantifying local drug concentration at live cell membranes

Fundamental equations for determining pharmacological parameters, such as the binding afnity of a ligand for its target receptor, assume a homogeneous distribution of ligand, with concentrations in the immediate vicinity of the receptor being the same as those in the bulk aqueous phase. It is, however, known that drugs are able to interact directly with the plasma membrane, potentially increasing local ligand concentrations around the receptor. We have previously reported an infuence of ligand-phospholipid interactions on ligand binding kinetics at the β2-adrenoceptor, which resulted in distinct “micro-pharmacokinetic” ligand profles. Here, we directly quantifed the local concentration of BODIPY630/650-PEG8-S-propranolol (BY-propranolol), a fuorescent derivative of the classical β-blocker propranolol, at various distances above membranes of single living cells using fuorescence correlation spectroscopy. We show for the frst time a signifcantly increased ligand concentration immediatel adjacent to the cell membrane compared to the bulk aqueous phase. We further show a clear role of both the cell membrane and the β2-adrenoceptor in determining high local BY-propranolol concentrations at the cell surface. These data suggest that the true binding afnity of BY-propranolol for the β2-adrenoceptor is likely far lower than previously reported and highlights the critical importance of understanding the “micro-pharmacokinetic” profles of ligands for membrane-associated proteins

Pooled extracellular receptor-ligand interaction screening using CRISPR activation.

Extracellular interactions between cell surface receptors are necessary for signaling and adhesion but identifying them remains technically challenging. We describe a cell-based genome-wide approach employing CRISPR activation to identify receptors for a defined ligand. We show receptors for high-affinity antibodies and low-affinity ligands can be unambiguously identified when used in pools or as individual binding probes. We apply this technique to identify ligands for the adhesion G-protein-coupled receptors and show that the Nogo myelin-associated inhibitory proteins are ligands for ADGRB1. This method will enable extracellular receptor-ligand identification on a genome-wide scale

Identifizierung VHL-assoziierter Veränderungen im klarzelligen Nierenzellkarzinom : Anwendung von kombinierten Genom- und Expressionsanalysen

Das sporadische Nierenzellkarzinom (NZK) ist ein heterogener solider Tumor, der traditionell basierend auf morphologischen Kriterien in weitere Subtypen unterteilt wird. In den letzten Jahren konnten unter Anwendung molekularer Hochdurchsatzanalysen genetische, transkriptionelle und translationale Alterationen identifiziert werden. Diese Marker eignen sich zum einen für die molekulare Klassifizierung des NZK und haben zum anderen prognostische Wertigkeit. Die isolierte Betrachtung genetischer, transkriptioneller und translationaler Veränderungen verhindert jedoch ein tieferes Verständnis für die komplexen Vorgänge der Karzinogenese. Wir fassen hier aktuelle Forschungsergebnisse zur molekularen Charakterisierung des NZK zusammen und stellen ein systembiologisches Konzept zur Identifizierung neuer Tumormarker vor. Diese könnten zukünftig Einsatz in der Diagnostik und Therapie des sporadischen NZK finden = Sporadic renal cell carcinoma (RCC) represents a heterogeneous tumor, which is traditionally classified into subtypes based on morphological criteria. In recent years high-throughput molecular analyses have been able to identify genomic and proteomic alterations in tumor cells. These markers are the basis for a molecular classification of RCC and bear prognostic value. However, an isolated consideration of genomic and proteomic alterations prevents deeper insights into the complex processes of carcinogenesis. Here we summarize recent studies focussing on this aspect of RCC and present a systems biology concept for the identification of novel tumor markers. These could be applied to improve future diagnosis and therapy of RCC

[Identification of VHL-associated changes in clear cell renal carcinoma: the application of combined genome and expression analyses]

Sporadic renal cell carcinoma (RCC) represents a heterogeneous tumor, which is traditionally classified into subtypes based on morphological criteria. In recent years high-throughput molecular analyses have been able to identify genomic and proteomic alterations in tumor cells. These markers are the basis for a molecular classification of RCC and bear prognostic value. However, an isolated consideration of genomic and proteomic alterations prevents deeper insights into the complex processes of carcinogenesis. Here we summarize recent studies focussing on this aspect of RCC and present a systems biology concept for the identification of novel tumor markers. These could be applied to improve future diagnosis and therapy of RCC

Detection of protein complex interactions via a Blue Native-PAGE retardation assay

We describe the Blue Native (BN)-PAGE retardation assay for the detection of interactions of biomolecules with protein complexes. Potential interactors of proteins are included in the BN gel matrix, resulting in retardation of proteins that interact with the added molecule. After validation using the T-cell antigen receptor, we applied the assay for a general identification of dextran interactors in combination with mass spectroscopy. The proteomic screen revealed triosephosphate isomerase oligomer as a dextranbinding, high MR complex

Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins.

Although the classification of cell types often relies on the identification of cell surface proteins as differentiation markers, flow cytometry requires suitable antibodies and currently permits detection of only up to a dozen differentiation markers in a single measurement. We use multiplexed mass-spectrometric identification of several hundred N-linked glycosylation sites specifically from cell surface-exposed glycoproteins to phenotype cells without antibodies in an unbiased fashion and without a priori knowledge. We apply our cell surface-capturing (CSC) technology, which covalently labels extracellular glycan moieties on live cells, to the detection and relative quantitative comparison of the cell surface N-glycoproteomes of T and B cells, as well as to monitor changes in the abundance of cell surface N-glycoprotein markers during T-cell activation and the controlled differentiation of embryonic stem cells into the neural lineage. A snapshot view of the cell surface N-glycoproteins will enable detection of panels of N-glycoproteins as potential differentiation markers that are currently not accessible by other means

Immunphänotypisierung ohne Antikörper: Neue Perspektiven in der Lymphomcharakterisierung

Ziel: Eine exakte Klassifikation hämatologischer Neoplasien ist Voraussetzung für eine korrekte Diagnose, Prognose und Therapiestrategie. Die Lymphomklassifikation war bis dahin limitiert durch die beschränkte Verfügbarkeit von Antikörpern gegen Oberflächenproteine, die in der Routinediagnostik an Paraffinmaterial anwendbar sind. Eine systematische und quantitative Analyse von Oberflächenproteinen ist notwendig, um neue Proteinmarker auf Lymphomsubtypen zu identifizieren. Methode: Neun Hodgkin- und Non-Hodgkin-B-Zelllinien vom diffus großzelligen und mediastinalen Typ wurden mittels sog. „Cell surface capture“ (CSC)-Technologie, einer massenspektrometriebasierten Methode, nach Zelloberflächenglykoproteinen untersucht. Selektionierte Proteine wurden mittels antikörperbasierter Methoden unter Einschluss von Durchflusszytometrie und Immunhistochemie auf Gewebechips validiert. Resultate: Insgesamt wurden 747 Transmembranproteine identifiziert, davon 142 CD- („cluster of differentiation“) annotierte Proteine. Mittels quantitativer CSC-Technologie wurde eine Gruppe unterschiedlich exprimierter Oberflächenglykoproteine zwischen Hodgkin- und Non-Hodgkin-B-Zelllinien nachgewiesen. Dabei wurden sowohl typische CD-Moleküle wie CD20 und CD30, aber auch weniger häufige Moleküle wie CD2 in Hodgkin-Lymphom- (HL-)Zelllinien identifiziert und mittels Immunhistochemie auf primären Zelllinien und Lymphomgewebe validiert. Ein Set von differenziell exprimierten Glykoproteinkandidaten wird aktuell auf Lymphomgewebechips untersucht. Schlussfolgerung: Die CSC-Technologie erlaubt, gleichzeitig mehrere hundert Oberflächenproteine auf Lymphomzelllinien nachzuweisen. Darüber hinaus können auch unbekannte, differenziell exprimierte Proteine identifiziert werden. Schlüsselwörter: Zelloberflächenglykoproteine - „Cell surface capture“ (CSC)-Technologie - Massenspektrometrie - Lympho