Jörg Schlaak - Academia.edu (original) (raw)

Papers by Jörg Schlaak

Research paper thumbnail of Proteomic Differences Between Hepatocellular Carcinoma and Nontumorous Liver Tissue Investigated by a Combined Gel-based and Label-free Quantitative Proteomics Study

Molecular & Cellular Proteomics, 2013

Proteomics-based clinical studies have been shown to be promising strategies for the discovery of... more Proteomics-based clinical studies have been shown to be promising strategies for the discovery of novel biomarkers of a particular disease. Here, we present a study of hepatocellular carcinoma (HCC) that combines complementary two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography (LC-MS)based approaches of quantitative proteomics. In our proteomic experiments, we analyzed a set of 14 samples (7 ؋ HCC versus 7 ؋ nontumorous liver tissue) with both techniques. Thereby we identified 573 proteins that were differentially expressed between the experimental groups. Among these, only 51 differentially expressed proteins were identified irrespective of the applied approach. Using Western blotting and immunohistochemical analysis the regulation patterns of six selected proteins from the study overlap (inorganic pyrophosphatase 1 (PPA1), tumor necrosis factor type 1 receptor-associated protein 1 (TRAP1), betaine-homocysteine S-methyltransferase 1 (BHMT)) were successfully verified within the same sample set. In addition, the up-regulations of selected proteins from the complements of both approaches (major vault protein (MVP), gelsolin (GSN), chloride intracellular channel protein 1 (CLIC1)) were also reproducible. Within a second independent verification set (n ‫؍‬ 33) the altered protein expression levels of major vault protein and betaine-homocysteine S-methyltransferase were further confirmed by Western blots quantitatively analyzed via densitometry. For the other candidates From the ‡Medizinisches Proteom-Center, Ruhr-Universitä t Bochum, The abbreviations used are: HCC, hepatocellular carcinoma; SILAC, stable isotope labeling by amino acids in cell culture; iTRAQ, isobaric tags for relative and absolute quantification; CDIT, culturederived isotope tags; NASH, nonalcoholic steatohepatitis; IEF, isoelectric focusing; ECL, Enhanced chemiluminescence; AB, antibody; RT, room temperature.

Research paper thumbnail of A structured proteomic approach identifies 14-3-3Sigma as a novel and reliable protein biomarker in panel based differential diagnostics of liver tumors

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2014

Research paper thumbnail of A practical data processing workflow for multi-OMICS projects

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2014

Multi-OMICS approaches aim on the integration of quantitative data obtained for different biologi... more Multi-OMICS approaches aim on the integration of quantitative data obtained for different biological molecules in order to understand their interrelation and the functioning of larger systems. This paper deals with several data integration and data processing issues that frequently occur within this context. To this end, the data processing workflow within the PROFILE project is presented, a multi-OMICS project that aims on identification of novel biomarkers and the development of new therapeutic targets for seven important liver diseases. Furthermore, a software called CrossPlatformCommander is sketched, which facilitates several steps of the proposed workflow in a semi-automatic manner. Application of the software is presented for the detection of novel biomarkers, their ranking and annotation with existing knowledge using the example of corresponding Transcriptomics and Proteomics data sets obtained from patients suffering from hepatocellular carcinoma. Additionally, a linear regression analysis of Transcriptomics vs. Proteomics data is presented and its performance assessed. It was shown, that for capturing profound relations between Transcriptomics and Proteomics data, a simple linear regression analysis is not sufficient and implementation and evaluation of alternative statistical approaches are needed. Additionally, the integration of multivariate variable selection and classification approaches is intended for further development of the software. Although this paper focuses only on the combination of data obtained from quantitative Proteomics and Transcriptomics experiments, several approaches and data integration steps are also applicable for other OMICS technologies. Keeping specific restrictions in mind the suggested workflow (or at least parts of it) may be used as a template for similar projects that make use of different high throughput techniques.

Research paper thumbnail of Individual profiling of circulating tumor cell composition and therapeutic outcome in patients with hepatocellular carcinoma

Translational Oncology, 2013

Background: Circulating tumor cells (CTC) could serve as a "liquid biopsy" for individualizing an... more Background: Circulating tumor cells (CTC) could serve as a "liquid biopsy" for individualizing and monitoring treatment in patients with solid tumors as recently shown by our group. We assessed which nonhematopoietic cell types are identifiable in the peripheral blood of patients with non-small cell lung cancer (NSCLC) and correlated those to clinical characteristics.

Research paper thumbnail of Identification of novel biomarker candidates by proteomic analysis of cerebrospinal fluid from patients with moyamoya disease using SELDI-TOF-MS

The aim of this study was the identification of novel biomarker candidates for the diagnosis of c... more The aim of this study was the identification of novel biomarker candidates for the diagnosis of cholangiocellular carcinoma (CCC) and its immunohistochemical differentiation from benign liver and bile duct cells. CCC is a primary cancer that arises from the epithelial cells of bile ducts and is characterized by high mortality rates due to its late clinical presentation and limited treatment options. Tumorous tissue and adjacent non-tumorous liver tissue from eight CCC patients were analyzed by means of twodimensional differential in-gel electrophoresis and massspectrometry-based label-free proteomics. After data analysis and statistical evaluation of the proteins found to be differentially regulated between the two experimental groups (fold change > 1.5; p value < 0.05), 14 candidate proteins were chosen for determination of the cell-typespecific expression profile via immunohistochemistry in a cohort of 14 patients. This confirmed the significant upregulation of serpin H1, 14-3-3 protein sigma, and stressinduced phosphoprotein 1 in tumorous cholangiocytes relative to normal hepatocytes and non-tumorous cholan-From the ‡Medizinisches Proteom-Center, Ruhr-Universitä t Bochum, 44801 Bochum, Germany; ¶Institut fü r Pathologie, Universitä tsklinikum Essen, Universitä t Duisburg-Essen, 45141 Essen, Germany; ʈKlinik fü r Gastroenterologie und Hepatologie, Universitä tsklinikum Essen, 45141 Essen, Universitä t Duisburg-Essen,

Research paper thumbnail of Proteomic Differences Between Hepatocellular Carcinoma and Nontumorous Liver Tissue Investigated by a Combined Gel-based and Label-free Quantitative Proteomics Study

Molecular & Cellular Proteomics, 2013

Proteomics-based clinical studies have been shown to be promising strategies for the discovery of... more Proteomics-based clinical studies have been shown to be promising strategies for the discovery of novel biomarkers of a particular disease. Here, we present a study of hepatocellular carcinoma (HCC) that combines complementary two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography (LC-MS)based approaches of quantitative proteomics. In our proteomic experiments, we analyzed a set of 14 samples (7 ؋ HCC versus 7 ؋ nontumorous liver tissue) with both techniques. Thereby we identified 573 proteins that were differentially expressed between the experimental groups. Among these, only 51 differentially expressed proteins were identified irrespective of the applied approach. Using Western blotting and immunohistochemical analysis the regulation patterns of six selected proteins from the study overlap (inorganic pyrophosphatase 1 (PPA1), tumor necrosis factor type 1 receptor-associated protein 1 (TRAP1), betaine-homocysteine S-methyltransferase 1 (BHMT)) were successfully verified within the same sample set. In addition, the up-regulations of selected proteins from the complements of both approaches (major vault protein (MVP), gelsolin (GSN), chloride intracellular channel protein 1 (CLIC1)) were also reproducible. Within a second independent verification set (n ‫؍‬ 33) the altered protein expression levels of major vault protein and betaine-homocysteine S-methyltransferase were further confirmed by Western blots quantitatively analyzed via densitometry. For the other candidates From the ‡Medizinisches Proteom-Center, Ruhr-Universitä t Bochum, The abbreviations used are: HCC, hepatocellular carcinoma; SILAC, stable isotope labeling by amino acids in cell culture; iTRAQ, isobaric tags for relative and absolute quantification; CDIT, culturederived isotope tags; NASH, nonalcoholic steatohepatitis; IEF, isoelectric focusing; ECL, Enhanced chemiluminescence; AB, antibody; RT, room temperature.

Research paper thumbnail of A structured proteomic approach identifies 14-3-3Sigma as a novel and reliable protein biomarker in panel based differential diagnostics of liver tumors

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2014

Research paper thumbnail of A practical data processing workflow for multi-OMICS projects

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2014

Multi-OMICS approaches aim on the integration of quantitative data obtained for different biologi... more Multi-OMICS approaches aim on the integration of quantitative data obtained for different biological molecules in order to understand their interrelation and the functioning of larger systems. This paper deals with several data integration and data processing issues that frequently occur within this context. To this end, the data processing workflow within the PROFILE project is presented, a multi-OMICS project that aims on identification of novel biomarkers and the development of new therapeutic targets for seven important liver diseases. Furthermore, a software called CrossPlatformCommander is sketched, which facilitates several steps of the proposed workflow in a semi-automatic manner. Application of the software is presented for the detection of novel biomarkers, their ranking and annotation with existing knowledge using the example of corresponding Transcriptomics and Proteomics data sets obtained from patients suffering from hepatocellular carcinoma. Additionally, a linear regression analysis of Transcriptomics vs. Proteomics data is presented and its performance assessed. It was shown, that for capturing profound relations between Transcriptomics and Proteomics data, a simple linear regression analysis is not sufficient and implementation and evaluation of alternative statistical approaches are needed. Additionally, the integration of multivariate variable selection and classification approaches is intended for further development of the software. Although this paper focuses only on the combination of data obtained from quantitative Proteomics and Transcriptomics experiments, several approaches and data integration steps are also applicable for other OMICS technologies. Keeping specific restrictions in mind the suggested workflow (or at least parts of it) may be used as a template for similar projects that make use of different high throughput techniques.

Research paper thumbnail of Individual profiling of circulating tumor cell composition and therapeutic outcome in patients with hepatocellular carcinoma

Translational Oncology, 2013

Background: Circulating tumor cells (CTC) could serve as a "liquid biopsy" for individualizing an... more Background: Circulating tumor cells (CTC) could serve as a "liquid biopsy" for individualizing and monitoring treatment in patients with solid tumors as recently shown by our group. We assessed which nonhematopoietic cell types are identifiable in the peripheral blood of patients with non-small cell lung cancer (NSCLC) and correlated those to clinical characteristics.

Research paper thumbnail of Identification of novel biomarker candidates by proteomic analysis of cerebrospinal fluid from patients with moyamoya disease using SELDI-TOF-MS

The aim of this study was the identification of novel biomarker candidates for the diagnosis of c... more The aim of this study was the identification of novel biomarker candidates for the diagnosis of cholangiocellular carcinoma (CCC) and its immunohistochemical differentiation from benign liver and bile duct cells. CCC is a primary cancer that arises from the epithelial cells of bile ducts and is characterized by high mortality rates due to its late clinical presentation and limited treatment options. Tumorous tissue and adjacent non-tumorous liver tissue from eight CCC patients were analyzed by means of twodimensional differential in-gel electrophoresis and massspectrometry-based label-free proteomics. After data analysis and statistical evaluation of the proteins found to be differentially regulated between the two experimental groups (fold change > 1.5; p value < 0.05), 14 candidate proteins were chosen for determination of the cell-typespecific expression profile via immunohistochemistry in a cohort of 14 patients. This confirmed the significant upregulation of serpin H1, 14-3-3 protein sigma, and stressinduced phosphoprotein 1 in tumorous cholangiocytes relative to normal hepatocytes and non-tumorous cholan-From the ‡Medizinisches Proteom-Center, Ruhr-Universitä t Bochum, 44801 Bochum, Germany; ¶Institut fü r Pathologie, Universitä tsklinikum Essen, Universitä t Duisburg-Essen, 45141 Essen, Germany; ʈKlinik fü r Gastroenterologie und Hepatologie, Universitä tsklinikum Essen, 45141 Essen, Universitä t Duisburg-Essen,