Ferdinand von Eggeling

Mass spectrometry meets chip technology: A new proteomic tool in cancer research?

DNA chip technologies are the most exiting genomic tools, which were developed within the last few years. It is, however, evident that knowledge of the gene sequence or the quantity of gene expression is not sufficient to predict the biological nature and function of a protein. This can be particularly important in cancer research where post‐translational modifications of a protein can specifically contribute to the disease. To address this problem, several proteomic tools have been developed. Currently the most widely used proteomic tool is two‐dimensional protein gel electrophoresis (2‐DE), which can display protein expression patterns to a high degree of resolution. As an alternative to 2‐DE, a preliminary study using a new technique was employed to generate protein expression patterns from whole tissue extracts. Surface‐enhanced laser desorption/ionization (SELDI) allows the retention of proteins on a solid‐phase chromatographic surface (Protein Chip® Array) with direct detection of retained proteins by time of flight‐mass spectrometry (TOF‐MS). Using this system, we analyzed eight cases of renal cell carcinoma (RCC) including normal, peripheral and central tumor tissue as well as four microdissected cases of cervical intraepithelial neoplasia (CIN) and three microdissected cases of cervix uteri carcinoma. Differentially expressed proteins were found by comparing the protein expression patterns generated using SELDI‐based TOF‐MS of tumor tissue with normal and neoplastic tissue, respectively. By applying this fast and powerful Protein Chip array technology it becomes possible to investigate complex changes at the protein level in cancer associated with tumor development and progression.

Spatial segmentation of imaging mass spectrometry data with edge-preserving image denoising and clustering.

In recent years, matrix-assisted laser desorption/ionization (MALDI)-imaging mass spectrometry has become a mature technology, allowing for reproducible high-resolution measurements to localize proteins and smaller molecules. However, despite this impressive technological advance, only a few papers have been published concerned with computational methods for MALDI-imaging data. We address this issue proposing a new procedure for spatial segmentation of MALDI-imaging data sets. This procedure clusters all spectra into different groups based on their similarity. This partition is represented by a segmentation map, which helps to understand the spatial structure of the sample. The core of our segmentation procedure is the edge-preserving denoising of images corresponding to specific masses that reduces pixel-to-pixel variability and improves the segmentation map significantly. Moreover, before applying denoising, we reduce the data set selecting peaks appearing in at least 1% of spectra. High dimensional discriminant clustering completes the procedure. We analyzed two data sets using the proposed pipeline. First, for a rat brain coronal section the calculated segmentation maps highlight the anatomical and functional structure of the brain. Second, a section of a neuroendocrine tumor invading the small intestine was interpreted where the tumor area was discriminated and functionally similar regions were indicated.

A Technical Triade for Proteomic Identification and Characterization of Cancer Biomarkers

Biomarkers are needed to elucidate the biological background and to improve the detection of cancer. Therefore, we have analyzed laser-microdissected cryostat sections from head and neck tumors and adjacent mucosa on ProteinChip arrays. Two differentially expressed proteins (P = 3.34 × 10−5 and 4.6 × 10−5) were isolated by two-dimensional gel electrophoresis and identified as S100A8 (calgranulin A) and S100A9 (calgranulin B) by in-gel proteolytic digestion, peptide mapping, tandem mass spectrometry analysis, and immunodepletion assay. The relevance of these single marker proteins was evaluated by immunohistochemistry. Positive tissue areas were reanalyzed on ProteinChip arrays to confirm the identity of these proteins. As a control, a peak with low P was identified as calgizzarin (S100A11) and characterized in the same way. This technical triade of tissue microdissection, ProteinChip technology, and immunohistochemistry opens up the possibility to find, identify, and characterize tumor relevant biomarkers, which will allow the movement toward the clonal heterogeneity of malignant tumors. Taking this approach, proteins were identified that might be responsible for invasion and metastasis.

Biomarker Discovery and Identification in Laser Microdissected Head and Neck Squamous Cell Carcinoma with ProteinChip® Technology, Two-dimensional Gel Electrophoresis, Tandem Mass Spectrometry, and Immunohistochemistry

Head and neck cancer is a frequent malignancy with a complex, and up to now not clear etiology. Therefore, despite of improvements in diagnosis and therapy, the survival rate with head and neck squamous-cell carcinomas is poor. For a better understanding of the molecular mechanisms behind the process of tumorigenesis and tumor progression, we have analyzed changes of protein expression between microdissected normal pharyngeal epithelium and tumor tissue by ProteinChip® technology. For this, cryostat sections from head and neck tumors (n = 57) and adjacent mucosa (n = 44) were laser-microdissected and analyzed on ProteinChip arrays. The derived mass spectrometry profiles exhibited numerous statistical differences. One peak significantly higher expressed in the tumor (p = 0.000029) was isolated by two-dimensional gel electrophoresis and identified as annexin V by in-gel proteolytic digestion, peptide mapping, tandem mass spectrometry analysis, and immuno-deplete assay. The relevance of this single marker protein was further evaluated by immunohistochemistry. Annexin-positive tissue areas were re-analyzed on ProteinChip arrays to confirm the identity of this protein. In this study, we could show that biomarker in head and neck cancer can be found, identified, and assessed by combination of ProteinChip technology, two-dimensional gel electrophoresis, and immunohistochemistry. In our experience, however, such studies only make sense if a relatively pure microdissected tumor tissue is used. Only then minute changes in protein expression between normal pharyngeal epithelium and tumor tissue can be detected, and it will become possible to educe a tumor-associated protein pattern that might be used as a marker for tumorigenesis and progression.

Disruption of ALX1 Causes Extreme Microphthalmia and Severe Facial Clefting: Expanding the Spectrum of Autosomal-Recessive ALX-Related Frontonasal Dysplasia

We present an autosomal-recessive frontonasal dysplasia (FND) characterized by bilateral extreme microphthalmia, bilateral oblique facial cleft, complete cleft palate, hypertelorism, wide nasal bridge with hypoplasia of the ala nasi, and low-set, posteriorly rotated ears in two distinct families. Using Affymetrix 250K SNP array genotyping and homozygosity mapping, we mapped this clinical entity to chromosome 12q21. In one of the families, three siblings were affected, and CNV analysis of the critical region showed a homozygous 3.7 Mb deletion containing the ALX1 (CART1) gene, which encodes the aristaless-like homeobox 1 transcription factor. In the second family we identified a homozygous donor-splice-site mutation (c.531+1G > A) in the ALX1 gene, providing evidence that complete loss of function of ALX1 protein causes severe disruption of early craniofacial development. Unlike loss of its murine ortholog, loss of human ALX1 does not result in neural-tube defects; however, it does severely affect the orchestrated fusion between frontonasal, nasomedial, nasolateral, and maxillary processes during early-stage embryogenesis. This study further expands the spectrum of the recently recognized autosomal-recessive ALX-related FND phenotype in humans.

Is there a higher incidence of maternal uniparental disomy 14 [upd(14)mat]? Detection of 10 new patients by methylation‐specific PCR

Maternal uniparental disomy for chromosome 14 [upd(14)mat] is associated with a characteristic phenotype including pre‐ and postnatal growth retardation, muscular hypotonia, feeding problems, motor delay, small hands and feet, precocious puberty and truncal obesity. Patients with upd(14)mat show features overlapping with Prader–Willi syndrome (PWS) and are probably underdiagnosed. Maternal upd(14) is frequently described in carriers of a Robertsonian translocation involving chromosome 14, but is also found in patients with a normal karyotype. Based on the above mentioned criteria we have identified six patients with upd(14)mat including two patients with a normal karyotype, one patient with a de novo Robertsonian translocation (14;21), one patient with a familial Robertsonian translocation (13;14) and two patients with a marker chromosome. In addition, we analyzed a cohort of 33 patients with low birth weight, feeding difficulties and consecutive obesity in whom PWS had been excluded by methylation analysis of SNRPN. In four of these patients (12%) we detected upd(14)mat. For rapid testing of upd(14)mat we analyzed the methylation status of the imprinted MEG3 locus. In conclusion, we recommend considering upd(14)mat in patients with low birth weight, growth retardation, neonatal feeding problems, muscular hypotonia, motor delay, precocious puberty and truncal obesity as well as in patients with a PWS like phenotype presenting with low birth weight, feeding difficulties and obesity.

The proteasomal subunit S6 ATPase is a novel synphilin-1 interacting protein—implications for Parkinson’s disease

Synphilin‐1 is linked to Parkinsons disease (PD), based on its role as an alpha‐synuclein (PARK1)‐interacting protein and substrate of the ubiquitin E3 ligase Parkin (PARK2) and because of its presence in Lewy bodies (LB) in brains of PD patients. We found that overexpression of synphilin‐1 in cells leads to the formation of ubiquitinated cytoplasmic inclusions supporting a derangement of the ubiquitin‐proteasome system in PD. We report here a novel specific interaction of synphilin‐1 with the regulatory proteasomal protein S6 ATPase (tbp7). Functional characterization of this interaction on a cellular level revealed colocalization of S6 and synphilin‐1 in aggresome‐like intracytoplasmic inclusions. Overexpression of synphilin‐1 and S6 in cells caused reduced proteasomal activity associated with a significant increase in inclusion formation compared to cells expressing syn‐philin‐1 alone. Steady‐state levels of synphilin‐1 in cells were not altered after cotransfection of S6 and colocal‐ization of synphilin‐1‐positive inclusions with lysosomal markers suggests the presence of an alternative lysosomal degradation pathway. Subsequent immunohistochemical studies in brains of PD patients identified S6 ATPase as a component of LB. This is the first study investigating the physiological role of synphilin‐1 in the ubiquitin protea‐some system. Our data suggest a direct interaction of synphilin‐1 with the regulatory complex of the protea‐some modulating proteasomal function.—Marx F. P., Soehn, A. S., Berg, D., Melle, C., Schiesling, C., Lang, M., Kautzmann, S., Strauss, K. M., Franck, T., Engelender, S., Pahnke, J., Dawson, S., von Eggeling F., Schulz, J. B., Riess, O., Krüger R. The proteasomal subunit S6 ATPase is a novel synphilin‐1 interacting protein—implications for Parkinsons disease. FASEB J. 21, 1759–1767 (2007)

Rapid detection of trisomy 21 by quantitative PCR

Chromosomal aneuploidy is a major cause of fetal loss and genetic disease. We have devised a polymerase chain reaction (PCR)-based test that allows prenatal detection of trisomy 21 in as few as 15 fetal cells within 1 day. A pair of fluorescein-tagged primers directs amplification of a 216-bp fragment of the human S100B gene on chromosome 21. Primers that direct amplification of a 165-bp fragment of the IGF1 gene on chromosome 12 are included to generate an internal standard for quantitation. After 31 cycles of PCR, the amounts of S100B and IGF1 amplification products are determined on an Automated Laser Fluorescent DNA Sequencer. In trisomic cells, the relative amount of the S100B product is approximately 1.5-fold higher than that from normal cells. The test may be useful for non-invasive prenatal diagnosis performed on fetal cells isolated from maternal blood.

Colon-Derived Liver Metastasis, Colorectal Carcinoma, and Hepatocellular Carcinoma Can Be Discriminated by the Ca2+-Binding Proteins S100A6 and S100A11

Background It is unknown, on the proteomic level, whether the protein patterns of tumors change during metastasis or whether markers are present that allow metastases to be allocated to a specific tumor entity. The latter is of clinical interest if the primary tumor is not known. Methodology/Principal Findings In this study, tissue from colon-derived liver metastases (n = 17) were classified, laser-microdissected, and analysed by ProteinChip arrays (SELDI). The resulting spectra were compared with data for primary colorectal (CRC) and hepatocellular carcinomas (HCC) from our former studies. Of 49 signals differentially expressed in primary HCC, primary CRC, and liver metastases, two were identified by immunodepletion as S100A6 and S100A11. Both proteins were precisely localized immunohistochemically in cells. S100A6 and S100A11 can discriminate significantly between the two primary tumor entities, CRC and HCC, whereas S100A6 allows the discrimination of metastases and HCC. Conclusions Both identified proteins can be used to discriminate different tumor entities. Specific markers or proteomic patterns for the metastases of different primary cancers will allow us to determine the biological characteristics of metastasis in general. It is unknown how the protein patterns of tumors change during metastasis or whether markers are present that allow metastases to be allocated to a specific tumor entity. The latter is of clinical interest if the primary tumor is not known.

Specific protein and miRNA patterns characterise tumour-associated fibroblasts in bladder cancer

PurposeTumour development and progression are strongly affected by interaction of tumour cells and tumour stroma. Different tumour models demonstrate a supportive effect of tumour-associated fibroblasts (TAF) on the tumour genesis. Aims of the present study are the isolation of TAF from primary urinary bladder tumour specimens and the proteomic and epigenetic characterisation.MethodsTAF were isolated from cultured urinary bladder tumour specimens. Therefore, primary tumour material was treated with EDTA followed by two separated detachment steps. Non-tumour fibroblasts were isolated from foreskin and normal bladder tissues. Proteins and total RNA were isolated from cultured fibroblasts. Protein pattern analyses were carried out by SELDI–TOF–MS. The miRNA expression profile was analysed by miRNA microarray.ResultsBy optimising cell culture routines, we achieved to isolate and subsequently cultivate TAF from primary tumour material of the urinary bladder. SELDI–TOF–MS measurements reveal distinct differences in the proteomic patterns of TAF and non-tumour fibroblasts. Microarray analyses indicate specific expression of several miRNAs in TAF and non-tumour fibroblasts.ConclusionIn summary, we determined proteomic and epigenetic differences between non-tumour fibroblasts and TAF of urinary bladder carcinoma and identified specific protein expression patterns as well as miRNA profiles of TAF in comparison with non-tumour fibroblasts. These findings provide more insights into the complex tumour network and a good starting point for the identification of markers for the prediction of tumour development and progression based on specific TAF expression patterns.