-
[show abstract]
[hide abstract]
ABSTRACT: Automated image analysis on virtual slides is evolving rapidly and will play an important role in the future of digital pathology. Due to the image size, the computational cost of processing whole slide images (WSIs) in full resolution is immense. Moreover, image analysis requires well focused images in high magnification.
We present a system that merges virtual microscopy techniques, open source image analysis software, and distributed parallel processing. We have integrated the parallel processing framework JPPF, so batch processing can be performed distributed and in parallel. All resulting meta data and image data are collected and merged. As an example the system is applied to the specific task of image sharpness assessment. ImageJ is an open source image editing and processing framework developed at the NIH having a large user community that contributes image processing algorithms wrapped as plug-ins in a wide field of life science applications. We developed an ImageJ plug-in that supports both basic interactive virtual microscope and batch processing functionality. For the application of sharpness inspection we employ an approach with non-overlapping tiles. Compute nodes retrieve image tiles of moderate size from the streaming server and compute the focus measure. Each tile is divided into small sub images to calculate an edge based sharpness criterion which is used for classification. The results are aggregated in a sharpness map.
Based on the system we calculate a sharpness measure and classify virtual slides into one of the following categories - excellent, okay, review and defective. Generating a scaled sharpness map enables the user to evaluate sharpness of WSIs and shows overall quality at a glance thus reducing tedious assessment work.
Using sharpness assessment as an example, the introduced system can be used to process, analyze and parallelize analysis of whole slide images based on open source software.
Diagnostic Pathology 01/2011; 6 Suppl 1:S16. · 1.64 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We attempted to establish a microscopy based tumour characterization providing insight into the genetics of cancer cells and in particular their DNA ploidy. The core classification defined semi-quantitative criteria for scoring the nuclear size ranging from small (core score 1) to giant nuclei (core score 4). By listing all nuclear sizes according to their relative frequencies it provided a measure for core size variability as a correlate of nuclear pleomorphism. Additionally, the mitosis size, their variability and the presence/abundance of tripolar and tetrapolar mitoses were determined. This classification was applied to 155 lung cancer samples from all major histologic types and the results were correlated with the analysis by DNA image cytometry and patient survival. The morphological assessments correlated highly significantly with the DNA ploidy parameters, e.g. small cell lung carcinomas showed the smallest values for nuclear size (mean core score of 1.18) and DNA content (DNA index mean of 2.08c) being highly significantly different from adenocarcinomas (1.95/3.10c), large cell lung carcinoma (2.00/3.26c) and squamous cell carcinoma (2.20/3.42c). In non-small cell lung carcinoma (NSCLC) in general and adenocarcinoma in particular, the core size variability correlated significantly with grading and survival. Furthermore, parameters indicative for chromosomal variability, i.e. 2c deviation index and 5c exceeding rate, were predictors of poor survival in NSCLC patients. As a complement to histologic tumour diagnosis the core classification should help to better stratify cancer subtypes.
Lung cancer (Amsterdam, Netherlands) 02/2009; 65(3):312-8. · 3.14 Impact Factor
-
Iver Petersen,
Christiane Schewe, Karsten Schlüns,
Manfred Dietel,
Norbert Speich,
Christoph Schmitt,
Magdolna Bollmann,
Karl Sotlar,
Burkhard Bültmann,
Maria T Dours-Zimmermann,
Barbara Padberg,
Dieter R Zimmermann
[show abstract]
[hide abstract]
ABSTRACT: The detection and typing of human papilloma virus (HPV) in pathology specimens is gaining increasingly in importance. In the context of the initiative for quality assurance in pathology (QuIP) of the German Society of Pathology and the Professional Association of German Pathologists, four panel laboratories with experience and expertise in polymerase chain reaction (PCR)-based HPV detection were selected to establish an inter-laboratory trial. In a first step, these laboratories performed an internal testing of their own methodologies, which comprised DNA sequencing, multiplex nested PCR and hybridization techniques. Material from 39 samples including paraffin sections and DNA preparations of tissues and plasmids were evaluated by each panel institute according to their own protocols. Despite the different methodologies, a high degree of inter-laboratory reliability was achieved. In this report, we summarise the results. Pretested specimens are available for the external trail and can be ordered from the steering institute via provitro GmbH Berlin ( http://www.provitro.de ). Supplementary data are online available at http://pathologie-ccm.charite.de (rubric "Forschung"), which includes a web-based photo gallery of HPV-associated lesions and their potential association with specific virus types. The initiative is intended to foster the quality assurance of molecular HPV analysis in pathology and its correlation with morphological changes.
Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin 10/2007; 451(3):701-16. · 2.49 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Insulin-like growth factor binding protein 7 (IGFBP-7) is considered a tumor suppressor in various cancers, but its role in colorectal cancer (CRC) is still uncertain. The aims of this study were to analyze the IGFBP-7 expression, and explore the mechanism responsible for the inactivation of IGFBP-7 in CRC.
mRNA expression was studied by RT-PCR and Northern blot analysis of cultured cells. Methylation status was analyzed by treatment with 5-aza-2'-deoxycytidine followed by sequencing of PCR products of sodium bisulfite-treated genomic DNA. IGFBP-7 protein expression was evaluated by immunohistochemistry (IHC) on tissue microarrays.
mRNA expression was lost in six out of eight CRC cell lines as compared to normal colon cells. DNA methylation was found in the region of exon 1 and intron 1 of IGFBP-7. In tumor tissue, 107 out of 279 samples showed a negative expression of IGFBP-7 by IHC, which was significantly associated with poor prognosis. The analysis of 37 paired cancerous and normal mucosa samples confirmed the downregulation in the tumors, but revealed variable basal expression levels of IGFBP-7 in normal mucosal samples.
DNA methylation is a mechanism responsible for IGFBP-7 gene silencing providing a target for therapeutic intervention of this tumor suppressor gene.
Journal of Cancer Research and Clinical Oncology 06/2007; 133(5):305-14. · 2.56 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Recent cDNA expression profiling analyses indicate that within specific organ cancers Cytokeratins (CKs) dysregulation may identify subgroups with distinct biological phenotypes. Our objectives in this study were (1) to test whether cytokeratins were also distinct on the protein level, (2) to evaluate these biomarkers in a series of well-characterised CRCs, (3) to apply hierarchical cluster analysis to immunohistochemical data.
Tissue microarrays (TMA) comprising 468 CRC specimens from 203 patients were constructed to evaluate CK5, CK7, CK8, CK13, CK14, CK16, CK17, CK18, CK19 and CK20. In total, 2919 samples were analyzed.
Unsupervised hierarchical clustering discovered subgroups represented by reduced CK8 and CK20 expression, that differed by a shorter patients survival. The evaluation of the specific biomarkers by Kaplan-Meier analysis showed that reduced CK8 expression (p<0.01) was significantly associated with shorter patients' survival, but was not an independent factor correlated with tumour stage (pT), grading (G) and nodal stage (pN).
Reduced coexpression of CK8 and CK20 may indicate an epithelial-mesenchymal transition (EMT) representing an important step in the development of more aggressive CRCs. In addition, multiplex analysis of TMAs together with immunohistochemistry (IHC) supplemented by hierarchical clustering are a useful, promising and very powerful tool for the identification of tumour subgroups with diagnostic and prognostic signatures.
Cellular oncology: the official journal of the International Society for Cellular Oncology 02/2006; 28(4):167-75. · 4.17 Impact Factor
-
Christiane Schewe,
Torsten Goldmann,
Marianne Grosser,
Albert Zink, Karsten Schlüns,
Stefan Pahl,
Timo Ulrichs,
Stefan H E Kaufmann,
Andreas Nerlich,
Gustavo B Baretton,
Manfred Dietel,
Ekkehard Vollmer,
Iver Petersen
[show abstract]
[hide abstract]
ABSTRACT: The present study is based on the initiative for quality assurance in pathology of the German Society of Pathology and the Professional Association of German Pathologists. Four panel laboratories with experience and expertise in polymerase chain reaction (PCR) detection of Mycobacterium tuberculosis were selected to establish the prerequisites for continuous external laboratory trials, in particular, by providing pre-tested specimens and evaluation criteria for participating institutes. In the first step, the four panel laboratories performed an internal trial to test their own reliability and reproducibility. Paraffin sections and DNA preparations from 34 tissues (25 clinical specimens and 9 controls) totalling to 66 samples were evaluated by each panel institute according to their own protocols. The methodologies differed and are described in detail. Despite these differences, a high degree of inter-laboratory reliability was achieved. In this report, we summarise our results including the correlation with the histology and provide recommendations for applying PCR-based methodology for the detection of mycobacterial DNA in surgical specimens. Supplementary data are available online at http://www.charite.de/ch/patho (rubric "Forschung"). Pre-tested specimens are now available for the external trial and can be ordered from the steering institute via Oligene (http://www.oligene.com/). All molecular pathology laboratories are invited to participate in this quality assurance initiative.
Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin 10/2005; 447(3):573-85. · 2.49 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Genomewide expression profiling has identified a number of genes expressed at higher levels in colorectal cancer (CRC) than in normal tissues. Our objectives in this study were: 1) to test whether genes were also distinct on the protein level; 2) to evaluate these biomarkers in a series of well-characterized CRCs; and 3) to apply hierarchical cluster analysis to the immunohistochemical data.
Tissue microarrays (TMAs) comprising 351 CRC specimens from 270 patients were constructed to evaluate the genes Adam10, Cyclin D1, Annexin II, NFKB, Casein kinase 2 beta (CK2B), YB-1, P32, Rad51, c-fos, IGFBP4, and Connexin26 (Cx26). In total, 3,797 samples were analyzed.
Unsupervised hierarchical clustering discovered subgroups of CRC that differed by tumor stage and survival. Kaplan-Meier analysis showed that reduced Cx26 expression was significantly associated with shorter patient survival and higher tumor grade (G1/G2 vs G3, P = .02), and Adam10 expression with a higher tumor stage (pT1/2 vs pT3/4, P = .04).
Our study highlights the potential of TMAs for a higher-dimensional analysis by evaluating serial sections of the same tissue core (three-dimensional TMA analysis). In addition, it endorses the use of immunohistochemistry supplemented by hierarchical clustering for the identification of tumor subgroups with diagnostic and prognostic signatures.
Neoplasia 09/2005; 7(8):741-7. · 5.95 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: To investigate the gene expression of 9 cDNA clones generated by suppression subtraction hybridization (SSH), Northern blot analysis was performed on a panel of immortalized bronchial epithelial cell lines, lung cancer cell lines and normal human bronchial epithelial cells (HBEC). The clones were located on chromosomes 1q, 2q, 3p, 3q, 4q and 14q representing regions that are frequently affected by DNA imbalances as shown by comparative genomic hybridization (CGH). Two were unknown (H24, H103) whereas the others matched to the Pest-containing nuclear protein (H52), Rp11-767C1 gene (H134), the hypothetical gene AK025444 (H238), Guanine nucleotide binding protein (G protein)/alpha inhibiting activity polypeptide 2 (H268), Laminin gamma 1 (Y45), the DEAD (Asp-Glu-Ala-Asp/His) box polypeptide 9 (Y162) and the heat shock 90 kDa protein 1, alpha (Y238). Northern blot results indicated that all of the studied clones showed differential up- or down-regulation in immortalized cells and lung cancer cell lines. Of those, clone Y238 representing HSP90alpha showed a clearly over-expressed transcript. Subsequently, semi-quantitative RT-PCR was used to further confirm the over-expression of Y238, indicating that HSP90alpha was significantly over-represented in 49 primary lung tumors as compared to 14 normal lung samples (P<0.01). CGH showed that the majority of studied lung cancer cell lines (71.4%) carried an overrepresentation at 14q32 where HSP90alpha is located suggesting that it may be affected by DNA copy number changes. The further characterization of these clones will provide us with valuable information on its role in lung carcinogenesis and may help to develop new diagnostic or therapeutic targets for this lethal disease.
Oncology Reports 08/2005; 14(1):229-34. · 1.84 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Comparative genomic hybridization was used to screen colorectal carcinomas for chromosomal aberrations that are associated with the metastatic phenotype of the lung. Specimens of 13 lung metastases, 6 primary tumors, 1 lymph node metastasis, 1 liver metastasis, and 1 ovarian metastasis were investigated and added to our CGH colon cancer tumor collective, comprising 85 tumor specimens from 56 patients (see CGH online tumor database at http://amba.charite.de/cgh). Lung metastases showed more alterations than liver metastases, particularly more deletions at 1p, 3p, 9q, 12q, 17q, 19p and 22q and gains at 2q, 5p, and chromosome 6. Comparing lung metastases with their corresponding primary tumors, particularly more deletions at 3p, 8p, 12q, 17q, and 21q21 and gains at 5p were observed. Based on our results, we wish to suggest a metastatic progression model. Specific subpopulations of metastatic cells have a distinct metastatic potential, which is reflected by a non-random accumulation of chromosomal alterations. Distinct alterations already exist within the primary tumor and this "ready to go package" gives the cells the metastatic potential to achieve the complex series of events needed for metastasis.
Clinical and Experimental Metastasis 02/2005; 22(7):533-8. · 3.52 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: To study p63 expression at mRNA transcript and protein levels in human lung cancers, including squamous cell lung carcinoma (SCC), adenocarcinoma, large cell lung carcinoma (LCLC) and small cell lung carcinoma (SCLC), or the corresponding metastatic foci. The relationship of p63 expression and alterations in p63 locus at chromosomal 3q27-29 was also determined.
p63 gene expression in 72 cases of SCC, adenocarcinoma, LCLC and SCLC was analyzed by cDNA microarray technology. Tissue microarray of specimens from 150 cases of primary lung cancer was prepared for immunohistochemical study for p63 protein. Possible chromosomal alterations at the p63 locus in 70 cases of primary lung cancer were studied by comparative genomic hybridization (CGH) technology.
p63 mRNA transcript expression was significantly increased by more than 10-fold in SCC, as compared with that in other histologic subtypes including adenocarcinoma, LCLC and SCLC. p63 mRNA expression in metastatic foci was also remarkably higher than that in their primary tumors (P < 0.001). Immunostaining showed that p63 protein expression was observed in 94.64% of SCC, whereas only one lung adenocarcinoma (1.79%) was positive. Immunopositivity was also demonstrated in 2 of the 4 LCLC cases studied. None of the SCLC cases was positive. There was a statistically significant difference in p63 expression between pT1 and pT2 tumors (P < 0.05). The CGH results showed that overrepresentation of p63 locus at chromosomal 3q27-29 was a typical finding in SCC. p63 immunopositivity also correlated significantly with pronounced gains of p63 locus at chromosomal 3q27-q29 (P < 0.000 1), suggesting that strong expression of p63 in lung SCC was associated with increased gene amplification.
p63 may play a role in oncogenesis of human lung squamous cell carcinoma and development of metastasis.
Zhonghua bing li xue za zhi Chinese journal of pathology 08/2004; 33(4):324-7.
-
[show abstract]
[hide abstract]
ABSTRACT: Overexpression of cyclooxygenase-2 is observed in a variety of malignancies including colorectal cancer. However, to date, cyclooxygenase-2 expression by advanced human colorectal cancers and their metastases has been poorly characterized. This study was designed to evaluate the rate of cyclooxygenase-2 overexpression in our tumor collection and to clarify its correlation with the chromosomal status at the cyclooxygenase-2 locus in colorectal cancer.
Seventy-four specimens were analyzed immunohistochemically using a monoclonal cyclooxygenase-2 antibody. The staining was scored semiquantitatively as: -, negative; +, weak; ++, moderate; and +++, strong positive. Of these, 45 specimens were analyzed using comparative genomic hybridization and immunohistochemistry. We correlated the cyclooxygenase-2 overexpression with the chromosomal gain of 1q25.2-q25.3 and patients survival and compared primary colorectal cancers and their paired metastases at the DNA and protein level.
Overexpression was observed in 58 percent of the cases (score > or = ++). Chromosomal gains at the cyclooxygenase-2 locus were clearly correlated with overexpression of the gene (P=0.009). Furthermore, the comparison of paired tumor samples showed additional overrepresentation in the metastases at the cyclooxygenase-2 locus, which could be confirmed by immunohistochemistry. Kaplan-Meier analysis showed that overexpression of cyclooxygenase-2 was significantly associated with poor survival and thus could serve as a prognostic marker.
We conclude that cyclooxygenase-2 is related with tumor progression and metastasis in colorectal cancer, which can be observed on protein level, and reflects chromosomal gain at the locus at 1q25.2-q25.3.
Diseases of the Colon & Rectum 02/2004; 47(1):70-7. · 3.13 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: In this study we investigated the RNA helicase A (RHA) gene localized on chromosome 1q25 in 15 lung cancer cell lines, 54 primary carcinomas, bronchial epithelial cells and normal lung. Both RT-PCR and real-time RT-PCR showed that RHA is over-expressed in tumour samples compared to normal lung tissues (p=0.01). There was a tendency for higher expression levels in small cell lung cancer compared to non-small cell carcinomas. Over-expression of Y-162 correlated with high grade tumours (p=0.023). However, there was no correlation with tumour stage and survival. Our observations are compatible with the role of RHA in lung cancer development.
Oncology Reports 02/2004; 11(1):253-8. · 1.84 Impact Factor
-
Glen Kristiansen,
Klaus-Jürgen Winzer,
Empar Mayordomo,
Joachim Bellach, Karsten Schlüns,
Carsten Denkert,
Edgar Dahl,
Christian Pilarsky,
Peter Altevogt,
Hans Guski,
Manfred Dietel
[show abstract]
[hide abstract]
ABSTRACT: CD24 is expressed in hematological malignancies as well as in a large variety of solid tumors including breast cancer. We aimed to evaluate CD24 protein expression in breast cancer and to correlate to clinicopathological data including patient survival.
Primary breast carcinomas (201) with a mean clinical follow-up time of 53 months were immunostained using a monoclonal CD24 antibody (Ab-2, clone 24C02). The staining was evaluated as negative versus positive for statistical analysis.
In invasive breast carcinomas, CD24 expression was observed in 84.6% of cases. In univariate survival analyses, a significant association of CD24 expression with shortened patient overall survival (5-year survival rate 91.9% versus 83.8%; P = 0.031; log rank test) and disease-free survival (5-year progression rate 88.3% versus 57.0%; P = 0.0008) was demonstrated. In multivariate analyses CD24, tumor grading and nodal status were significant prognostic parameters for shortened disease-free survival.
Our data suggest that CD24 expression in primary breast cancer as detected by immunohistochemistry might be a new marker for a more aggressive breast cancer biology.
Clinical Cancer Research 11/2003; 9(13):4906-13. · 7.74 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Expression of MCAM is observed in a variety of human malignancies. We aimed to determine the rate of MCAM expression in our non-small cell lung cancer (NSCLC) collection and to clarify its correlation with clinicopathological parameters and patient survival. 85 NSCLC were analysed immunohistochemically using a monoclonal MCAM antibody (clone N1238) on an NSCLC tissue micro array. The staining was semiquantitatively scored. We found MCAM expression in 51% of NSCLC, preferentially squamous cell carcinomas (p=0.004). No other correlations to tumour size, grade, or stage were found. Univariate survival analysis showed no significant differences of MCAM positive and negative tumours. In adenocarcinomas however, MCAM positivity was significantly associated with shorter patient survival (p=0.016). We conclude, that MCAM is expressed in a high proportion of NSCLC and might be predictive of shortened patient survival in adenocarcinomas of the lung. Colour figure can be viewed on http://www.esacp.org/acp/2003/25-2/kristiansen.htm
Analytical cellular pathology: the journal of the European Society for Analytical Cellular Pathology 02/2003; 25(2):77-81.
-
[show abstract]
[hide abstract]
ABSTRACT: Suppression subtractive hybridization (SSH) was applied to identify differentially expressed genes in the SV40LT immortalized human bronchial epithelial cell line Y-BE, with normal human bronchial epithelial cells (HBEC) as a control. Two cDNA libraries of up- and downregulated genes were generated, comprising 218 known genes and 131 unknown genes in total. The expression of 22 clones from the 2 libraries was investigated by Northern blot analysis, and 86.4% (19/22) of them showed differential expression between Y-BE cells and HBEC. Although the Y-BE cells are nontumorigenic in nude mice, Comparative genomic hybridization (CGH) detected some DNA imbalances in Y-BE cells that were similar to lung cancer cells. Our data demonstrate that the studied cell line Y-BE and SSH is a reliable approach for identifying new genes that are associated with immortalization and early tumor development that may help to understand the pathogenesis of lung cancer.
International Journal of Cancer 02/2003; 103(2):194-204. · 5.44 Impact Factor
-
CARS 2003. Computer Assisted Radiology and Surgery. Proceedings of the 17th International Congress and Exhibition, London, June 25-28, 2003; 01/2003
-
[show abstract]
[hide abstract]
ABSTRACT: CD24 is a small heavily glycosylated glycosylphosphatidylinositol-linked cell surface protein, which is expressed in hematological malignancies as well as in a large variety of solid tumors. Very recently its expression in ovarian cancer has been found on RNA level by chip analysis. We evaluated CD24 protein expression by immunohistochemistry in 9 normal ovaries and 69 epithelial ovarian tumors (5 adenomas, 8 borderline tumors, and 56 carcinomas) with known follow-up data. Surface epithelium of normal ovaries as well as adenomas did not express CD24. In borderline tumors CD24 was expressed in membrane in 75% of cases, whereas cytoplasmic expression was detected in only one of nine cases. In invasive ovarian carcinomas, a membranous expression was detected in 84% and a cytoplasmic expression in 59% of cases. In univariate survival analysis of all invasive ovarian carcinomas, a highly significant association of increased cytoplasmic CD24 expression with shortened patient survival (mean 98 months versus 37 months, P = 0.0002, log rank test) was demonstrated. Other significant prognostic parameters were International Federation of Gynecology and Obstetrics (FIGO) stage, Silverberg grade, patient age, undifferentiated histological type, and metastatic disease. We did not detect a significant correlation of CD24 with these clinicopathological parameters. In multivariate analysis, only CD24 and FIGO stage were independent prognostic parameters. Our data suggest that the expression of CD24 as detected by immunohistochemistry is a new independent molecular marker for shortened survival time of patients with epithelial ovarian carcinomas.
American Journal Of Pathology 11/2002; 161(4):1215-21. · 4.89 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The genetic changes involved in the pathogenesis of ovarian carcinoma are not completely understood. To investigate this matter, we studied paraffin-embedded, microdissected tissue of 47 ovarian epithelial tumors (9 adenomas, 11 tumors of low malignant potential [LMP], 14 serous carcinomas, and 13 nonserous carcinomas) using comparative genomic hybridization (CGH). (The primary data used in this study are available at our CGH online tumor database at http://amba.charite.de/cgh.) Chromosomal imbalances were found in 1 serous adenoma and in 7 LMP tumors. In the latter the alterations appeared randomly and showed no overlap with alterations found in invasive carcinomas. Although the mean aberration number of low-grade serous carcinomas was comparable to LMP tumors, the imbalances of the former occurred with high incidence (>50%) and were found at different localizations. High-grade serous carcinomas had more than twice as much chromosomal imbalances as low-grade serous carcinomas and also had pronounced alterations. In serous carcinomas, gains were found on 3q, 6p, 7, 8q, and 20, and losses were found on 4q, 6q, 12q, 13q, and 16q. Comparing serous and nonserous carcinomas, the mean aberration number was comparable, but the number of high incidence changes was lower, and the most frequent imbalances were losses on 13q and gains on 20p. Overlapping alterations occurring in serous and nonserous carcinomas were gains on 3q and 6p, as well as losses on 4q. Chromosomal imbalances associated with poor prognosis of ovarian carcinomas were gains on 6p, 7q, and 13q and losses on 15q, 17p, 18q, and 21q. Our data indicate that serous LMP tumors and invasive carcinomas have different genetic aberrations, indicating that invasive carcinomas do not arise from preexisting serous LMP tumors. On the other hand, there are common genetic abnormalities in serous and nonserous carcinomas, suggesting that they have very early lesions in common but take different paths of further development.
Human Pathlogy 06/2002; 33(6):632-41. · 2.88 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: S100 proteins form a growing subfamily of proteins related by Ca2+-binding motifs to the Efhand Ca2+-binding protein superfamily. By analyzing a human lung cancer cell line subtraction cDNA library, we have identified and characterized a new member of the human S100 family that we named S100A14 (GenBank acc. no. NM_020672). It encodes a mRNA present in several normal human tissues of epithelial origin, with the highest level of expression in colon. The full-length cDNA is 1067 nt in length, with a coding region predicting a protein of 104 amino acids that is 68% homologous to the S100A13 protein. The deduced amino acid sequence of the human S100A14 and its mouse homolog (identified as GenBank entry) contains two EF-hand Ca2+-binding domains, a myristoylation motif, a glycosylation site, and several potential protein kinase phosphorylation sites. We have mapped this gene to human chromosome 1q21, within a region where at least 15 other S100 genes are tightly clustered. A 3.2-kb genomic fragment containing the entire S100A14 was cloned and sequenced. The gene is split into four exons and three introns spanning a total of 2165 bp of genomic sequence. We examined the intracellular distribution of the epitope-tagged S100A14 protein in two human lung carcinoma cell lines and one immortalized monkey cell line. Pronounced staining was observed in the cytoplasm, suggesting an association with the plasma membrane and in the perinuclear area. We also provide evidence for heterogenic expression of S100A14 in tumors, demonstrating its overexpression in ovary, breast, and uterus tumors and underexpression in kidney, rectum, and colon tumors, a pattern suggesting distinct regulation with potentially important functions in malignant transformation.
Genomics 05/2002; 79(4):513-22. · 3.02 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Comparative genomic hybridization (CGH) was used to screen 54 advanced colon carcinomas. i.e., 24 primary tumors and 30 metastases, for chromosomal alterations. Using a sensitive statistical method for the determination of DNA imbalances and histograms for analysis of the incidence of changes, we identified the DNA over-representation of chromosome 20q as the most common alteration being present in 100% of cases. High incidence deletions were observed on 18q21-18q23 (96%), 4q27-4q28 (96%), 4p14 (87%), 5q21 (81%), 1p21-1p22 (72%), 21q21 (74%), 6q16 (72%), 3p12 (66%), 8p24-8p21 (66%), 9p21 (64%), 11q22 (64%), and 14q13-14q21 (64%). Further frequent over-representation was found on 7q12-7q11.2 (75%), 16p11-16p12 (70%), 19p13 (70%), 9q34 (67%), 19q13 (67%), 13q34 (64%), 13q13 (64%), 17q21 (59%), 22q11 (61%), 8q24 (57%), and 1q21 (57%). Pronounced DNA gains and losses being defined as regions in which the ratio profiles exceeded the values of 1.5 and 0.5, respectively, frequently colocalized with peaks of incidence curve. The use of difference histograms for the comparison of tumor subgroups as well as case-by-case histogram for the analysis of 15 paired tumor samples identified several of the above alterations as relevant for tumor progression and metastasis formation. The study identified additional loci and delineates more precisely those that have been previously reported. For comparative purposes, we have made our primary data (ratio profiles, clinicopathological parameters, histograms) available at the interactive web site http://amba.charite.de/cgh, where the incidence of changes can be determined at individual loci and additional parameters can be applied for the analysis of our CGH results.
Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin 03/2002; 440(2):187-94. · 2.49 Impact Factor
