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PubMed2001

[Organization and contents of future research in pathology].

The organisation of research in Pathology in the future will be driven by the pressure for profitableness. This situation is already now leading to a continuous shifting of capacity from "non profitable" research (and teaching) to diagnostics. Since research continues to be a central future goal of the university institutes of Pathology, we have to claim that all our institutes shall have a financially incontestable research unit (at least 1 x BAT1 and 1 x BAT2, 1-2 BATV and consumables for approx. TDM75/year) and appropriate space. Additionally, academically orientated full pathologists and fellows, research assistants on grant money and M.D. students will perform research. One of the central future goals must be increase in motivation of researchers through output-orientated individual support and the enhancement of their career expectations. Research planned by politicians ("planned research") can--as "planned economy"--not be successful. Main goal of our future research efforts in the postgenomic era will be further clarification of the molecular basis of diseases. Applied research will be driven by the need for molecular classifications including individual prediction of prognosis, progression and choice and response to therapy. The future face of Pathology entirely depends on the fact, how actively this type of research is done in our labs and, consequently, how well we will be trained to do non-morphologic diagnostics on tissue in the future.

Humans↗
PubMedDate not supplied

Neurofibromatosis. Nosological considerations.

The neurofibromatosis (NF) represent a set of conditions having different clinical manifestations, prognosis and inheritance. It has been presented--on clinical grounds--seven types of NF, but for only two of these National Institute of Health Consensus Development Conference (NIHCDC) advent a set of diagnostic criteria. The genes responsible for NF1 and NF2 were mapped to the long arm of chromosome 17 (17q11.2) and respectively 22 (22q11.2), and their protein product (neurofibromin and respectively merlin or schwanomin) was identified. Recent studies are proved that NF1 and NF2 genes act as a tumour suppressor gene. Up to now, only a limited number of mutations in these genes have been characterized but even in these cases the genotype/fenotype correlation has not provided enough information to allow speculation on the etiologic role NF1 or NF2 mutations might play in the variant forms of NF. Further studies are required to elucidate the genes functions and mutation spectrum. This should provide a framework for the molecular classification and diagnosis and the development of new therapy for NF.

Chromosomes, Human, Pair 17↗
PubMed2003

Kernel Cox regression models for linking gene expression profiles to censored survival data.

In functional genomics, one important problem is to relate the microarray gene expression profiles to various clinical phenotypes from patients. The success has been demonstrated in molecular classification of cancer in which gene expression data serve as predictors and different types of cancer are the binary or multi-categorical outcome variable. However, there has been less research in linking gene expression profiles to other types of phenotypes, in particular, the censored survival data such as patients' overall survival or cancer relapse times. In the paper, we develop a kernel Cox regression model for relating gene expression profiles to censored phenotypes in the framework the penalization method in terms of function estimation in reproducing kernel Hilbert spaces. To circumvent the problem of censoring, we use the negative partial likelihood as a loss function in the estimation procedure. The functional combinations of the original gene expression data identified by the method are highly correlated with the patients' survival times and at the same time account for the variability in the gene expression levels. We apply our method to data sets from diffuse large B-cell lymphoma, lung adenocarcinoma and breast carcinoma studies to verify its effectiveness. The results from these analyses indicate that the proposed method works very well in identifying subgroups of patients with different risks of death or relapse and in predicting the risk of relapse or death based on the gene expression profiles measured from the tumor samples taken from the patients.

Artificial Intelligence↗
PubMedDate not supplied

[Gene expression profiles of protein kinases and phosphatases obtained by hybridization with cDNA arrays: molecular portrait of human prostate carcinoma].

Hybridization with cDNA arrays was used to obtain expression profiles of 263 protein-tyrosine kinase (PTK), protein-tyrosine phosphatase (PTP), dual-specific phosphatase (DuSP), and other genes for the normal prostate tissue, primary prostate carcinomas (PC) of 84 patients, 7 xenografts, and 5 carcinoma cell lines. Analysis of 96 profiles revealed eight clusters of genes coexpressed in PC (coefficient of correlation r > 0.7). According to the known functions of their genes, the clusters were designated as proliferating-cell (CDC42, TOP2A, FGFR3, MYC, etc.), neoangiogenesis and blood-cell (LCK, VAV1, KDR, VEGF, MMP9, SYK, PTPRS, and FLT4), invasion-1 and invasion-2 (ADAM17, TRPM2, DUSP6, VIM, CAV1, CAV2, JAK1, PTPNS1, FYN, and PDGFB), HER2, and PSA/PSM/HER3. Basing on expression profiles of 66 genes, a molecular classification of PC was constructed and allowed discrimination between PC and cell lines or xenografts at 98.9% probability. The results suggested that, along with PSA, PSM (FOLH1), kallikrein-2, and a-2-macroglobulin, cell signaling genes EGFR, HER2, HER3, TOP2, KRT8, KRT18, VEGF, CD44, VIM, CAV1, and CAV2 may serve as diagnostic and prognostic markers in PC. The HER2, VEGF, and CD44 genes and the MMP and ADAM families were assumed to be promising targets for inhibitors of PC cell proliferation and metastasis.

Gene Expression Regulation, Neoplastic↗
PubMedDate not supplied

[Differential gene expression analysis by DNA microarrays technology and its application in molecular oncology].

Accumulation of genetic and epigenetic aberrations leads to malignant transformation of normal cells. Functional studies of cancer using genomic and proteomic tools will help to reveal the true complexity of the processes leading to cancer development in humans. Until recently, diagnosis and prognosis of cancer was based on conventional pathologic criteria and epidemiological evidence. Certain tumors were divided only into relatively broad histological and morphological subcategories. Rapidly developing methods of differential gene expression analysis promote the search for clinically relevant genes changing their expression levels during malignant transformation. DNA microarrays offer a unique possibility to rapidly assess the global expression picture of thousands genes in any given time point and compare the detailed combinatory analysis results of global expression profiles for normal and malignant cells at various functional stages or separate experimental conditions. Acquisition of such "genetic portraits" allows searching for regularity and difference in expression patterns of certain genes, understanding their function and pathological importance, and ultimately developing the "molecular nosology" of cancer. This review describes the basis of DNA microarray technology and methodology, and focuses on their applications in molecular classification of tumors, drug sensitivity and resistance studies, and identification of biological markers of cancer.

Biomarkers, Tumor↗
PubMed2003

Phenotype versus genotype in gliomas displaying inter- or intratumoral histological heterogeneity.

PURPOSE: Molecular classification of gliomas is becoming increasingly important clinically as an adjunct to histopathological diagnosis. Whereas histological heterogeneity of gliomas is well recognized, less is known of the relationship between histological heterogeneity and genetic alterations. Our objective was to investigate the relationship between genotype and phenotype for markers of potential clinical utility in histologically heterogeneous gliomas. EXPERIMENTAL DESIGN: We have used laser capture microdissection to sample the various histological phenotypes present in 42 tumors from 25 glioma cases with either inter- or intratumoral histological heterogeneity, and multiple simultaneous PCR amplification of microsatellite markers and capillary electrophoresis to determine allelic imbalance in chromosomes 1p, 19q, 17p, 10p, and 10q. RESULTS: Loss of 1p36 and 19q13 was seen only in oligodendroglial histology in 7 of 13 oligodendrogliomas. 17p13 loss was found in 14 of 41 tumors in astrocytic, oligoastrocytic, oligodendroglial, and glioblastomatous histologies. Chromosome 10 loss was seen in all of the high-grade histologies in 7 of 7 glioblastomas with an oligodendroglial component and in 1 of 5 low-grade oligodendroglial regions present within high-grade tumors. Seven tumors from 5 cases had no detectable losses of any markers investigated. In 13 tumors with intratumoral heterogeneity, identical genetic losses were present in all areas of histological differentiation. Additional losses were seen in some but not all of the histologies within 2 tumors and were associated with progression in 3 cases. CONCLUSIONS: The gliomas in this study were more homogeneous in their genotype than their histological phenotype with regions of differing histological subtype indistinguishable by the genetic markers investigated, supporting a monoclonal origin of these tumors.

Alleles↗
PubMed2003

Advances in biology and therapy of multiple myeloma.

Even during this past year, further advances have been made in understanding the molecular genetics of the disease, the mechanisms involved in the generation of myeloma-associated bone disease and elucidation of critical signaling pathways as therapeutic targets. New agents (thalidomide, Revimid, Velcade) providing effective salvage therapy for end-stage myeloma, have broadened the therapeutic armamentarium markedly. As evidenced in Section I by Drs. Kuehl and Bergsagel, five recurrent primary translocations resulting from errors in IgH switch recombination during B-cell development in germinal centers involve 11q13 (cyclin D1), 4p16.3 (FGFR3 and MMSET), 6p21 (cyclin D3), 16q23 (c-maf), and 20q11 (mafB), which account for about 40% of all myeloma tumors. Based on gene expression profiling data from two laboratories, the authors propose 5 multiple myeloma (MM) subtypes defined by the expression of translocation oncogenes and cyclins (TC molecular classification of MM) with different prognostic implications. In Section II, Drs. Barillé-Nion and Bataille review new insights into osteoclast activation through the RANK Ligand/OPG and MIP-1 chemokine axes and osteoblast inactivation in the context of recent data on DKK1. The observation that myeloma cells enhance the formation of osteoclasts whose activity or products, in turn, are essential for the survival and growth of myeloma cells forms the basis for a new treatment paradigm aimed at reducing the RANKL/OPG ratio by treatment with RANKL inhibitors and/or MIP inhibitors. In Section III, Dr. Fenton reviews apoptotic pathways as they relate to MM therapy. Defects in the mitochrondrial intrinsic pathway result from imbalances in expression levels of Bcl-2, Bcl-XL and Mcl-1. Mcl-1 is a candidate target gene for rapid induction of apoptosis by flavoperidol. Antisense oglionucleotides (ASO) lead to the rapid induction of caspace activity and apoptosis, which was potentiated by dexamethasone. Similar clinical trials with Bcl-2 ASO molecules alone and in combination with doxorubicin and dexamethasone or thalidomide showed promising results. The extrinsic pathway can be activated upon binding of the ligand TRAIL. OPG, released by osteoblasts and other stromal cells, can act as a decoy receptor for TRAIL, thereby blocking its apoptosis-inducing activity. MM cells inhibit OPG release by stromal cells, thereby promoting osteoclast activation and lytic bone disease (by enhancing RANKL availability) while at the same time exposing themselves to higher levels of ambient TRAIL. Thus, as a recurring theme, the relative levels of pro- versus anti-apoptotic molecules that act in a cell autonomous manner or in the milieu of the bone marrow microenvironment determine the outcome of potentially lethal signals. In Section IV, Dr. Barlogie and colleagues review data on single and tandem autotransplants for newly diagnosed myeloma. CR rates of 60%-70% can be reached with tandem transplants extending median survival to approximately 7 years. Dose adjustments of melphalan in the setting of renal failure and age > 70 may be required to reduce mucositis and other toxicities in such patients, especially in the context of amyloidosis with cardiac involvement. In Total Therapy II the Arkansas group is evaluating the role of added thalidomide in a randomized trial design. While data are still blinded as to the contribution of thalidomide, the overriding adverse importance of cytogenetic abnormalities, previously reported for Total Therapy I, also pertain to this successor trial. In these two-thirds of patients without cytogenetic abnormalities, Total Therapy II effected a doubling of the 4-year EFS estimate from 37% to 75% (P <.0001) and increased the 4-year OS estimate from 63% to 84% (P =.0009). The well-documented graft-vs-MM effect of allotransplants can be more safely examined in the context of non-myeloablative regimens, applied as consolidation after a single autologous transplant with melphalan 200 mg/m(2), have been found to be much better tolerated than standard myeloablative conditioning rege conditioning regimens and yielding promising results even in the high-risk entity of MM with cytogenetic abnormalities. For previously treated patients, the thalidomide congener Revimid and the proteasome inhibitor Velcade both are active in advanced and refractory MM (approximately 30% PR). Gene expression profiling (GEP) has unraveled distinct MM subtypes with different response and survival expectations, can distinguish the presence of or future development of bone disease, and, through serial investigations, can elucidate mechanisms of actions of new agents also in the context of the bone marrow microenvironment. By providing prognostically relevant distinction of MM subgroups, GEP should aid in the development of individualized treatment for MM.

Bone Diseases↗
PubMed2004

[Relationship between the expression of O6-methylguanine-DNA methyltransferase in glioma and the survival time of patients].

BACKGROUND & OBJECTIVE: Previous studies showed that the DNA-repair enzyme O(6)-methylguanine-DNA methyltransferase (MGMT) is one of drug resistant factors that affect chemosensibility of glioma. This study was to analyze the relationship between the expression of MGMT in glioma and the survival time of patients,and supply references to make molecular classification for glioma based on drug resistant mechanism. METHODS: MGMT expression in 311 glioma specimens was examined by tissue array technology and immunohistochemistry method, all patients had been followed up for 5 years, and the materials were analyzed statistically. RESULTS: The positive expression of MGMT was 126 in 311 gliomas (40.51%), among them, 61 in 121 astrocytomas (50.41%), 18 in 70 oligodendrogliomas (25.71%), 18 in 64 oligoastrocytomas (28.13%), 29 in 56 glioblastomas (51.79%); 68 in 186 grade I-II gliomas (36.56%), and 58 in 125 grade III-IV gliomas (46.40%). The difference of MGMT expression between grade I-II and grade III-IV gliomas was significant (P< 0.001). According to Kaplan-Meier's survival curves and log-rank test, patients with MGMT expression showed a shorter survival time than those with no MGMT expression (P< 0.05). CONCLUSION: MGMT expression in glioma correlates with histopathological type and tumor grade. Patients with MGMT expression show a shorter survival time than those with no MGMT expression.

Adolescent↗
PubMed2005

Gene expression profiles in prostate cancer: association with patient subgroups and tumour differentiation.

Prostate carcinoma is the most common cancer of western men and is a markedly heterogeneous disease. The aim of this study was to identify signatures of differentially expressed genes in prostate cancer using DNA microarray technology, evaluating expression profiles in matched pairs of benign and malignant tissue. Samples were collected from 33 radical prostatectomies, and 52 specimens were included, representing 29 histologically verified primary tumours, 19 paired samples of malignant and benign tissue, and 4 non-paired benign tissue samples. Microarray analysis was performed using an expanded sequence verified set of 40,000 human cDNA clones, revealing several genes with significant differences between malignant and benign tissue, including recently reported genes like alpha-methylacyl-CoA racemase (AMACR) and hepsin, as well as genes relevant for tumour development and progression. Leave out cross validation (LOCV) test correctly predicted tumour or benign tissue in 47 (90.3%) out of 52 cases, significantly better than cross validation tests using randomly permuted tissue labels. Unsupervised clustering analysis revealed 3 distinct patient clusters significantly associated with Gleason score, and high grade tumours (Gleason score >/=7) accumulated in cluster 1 (C1). Gene expression profiles correctly predicted 100% of tumour samples segregating to C1, as also validated by LOCV. Gene expression profiles were analysed in filtered and floored datasets with similar results, and a pair-wise design was also tested. Gene expression profiles provided tumour clusters linked to differentiation, and revealed novel markers relevant for molecular classification, grading and therapy of prostate cancer.

Cluster Analysis↗
PubMed2005

Gene expression profiling in lymphoma diagnosis and research.

Gene expression profiling in the past 5 years has generated a large amount of data on a variety of malignancies. Unique gene expression signatures have been identified for the more common types of non-Hodgkin lymphoma (NHL), including clinically and biologically important subsets that have not been defined before. In addition, molecularly defined prognosticators have also been constructed for the major types of NHL and these prognosticators provide added value to the widely used International Prognostic Index. The new information should be included in our evaluation of NHL patients, especially when conducting clinical trials. Studies are ongoing to validate and refine these diagnostic and prognostic signatures and to develop platforms that are suitable for routine clinical applications. Similar studies will be performed on the less common types of NHL to complete the molecular classification of NHLs. It is also anticipated that gene expression profiling studies will lead to the identification of novel targets for the development of new therapeutic agents for NHL.

Gene Expression Profiling↗
PubMed2005

Role of gene expression profiling for diagnosing acute leukemias.

Cytomorphology and cytochemistry in combination with multiparameter immunophenotyping today are the standard methods for establishing the diagnosis of acute leukemias. In addition, cytogenetics, fluorescence in situ hybridization, and polymerase chain reaction based assays provide important information regarding biologically defined and prognostically relevant subgroups and allow a comprehensive diagnosis of well defined subentities. With regard to the clinical setting a better understanding of the clinical course of distinct biologically defined disease subtypes is needed to select disease-specific therapeutic approaches. Paralleling the increase in knowledge on deregulated pathways in leukemia the development of new therapeutics is accelerated and therefore requires a detailed and comprehensive diagnostic tool. Revealing and quantifying the expression status of many ten thousands of genes in a single analysis the microarray technology holds this potential to become an essential tool for the molecular classification of leukemias. It may therefore be used as a routine method for diagnostic purposes in the near future. Furthermore, it is anticipated that new biologically defined and clinically relevant subtypes of leukemia will be identified based on gene expression profiling. This method may therefore guide therapeutic decisions.

Acute Disease↗
PubMed2005

[Genotype-phenotype associations in inflammatory bowel disease].

Inflammatory bowel disease has traditionally been categorized as either ulcerative colitis or Crohn's disease on the basis of clinical, radiological and histological criteria. Emerging data suggest that inflammatory bowel disease comprises a heterogenous family of inflammatory disorders in which the specific clinical manifestations of disease are determined by the interaction of genetic and environmental factors. Interactions of susceptibility and modifying genes influence the specific features of disease phenotype, penetrance, location, behavior, and complication. CARD15/NOD2 mutations are significantly associated with ileal location, whereas certain HLA haplotypes are associated with colonic disease. The associations with CARD15/ND2 mutations and early age at onset, as well as disease behavior (stricturing, fistulizing type) are less consistent. Distinct HLA alleles contribute to the occurrence of extraintestinal manifestation. With the increasing number of genotype-phenotype relationship, it is hoped that a molecular classification can be created, in which various disease subtypes are categorized according to their specific genotypes. In the future, such sheme may permit early, accurate diagnosis, prediction of disease course, complications, prognosis, as well as treatment response.

Age of Onset↗
PubMedDate not supplied

Characterization of genes with increased expression in human glioblastomas.

In the present study, we have used the gene expression data available in the SAGE database in an attempt to identify glioblastoma molecular markers. Of 129 genes with more than 5-fold difference found by comparison of nine glioblastoma with five normal brain SAGE libraries, 44 increased their expression in glioblastomas. Most corresponding proteins were involved in angiogenesis, host-tumor immune interplay, multidrug resistance, extracellular matrix (ECM) formation, IGF-signalling, or MAP-kinase pathway. Among them, 16 genes had a high expression both in glioblastomas and in glioblastoma cell lines suggesting their expression in transformed cells. Other 28 genes had an increased expression only in glioblastomas, not in glioblastoma cell lines suggesting an expression possibly originated from host cells. Many of these genes are among the top transcripts in activated macrophages, and involved in immune response and angiogenesis. This altered pattern of gene expression in both host and tumor cells, can be viewed as a molecular marker in the analysis of malignant progression of astrocytic tumors, and as possible clues for the mechanism of disease. Moreover, several genes overexpressed in glioblastomas produce extracellular proteins, thereby providing possible therapeutic targets. Further characterization of these genes will thus allow them to be exploited in molecular classification of glial tumors, diagnosis, prognosis, and anticancer therapy.

Biomarkers, Tumor↗
PubMed2005

Proteomic profiling of mature CD10+ B-cell lymphomas.

Proteomic profiling with protein-chip technology has been used successfully to discover biomarkers with potential clinical usefulness in several cancer types. Little proteomic study has been done in B-cell lymphomas. We determined whether the expression of a set of proteins by protein-chip technology coupled with new informatics tools could be used to build a model to molecularly classify B-cell lymphoma subgroups. We used surface-enhanced laser desorption/ionization time-of-flight mass spectrometry to analyze 18 CD10+ B-cell lymphomas, including 6 grade 1 (G1) follicular lymphomas (FLs), 7 grade 3 (G3) FLs, and 5 Burkitt lymphomas. We used 7 reactive follicular hyperplasia cases as a control group. By using SAX2 ProteinChip arrays (Ciphergen Biosystems, Fremont, CA), we found a unique protein expression profile for each type of lesion. Two-way hierarchical clustering analysis of these protein expression profiles differentiated reactive follicular hyperplasia, FL, and Burkitt lymphoma, with 5 major clusters of differentially expressed protein peaks. In addition, we identified histone H4 as a potential differentially expressed protein marker that seems to distinguish G1 from G3 FL. To our knowledge, this is the first proteomic study using protein-chip technology for molecular classification of B-cell lymphoma subtypes with clinical samples.

Biomarkers, Tumor↗
PubMed2005

Apert syndrome with preaxial polydactyly showing the typical mutation Ser252Trp in the FGFR2 gene.

The Apert syndrome is characterized by craniosynostosis and syndactyly of hands and feet. Although most cases are sporadic, an autosomal dominant mode of inheritance is well documented. Two mutations in the FGFR2 gene (Ser252Trp and Pro253Arg) account for most of the cases. We report a patient with a rare form of Apert syndrome with polydactyly. The proposita has turribrachycephaly. complete syndactyly of 2nd to 5th digits ("mitten hands" and cutaneous fusion of all toes). The X-rays revealed craniosynostosis of the coronal suture and preaxial polydactyly of hands and feet with distal bony fusion. Molecular analysis found a C755G transversion (Ser252Trp) in the FGFR2 gene. Only eight patients with Apert syndrome and preaxial polydactyly have been reported and this is the first case in which molecular diagnosis is available. On the basis of the molecular findings in this patient, polydactyly should be considered part of the spectrum of abnormalities in the Apert syndrome. This assertion would establish the need for a new molecular classification of the acrocephalopolysyndactylies.

Acrocephalosyndactylia↗
PubMed2006

Building a European biomedical grid on cancer: the ACGT Integrated Project.

This paper presents the needs and requirements that led to the formation of the ACGT (Advancing Clinico Genomic Trials) integrated project, its vision and methodological approaches of the project. The ultimate objective of the ACGT project is the development of a European biomedical grid for cancer research, based on the principles of open access and open source, enhanced by a set of interoperable tools and services which will facilitate the seamless and secure access to and analysis of multi-level clinico-genomic data, enriched with high-performing knowledge discovery operations and services. By doing so, it is expected that the influence of genetic variation in oncogenesis will be revealed, the molecular classification of cancer and the development of individualised therapies will be promoted, and finally the in-silico tumour growth and therapy response will be realistically and reliably modelled. Its main design decisions and results at its current stage of development are presented.

Biomedical Research↗
PubMed1989

[Monoclonal antibodies in diagnosis and therapy].

The value of monoclonal antibodies (mAb) produced against renal, bladder and prostate cancer antigens is demonstrated. These mAb allow a molecular classification of urological cancers as well as therapeutic approaches in cancer treatment. Anti-T-cell mAb can also be used in cellular rejection of kidney transplants.

Antibodies, Monoclonal↗
PubMed1993

Advances in the diagnosis of acute leukemia.

The diagnosis and monitoring of acute leukemia requires a multiparameter approach. Although the foundation of diagnosis continues to depend on morphologic and cytochemical determinations, the importance of immunologic, cytogenetic, and molecular classifications is beginning to be emphasized and addressed worldwide. In addition to aiding in the diagnosis of acute leukemia, the information gained by these studies increases the understanding of the pathobiology of these neoplasms.

Acute Disease↗