Biomedical subjects

R Simon

Publications and source records attributed to R Simon.

At least 55 records · Page 3Linked to original sources

PubMed2001

Combinatorial peptide libraries and biometric score matrices permit the quantitative analysis of specific and degenerate interactions between clonotypic TCR and MHC peptide ligands.

The interaction of TCRs with MHC peptide ligands can be highly flexible, so that many different peptides are recognized by the same TCR in the context of a single restriction element. We provide a quantitative description of such interactions, which allows the identification of T cell epitopes and molecular mimics. The response of T cell clones to positional scanning synthetic combinatorial libraries is analyzed with a mathematical approach that is based on a model of independent contribution of individual amino acids to peptide Ag recognition. This biometric analysis compares the information derived from these libraries composed of trillions of decapeptides with all the millions of decapeptides contained in a protein database to rank and predict the most stimulatory peptides for a given T cell clone. We demonstrate the predictive power of the novel strategy and show that, together with gene expression profiling by cDNA microarrays, it leads to the identification of novel candidate autoantigens in the inflammatory autoimmune disease, multiple sclerosis.

Amino Acid Motifs↗

PubMed2001

Patterns of her-2/neu amplification and overexpression in primary and metastatic breast cancer.

BACKGROUND: Only 25% of patients with HER-2/neu-positive metastatic breast tumors respond favorably to trastuzamab (Herceptin) treatment. We hypothesized that a high failure rate of patients on trastuzamab could result if some of the metastases were HER-2 negative and these metastases ultimately determine the course of the disease. METHODS: We used tissue microarrays (TMAs) containing four samples each from 196 lymph node-negative primary tumors, 196 lymph node-positive primary tumors, and three different lymph node metastases from each lymph node-positive tumor to estimate HER-2 gene amplification by fluorescence in situ hybridization (FISH) and Her-2 protein overexpression by immunohistochemistry (IHC). RESULTS: FISH and IHC analyses gave the same result with respect to HER-2 status for 93.7% of the tissues contained in the TMAs. Tissue samples were, therefore, considered to be HER-2 positive if they were positive for either HER-2 DNA amplification or Her-2 protein expression and HER-2 negative if both FISH and IHC gave a negative result. The HER-2 status of lymph node-positive primary tumors was maintained in the majority of their metastases. For HER-2-positive primary tumors, 77% (95% confidence interval [CI] = 59% to 90%) had entirely HER-2-positive metastases, 6.5% (95% CI = 8% to 21%) had entirely HER-2-negative metastases, and 16.3% (95% CI = 5% to 34%) had a mixture of HER-2-positive and HER-2-negative metastases. For HER-2-negative primary tumors, 95% (95% CI = 88% to 98%) had metastases that were entirely negative for HER-2. CONCLUSIONS: Our data suggest that differences in HER-2 expression between primary tumors and their lymph node metastases cannot explain the high fraction of nonresponders to trastuzamab therapy.

Antibodies, Monoclonal↗

PubMed2001

Combinatorial peptide libraries as an alternative approach to the identification of ligands for tumor-reactive cytolytic T lymphocytes.

The recent identification of molecularly defined human tumor antigens recognized by autologous CTLs has opened new opportunities for the development of antigen-specific cancer vaccines. Despite extensive work, however, the number of CTL-defined tumor antigens that are suitable targets for generic vaccination of cancer patients is still limited, mostly because of the painstaking and lengthy nature of the procedures currently used for their identification. A novel approach is based on the combined use of combinatorial peptide libraries in positional scanning format (positional scanning synthetic combinatorial peptide libraries, PS-SCLs) and tumor-reactive CTL clones. To validate this approach, we herein analyzed in detail the recognition of PS-SCLs by Melan-A-specific CTL clones. Our results indicate that, at least for some clones, most of the amino acids composing the native antigenic peptide can be identified through the use of PS-SCLs. Interestingly, this analysis also allowed the identification of peptide analogues with increased antigenic activity as well as agonist peptides containing multiple amino-acid substitutions. In addition, biometrical analysis of the data generated by PS-SCL screening allowed the identification of the native ligand in a public database. Overall, these data demonstrate the successful use of PS-SCLs for the identification and optimization of tumor-associated CTL epitopes.

Amino Acid Sequence↗

PubMed2001

A molecular link between stem cell regulation and floral patterning in Arabidopsis.

The homeotic gene AGAMOUS (AG) has dual roles in specifying organ fate and limiting stem cell proliferation in Arabidopsis flowers. We show that the floral identity protein LEAFY (LFY), a transcription factor expressed throughout the flower, cooperates with the homeodomain protein WUSCHEL (WUS) to activate AG in the center of flowers. WUS was previously identified because of its role in maintaining stem cell populations in both shoot and floral meristems. The unsuspected additional role of WUS in regulating floral homeotic gene expression supports the hypothesis that floral patterning uses a general meristem patterning system that was present before flowers evolved. We also show that AG represses WUS at later stages of floral development, thus creating a negative feedback loop that is required for the determinate growth of floral meristems.

AGAMOUS Protein, Arabidopsis↗

PubMed2001

High-throughput tissue microarray analysis of 3p25 (RAF1) and 8p12 (FGFR1) copy number alterations in urinary bladder cancer.

Studies by comparative genomic hybridization revealed that the chromosomal regions 3p25 and 8p11-p12 are recurrently amplified in bladder cancer. To investigate the prevalence of DNA copy number alterations in these chromosomal regions and study their clinical significance, we used probes for the RAF1 (3p25) and FGFR1 (8p12) genes for fluorescence in situ hybridization. A tissue microarray containing 2317 tumors was analyzed. The analysis revealed RAF1 amplification in 4.0% and FGFR1 amplification in 3.4% of interpretable tumors. In addition, deletions were found at the 3p25 locus in 2.2% and at the 8p11-12 locus in 9.9% of interpretable tumors. Both amplifications and deletions of RAF1 and FGFR1 were significantly associated with high tumor grade (P < 0.0001), advanced stage (P < 0.0001), and poor survival (P < 0.05) if tumors of all of the stages where analyzed together. RAF1 amplifications were associated with subsequent tumor progression in pT1 carcinomas (P < 0.05). The marked differences in the frequency of all of the analyzed changes between pTa grade 1/grade 2 and pT1-4 carcinomas support the concept of these tumor groups representing different tumor entities.

Chromosomes, Human, Pair 3↗

PubMed2001

Gene-expression profiles in hereditary breast cancer.

BACKGROUND: Many cases of hereditary breast cancer are due to mutations in either the BRCA1 or the BRCA2 gene. The histopathological changes in these cancers are often characteristic of the mutant gene. We hypothesized that the genes expressed by these two types of tumors are also distinctive, perhaps allowing us to identify cases of hereditary breast cancer on the basis of gene-expression profiles. METHODS: RNA from samples of primary tumor from seven carriers of the BRCA1 mutation, seven carriers of the BRCA2 mutation, and seven patients with sporadic cases of breast cancer was compared with a microarray of 6512 complementary DNA clones of 5361 genes. Statistical analyses were used to identify a set of genes that could distinguish the BRCA1 genotype from the BRCA2 genotype. RESULTS: Permutation analysis of multivariate classification functions established that the gene-expression profiles of tumors with BRCA1 mutations, tumors with BRCA2 mutations, and sporadic tumors differed significantly from each other. An analysis of variance between the levels of gene expression and the genotype of the samples identified 176 genes that were differentially expressed in tumors with BRCA1 mutations and tumors with BRCA2 mutations. Given the known properties of some of the genes in this panel, our findings indicate that there are functional differences between breast tumors with BRCA1 mutations and those with BRCA2 mutations. CONCLUSIONS: Significantly different groups of genes are expressed by breast cancers with BRCA1 mutations and breast cancers with BRCA2 mutations. Our results suggest that a heritable mutation influences the gene-expression profile of the cancer.

Algorithms↗

PubMed2001

Clinical trial designs for cytostatic agents: are new approaches needed?

Preclinical data suggest that some new anticancer agents directed at novel targets demonstrate tumor growth inhibition but not tumor shrinkage. Such cytostatic agents may offer clinical benefits for patients in the absence of tumor shrinkage. In addition, lower doses of some of these agents may be just as effective as higher doses, implying that toxicity may not be an ideal end point for dose finding. Because of these factors, the sequence and design of traditional phase I, II, and III trials used for cytotoxic agents (which typically shrink tumors and in a dose-dependent manner) may not be appropriate for cytostatic agents. This article discusses options for modifying trial designs to accommodate cytostatic agents. Examples are given where these options have been tried or are currently being tried. Recommendations given for choosing among the trial designs depend on what is known preclinically about the agents (eg, does one have a validated and reproducible biologic end point that can be used to guide a dose escalation?), what is known about the patient population being studied (eg, does one have a well-documented historical progression-free survival rate at 1 year for comparison with the experience of the new agent?), and the numbers of agents and patients available for participation in trials. Planned and ongoing trials will test the utility of some of these new approaches.

Antineoplastic Agents↗

PubMed2001

Cytogenetic analysis of multifocal bladder cancer supports a monoclonal origin and intraepithelial spread of tumor cells.

Bladder cancer is often characterized by a multifocal growth pattern. This observation has given rise to the hypothesis of "field cancerization," predicting a polyclonal origin of multiple tumors rising from an area of independently transformed mucosa cells. On the other hand, genetic studies suggested a monoclonal origin. To address these contradictory hypotheses, we performed comparative genomic hybridization (CGH) on 32 tumors originating from six bladder cystectomy specimens. All tumors derived from the same patient showed a set of 7-13 identical chromosomal aberrations and additional individual alterations. Most striking were the findings of 17p losses in all (32 of 32) tumors of the six cystectomy specimens and 20p gains in all tumors of four bladders, as well as an unexpected high number of chromosomal changes (20.4 alterations per tumor on average). To clarify a possible role of the TP53 tumor suppressor gene on 17p13, we applied immunohistochemistry and sequence analysis on the tumors and additional 52 mucosa samples. Identical TP53 mutations and protein overexpression was found in individual tumors only as well as in mucosa samples from continuous areas. Our results not only provide further evidence for a monoclonal origin of multifocal bladder cancer but also point at intraepithelial migration of tumor cells carrying specific chromosomal aberrations.

Cell Movement↗

PubMed2001

Control of cell fate in plant meristems.

In contrast to animals, plants do not stop to initiate organs with the end of embryogenesis. Instead, most of the growth and development of higher plants will take place during later phases following germination of the seed. Plant development depends on the activity of two meristems, the root meristem and the shoot apical meristem (SAM), that are located at opposite ends of the plant embryo. These meristems serve as a source of pluripotent stem cells and, in case of the SAM, provide a centre for repetitive organ initiation. In order to maintain the SAM throughout plant life, the cells that are lost from the meristem through organ initiation and differentiation have to be replaced from the stem cell population. In this paper, we will discuss recent results indicating that the fate of stem cells in plant meristems is controlled by directional signalling systems.

Animals↗

PubMed2001

Distal chromosome 17 gains in neuroblastomas detected by comparative genomic hybridization (CGH) are associated with a poor clinical outcome.

PROCEDURE: To establish the significance of chromosome 17 aberrations in the biology of neuroblastomas, the fresh-frozen material of 53 primary neuroblastomas (average patient age: 20.8 months; stage 1 or 2: n = 10; stage 3: n = 10; stage 4: n = 10; stage 4s: n = 23) was studied by means of comparative genomic hybridization (CGH). Follow-up data were available for 52 of 53 cases studied (average follow-up period: 26.4 months). Except for one, all cases had previously been analyzed for MYCN status (semiquantitative Southern blot analysis). Studies of LOH 1p36 (VNTR-PCR) had been performed on 28 of 53 cases. RESULTS: Chromosome 17 gains were detected in 46 of 53 (86.8%) cases. Whole chromosome gains were mostly restricted to localized tumors (stage 1 or 2: 9 of 10 cases; stage 4s:19 of 23; stage 3: 2 of 10; stage 4:0 of 10 cases), whereas distal 17 gains were significantly associated with clinically advanced tumor stages and patients aged over 1 year at diagnosis. Univariate analyses revealed a statistically significant correlation of distal 17q gains with overall survival (P< 0.01, MYCN amplification: P< 0.01; 1p deletion: P< 0.01) and an elevated recurrency rate (17q: P= 0.02, MYCN amplification: P = 0.05; 1p deletion P= 0.3). There was a strong coincidence of distal 17q gains and 1p deletion or MYCN amplification (P < 0.01). CONCLUSION: Our data indicate that distal chromosome 17q gains are of major prognostic relevance for neuroblastoma patients. However, studies on a larger series of tumors have to be performed to assess whether or not these alterations are independent prognostic markers of a poor clinical outcome.

Child↗

PubMed2001

Comparative genomic hybridization in pineal parenchymal tumors.

Nine pineal parenchymal tumors were studied by comparative genomic hybridization. These consisted of three pineocytomas (WHO grade II), three pineal parenchymal tumors of intermediate differentiation (WHO grade III), and three pineoblastomas (WHO grade IV). An average of 0 chromosomal changes per pineocytoma, 5.3 per pineal parenchymal tumor of intermediate differentiation (3.3 gains vs. 2.0 losses), and 5.6 per pineoblastoma (2.3 gains vs. 3.3 losses) were found. The most frequent DNA copy number changes among pineal parenchymal tumors of intermediate differentiation and pineoblastomas were gains of 12q (3/6 cases), 4q, 5p, and 5q (2/6 cases each), as well as losses of 22 (4/6 cases), 9q, and 16q (2/6 cases each). Among pineal parenchymal tumors of intermediate differentiation, the most common chromosomal imbalances were +4q, +12q, and -22 (2/3 cases each), and in pineoblastomas -22 (2/3 cases). Five high level gains were identified, all of them in pineoblastomas; these were found on 1q12-qter, 5p13.2-14, 5q21-qter, 6p12-pter, and 14q21-qter. Clinically, all patients with pineocytomas and pineal parenchymal tumors of intermediate differentiation were alive after a mean observation time of 142 and 55 months, respectively, whereas all patients with pineoblastomas had died after an average of 17 months. Our findings suggest that pineal parenchymal tumors of intermediate differentiation are cytogenetically more similar to pineoblastomas and prognostically more similar to pineocytomas. Furthermore, imbalances in higher-grade pineal parenchymal tumors mainly affect gains of 12q and losses of chromosome 22.

Adult↗

PubMed2001

Functional domains in plant shoot meristems.

The development of higher plants depends on the activity of a shoot apical meristem. Organs are formed on the flanks of the meristem, while pluripotent stem cells are found in a separate domain in the meristem centre. Further domains are distinguished by the expression patterns of genes that control the development of the shoot meristem. Although most plant cells are immobile, their relative position within a meristem, and therefore also their function, can change after cell divisions. To maintain an active shoot meristem throughout plant life, the cells in the meristem need constantly to assess their position, transmit this information to others, and readjust their gene expression profiles and their fate. Some of the genes that permit intercellular communication have been isolated. They enable the flow of information in and between meristem regions via ligands and receptor proteins to transcription factors, that ultimately control the fate of cells in the centre of the meristem.

Animals↗

PubMed2001

Ductal invasive G2 and G3 carcinomas of the breast are the end stages of at least two different lines of genetic evolution.

Ductal invasive grade (G) 2 and G3 carcinomas represent the majority of invasive breast cancers. Previous morphological and cytogenetic studies have provided evidence that ductal invasive G2 carcinoma may originate from at least two different genetic pathways. The aim of this study was to evaluate further the heterogeneity of G2 breast cancer in comparison with G3 cancers by cytogenetic and quantitative analysis. To this end, 35 cases of ductal invasive G2 and 42 cases of ductal invasive G3 carcinomas were investigated by means of comparative genomic hybridization (CGH) and these findings were correlated with DNA ploidy status, mitotic activity index (MAI), mean nuclear area (MNA), volume per lumen (VPL), and clinico-pathological parameters. The findings of this study demonstrate that ductal invasive G2 carcinomas, in contrast to ductal invasive G3 carcinomas, have to be interpreted as the morphological end stage resulting from two different cytogenetic and morphological pathways; the loss of 16q material is the cytogenetic key event in the evolution of a subgroup of this entity. By correlating genetic alterations with DNA ploidy status, an extended morphology-based cytogenetic progression model is presented, with early and late genetic alterations in the pathogenesis of breast cancer. The correlation with MAI gives rise to the hypothesis that these different genetic pathways significantly differ in their proliferation rate. Further studies will be required to elucidate which genes contribute to an altered proliferation rate in these subgroups and to the associated prognosis.

Breast Neoplasms↗

PubMed2001

Molecular mimicry and antigen-specific T cell responses in multiple sclerosis and chronic CNS Lyme disease.

The concept of molecular mimicry provides and elegant framework as to how cross-reactivity between antigens from a foreign agent with self proteins may trigger autoimmune diseases. While it was previously thought that sequence and structural homology between foreign and self proteins or the sharing of T cell receptor (TCR) and MHC-binding motifs are required for molecular mimicry to occur, we have shown that even completely unrelated peptide sequences may lead to cross-recognition by T cells. The use of synthetic combinatorial peptide libraries in the positional scanning format (PS-SCL) together with novel biometric prediction approaches has allowed us to describe the recognition profiles of individual autoreactive T cell clones (TCC) with unprecedented accuracy. Through studies of myelin-specific TCC as well as clones from the nervous system of patients suffering from chronic central nervous (CNS) Lyme disease it has become clear that at least some T cells are more degenerate than previously anticipated. These data will not only help us to redefine what constitutes specific T cell recognition, but also allow us to study in more detail the biological role of molecular mimicry. A recent clinical trial with an altered peptide ligand (APL) of one of the candidate myelin basic protein (MBP) epitopes in MS (amino acids 83-99) has shown that such a modified MBP peptide may not only have therapeutic efficacy, but also bears the potential to exacerbate disease. Thus, we provide firm evidence that the basic principles of cross-recognition and their pathogenetic significance are relevant in MS.

Amino Acid Sequence↗

PubMed2001

Function of plant shoot meristems.

Growth and development of higher plants is directed by the continuous activity of meristems, sites of sustained cell division. Organs are formed at the flanks of the shoot meristem, while the central region contains pluripotent stem cells. The developmental programme of the meristem is coordinated by interactions between cells in separate regions of meristems, and some of the genes involved have been studied. Transcription factors can be exchanged between meristem cell layers. The control of stem cell fate involves a ligand/receptor interaction that regulates the activity of a transcription factor, and genes expressed in organ primordia can feedback to restrict the activity of meristematic genes.

Cell Communication↗

PubMed2001

[Vascularized fibula transplantation in orthopedic oncology. Personal experience and review of the literature].

Primary malignant bone tumors can be treated predominantly with limb salvage. After resection of large articular segments adjacent to the dia- or metaphysis of long bones modular endoprosthetic devices are most commonly used for reconstruction. In case non-vascularized corticocancellous bone is transplanted in order to bridge extensive bone defects, the risk of pseudarthrosis and fracture of the donor bone is significantly higher in comparison to a free vascularized transplant. From 1988 until 1999 we treated 20 patients with extensive bone defects after resection of tumors affecting the upper and lower extremity using a vascularized fibular graft. In this retrospective analysis we collected the data focusing on bone integration and functional outcome. The graft union was classified according to the standards of the "International Symposium of Limb Salvage". Evaluation of the functional outcome was quantified using the Enneking-score. The stabilisation of the transplant was obtained exclusively by plate fixation in the upper extremity. In 10 in a total of 12 patients the reconstruction using a vascularized fibula transfer was reinforced with an allograft in the lower extremity. The functional evaluation score reached 73% of normal function at the last follow-up. After 18 months the radiographic evaluation of graft union was "excellent" in 75%, "good" in 11%, "fair" in 6% and "poor" in 9% according to the criteria of the ISOLS. Main complications were graft fracture in of 15% and pseudarthrosis in 14.3%. Reconstruction of extensive bone defects using free vascularized fibula grafts are a demanding operative procedure. The procedure combines a biologic form of reconstruction with a legitimate expectation of good long term outcome and a relatively low rate of complications.

Adolescent↗

PubMed2001

GEST: a gene expression search tool based on a novel Bayesian similarity metric.

Gene expression array technology has made possible the assay of expression levels of tens of thousands of genes at a time; large databases of such measurements are currently under construction. One important use of such databases is the ability to search for experiments that have similar gene expression levels as a query, potentially identifying previously unsuspected relationships among cellular states. Such searches depend crucially on the metric used to assess the similarity between pairs of experiments. The complex joint distribution of gene expression levels, particularly their correlational structure and non-normality, make simple similarity metrics such as Euclidean distance or correlational similarity scores suboptimal for use in this application. We present a similarity metric for gene expression array experiments that takes into account the complex joint distribution of expression values. We provide a computationally tractable approximation to this measure, and have implemented a database search tool based on it. We discuss implementation issues and efficiency, and we compare our new metric to other standard metrics.

Bayes Theorem↗

PubMed2001

Penetrating esophageal injuries: multicenter study of the American Association for the Surgery of Trauma.

OBJECTIVE: The purpose of this study was to define the period of time after which delays in management incurred by investigations cause increased morbidity and mortality. The outcome study is intended to correlate time with death from esophageal causes, overall complications, esophageal related complications, and surgical intensive care unit length of stay. METHODS: This was a retrospective multicenter study involving 34 trauma centers in the United States, under the auspices of the American Association for the Surgery of Trauma Multi-institutional Trials Committee over a span of 10.5 years. Patients surviving to reach the operating room (OR) were divided into two groups: those that underwent diagnostic studies to identify their injuries (preoperative evaluation group) and those that went immediately to the OR (no preoperative evaluation group). Statistical methods included Fisher's exact test, Student's T test, and logistic regression analysis. RESULTS: The study involved 405 patients: 355 male patients (86.5%) and 50 female patients (13.5%). The mean Revised Trauma Score was 6.3, the mean Injury Severity Score was 28, and the mean time interval to the OR was 6.5 hours. There were associated injuries in 356 patients (88%), and an overall complication rate of 53.5%. Overall mortality was 78 of 405 (19%). Three hundred forty-six patients survived to reach the OR: 171 in the preoperative evaluation group and 175 in the no preoperative evaluation group. No statistically significant differences were noted in the two groups in the following parameters: number of patients, age, Injury Severity Score, admission blood pressure, anatomic location of injury (cervical or thoracic), surgical management (primary repair, resection and anastomosis, resection and diversion, flaps), number of associated injuries, and mortality. Average length of time to the OR was 13 hours in the preoperative evaluation group versus 1 hour in the no preoperative evaluation group (p < 0.001). Overall complications occurred in 134 in the preoperative evaluation group versus 87 in the no preoperative evaluation group (p < 0.001), and 74 (41%) esophageal related complications occurred in the preoperative evaluation group versus 32 (19%) in the no preoperative evaluation group (p = 0.003). Mean surgical intensive care unit length of stay was 11 days in the preoperative evaluation group versus 7 days in the no preoperative evaluation group (p = 0.012). Logistic regression analysis identified as independent risk factors for the development of esophageal related complications included time delays in preoperative evaluation (odds ratio, 3.13), American Association for the Surgery of Trauma Organ Injury Scale grade >2 (odds ratio, 2.62), and resection and diversion (odds ratio, 4.47). CONCLUSION: Esophageal injuries carry a high morbidity and mortality. Increased esophageal related morbidity occurs with the diagnostic workup and its inherent delay in operative repair of these injuries. For centers practicing selective management of penetrating neck injuries and transmediastinal gunshot wounds, rapid diagnosis and definitive repair should be made a high priority.

Adolescent↗