Thomas M Halder - Academia.edu (original) (raw)

Papers by Thomas M Halder

Dermatologie, 1998

HLA ist ein Akronym fur humanes Leukozyten Antigen. Diese Proteine werden im Bereich des Haupt- H... more HLA ist ein Akronym fur humanes Leukozyten Antigen. Diese Proteine werden im Bereich des Haupt- Histokompatibilitats-Komplexes auf Chromosom 6 kodiert und bilden ein hochpolymorphes System: Sie werden grob in Klasse-I- und -II-Molekule eingeteilt; bei letzteren unterscheidet man zwischen DR-, DQ- und DP-Molekulen, von denen jeweils eine Vielzahl von Allelen existiert. Die physiologische Rolle dieser Molekule besteht darin, korperfremde Proteine nach intrazellularem Verdau spezialisierten T-Lymphozyten zu prasentieren [4]. Wie durch Rontgenstruktur- analysen gezeigt werden konnte, werden die prozessierten Proteine in Form von Peptiden in einer Bindungsgrube des HLA-Molekuls gebunden und auf diese Weise allelspezifischen T-Zellen prasentiert. Pathogene, die ins Zytosol gelangen (z. B. Viren und manche Bakterien), werden dort prozessiert und von ubiquitar vorkommenden HLA-Klasse-I-Molekulen fur die Erkennung durch zytotoxische CD8+ T-Zellen prasentiert.

The denitrifying “Aromatoleum aromaticum ” strain EbN1 was demonstrated to utilize p-ethylphenol ... more The denitrifying “Aromatoleum aromaticum ” strain EbN1 was demonstrated to utilize p-ethylphenol under anoxic conditions and was suggested to employ a degradation pathway which is reminiscent of known anaerobic ethylbenzene degradation in the same bacterium: initial hydroxylation of p-ethylphenol to 1-(4-hydroxyphenyl)-ethanol followed by dehydrogenation to p-hydroxyacetophenone. Possibly, subsequent carboxylation and thio-lytic cleavage yield p-hydroxybenzoyl-coenzyme A (CoA), which is channeled into the central benzoyl-CoA pathway. Substrate-specific formation of three of the four proposed intermediates was confirmed by gas chromato-graphic-mass spectrometric analysis and also by applying deuterated p-ethylphenol. Proteins suggested to be involved in this degradation pathway are encoded in a single large operon-like structure (15 kb). Among them are a p-cresol methylhydroxylase-like protein (PchCF), two predicted alcohol dehydrogenases (ChnA and EbA309), a biotin-dependent carboxy...

International Immunology, Dec 1, 1998

Glutamic acid decarboxylase (GAD 65) has been implicated as a targeted self antigen in the immune... more Glutamic acid decarboxylase (GAD 65) has been implicated as a targeted self antigen in the immune destruction of pancreatic β cells. T cell responses to GAD 65 peptides have been detected in both patients with type I diabetes and in the non-obese diabetic (NOD) mouse. To establish which GAD 65 epitopes are important in the immunopathogenesis of disease we initially compared T cell responses to GAD 65 epitopes in conditions of disease susceptibility and protection. T cell responses to GAD 65 peptides were measured in monozygotic twin pairs selected on the basis of disease discordance and T cell recognition of immunogenic regions of GAD 65. Peptides of interest were then used to immunize susceptible NOD mice and H2-E transgenic NOD mice which are protected from diabetes. A differential response to the epitope GAD 65 521-535 discriminated diabetic from non-diabetic human twins as well as susceptible from protected mice. This epitope as well as GAD 505-519 induces T cell responses despite binding the type I diabetes associated HLA-DQA1*0301/DQB1*0302 product with low affinity. Since DQ-restricted T cell responses are difficult to study in humans, HLA-DQ8 transgenic mice were then used: GAD epitopes 521-535 and 505-519 induced responses in DQ8 transgenic mice and T cell lines were established. Long-term T cell lines against GAD 505-519 were HLA-DQ restricted, and responded to peptide with a strong IFN-γ and IL-10 response. The findings implicate GAD 521-535 as a possible target peptide in pathogenesis and are compatible with a model whereby self-reactive T cells specific for low-affinity peptide-MHC complexes may escape thymic negative selection.

Already before the occurrence of pathological symptoms in the development of severe diseases chan... more Already before the occurrence of pathological symptoms in the development of severe diseases changes in the proteome pattern in the plasma of patients can be observed. Therefore, to follow these pathological changes, plasma samples from several time points should be analysed before clinical symptoms arise. Future patients can be statistically expected within the pool of periodical blood donors. From the biobank (blood donor centre of the Bavarian red cross) colon cancer patients can be derived out of a pool of nearly 300,000 donors every year.

American Peptide Symposia, 2002

Cancer research, 1997

Endogenous peptides bound to the constitutively expressed MHC class II molecules HLA-DR and HLA-D... more Endogenous peptides bound to the constitutively expressed MHC class II molecules HLA-DR and HLA-DQ of the melanoma cell line FM3 were examined. By a combination of analytical methods (narrow bore and capillary reversed-phase high-performance liquid chromatography with subsequent spotting on polyvinylidene difluoride membranes, matrix-assisted laser desorption ionization mass spectrometry, and Edman microsequencing), we were able to isolate and identify a panel of HLA-DR4/2 (HLA-DRB1*0401/0201/DRB5*0101)-associated self-peptides from the melanoma cell line FM3. Among ubiquitously HLA-DR-associated peptides such as peptides from the class II-associated invariant chain peptide region of the invariant chain, HLA-class I, the transferrin receptor, and the IFN-gamma receptor, we identified several potential tumor-associated antigens stemming from the MHC class I-restricted tumor antigen gp100, the Ca2(+)-binding protein annexin II, and proteins from the hsp70 family. Chinese hamster ovary...

Blood, 2000

The HLA-DR-associated peptides from peripheral blood mononuclear cells of 2 patients with plasmac... more The HLA-DR-associated peptides from peripheral blood mononuclear cells of 2 patients with plasmacytoma and 1 with chronic myeloid leukemia were isolated, identified, and compared. Several were identified as derivatives of the defensin family. Defensins (or human neutrophil peptides [HNP]) are antimicrobial, cationic peptides of 29 to 35 amino acids in length and are the major constituents of the azurophilic granules of human neutrophils. Using peripheral blood cells from leukapheresis, containing about 90% of polymorphonuclear cells, we could identify HNP-1, -2, and -4 and propeptides of up to 49 amino acids in length, eluted from HLA class II molecules. Binding of isolated and synthetic defensin peptides to various HLA-DR alleles using an in vitro binding/competition assay based on size exclusion chromatography revealed that defensin may bind into the peptide-binding groove. In a T-cell competition assay, defensins were able to reduce the proliferation of an HLA-DR-restricted T-cel...

Journal of immunology (Baltimore, Md. : 1950), 1993

Naturally processed MHC class II-associated peptides proved to be heterogeneous in size, varying ... more Naturally processed MHC class II-associated peptides proved to be heterogeneous in size, varying from 13 to 25 amino acids. Truncation variants suggested sequence motifs that afford the amino termini to be shifted for obtaining an alignment: a 9- to 11-residue core region that is bordered by primary anchor residues is surrounded by extra sequences of variable lengths and hitherto unknown functions. Herein we present bulk sequencing analyses of self-peptides from four HLA-DR alleles and HLA-DQw7 clearly showing that the length of most of the NH2-terminal preanchor sequence is limited to 1 to 3 residues. Most strikingly, proline is the dominant residue reappearing at positions 2 and 3 in any allele. Proline revealed to function as a stop signal for NH2-terminal trimming as well as a secondary anchor: crude cytosolic and endosomal peptide fractions could be processed by aminopeptidases in vitro, whereupon DR1 binding peptides with increased affinity were generated. In addition, aminope...

European Journal of Biochemistry, 1996

Major histocompatibility complex (MHC) class I1 molecules present peptide antigens to CD4'-T cell... more Major histocompatibility complex (MHC) class I1 molecules present peptide antigens to CD4'-T cells. These heterogeneous peptides are derived from internalized exogenous proteins or from endogenous membrane proteins that are processed by the antigen-presenting cell. Peptides are bound to the MHC class I1 molecules in an extended conformation and extend out of the binding groove. The aim of this study was to estimate the influence of every amino acid in all the possible undecapeptide amides (2.O48X1Oi4 individuals) on the binding to human MHC-DRBI*OlOl molecules (HLA-DRI) and to identify new peptide ligands. 220 undecapeptide sublibraries, O/X,,, each composed of ten degenerate positions and one defined position, were screened for binding to isolated HLA-DR1 , Competition of the sublibraries with a fluorescence-labeled peptide ligand allowed definition of the amino acids favourable or unfavourable for DR1-binding at every sequence position. From the activity pattern of the undecapeptide library, 54 individual peptides were deduced (27 potential hits and 27 potential falls) and prepared by chemical synthesis. As anticipated, 27 positive and 27 negative results were obtained from the competition experiments. The 27 peptides that bind obey the rules for the HLA-DR1-binding motif. The synthetic peptide library approach proved to be valuable for the design of synthetic MHC class I1 ligands and thus can be considered as a basis for drug design in immunotherapy.

Prostate Cancer - From Bench to Bedside, 2011

Tissue Antigens, 2008

Printed in Denmark .All rights reserved Human monoclonal antibody with T-cell-like specificity re... more Printed in Denmark .All rights reserved Human monoclonal antibody with T-cell-like specificity recognizes MHC class I selfpeptide presented by HLA-DR1 on activated cells Abstract: Alloreactive T cells recognize peptides presented in the binding groove of major histocompatibility complex molecules (NMCs), whereas B cells mainly recognize the MHCs independent of bound peptides. Here, we demonstrate that the human B-cell repertoire comprises B cells which can be stimulated during pregnancy to produce antibodies reacting with MHCs in a way similar to T cells The human monoclonal antibody ULdA1 recognizes DRl(DRA/DRB1*0101) molecules on Iymphoblastoid cell lines only if they co-express HLA42 or if they have been loaded with HLA-A2derived peptides. The effect of the HLA-A2 peptide 105-117 on UL-5A1 reactivity was specific, time and dose-dependent. Reactivity increased when naturally processed peptides were removed from DR1 molecules before the HLA-M peptide 105-117 was loaded. ULdA1 reacted specifically with cells that had been activated. The results imply a role of activation of cells in peptide processing andor loading.

PROTEOMICS, 2005

Renal cell carcinoma (RCC) representing the most common neoplasia of the kidney in Western countr... more Renal cell carcinoma (RCC) representing the most common neoplasia of the kidney in Western countries is a histologic diverse disease with an often unpredictable course. The prognosis of RCC is worsened with the onset of metastasis, and the therapies currently available are of limited success for the treatment of metastatic RCC. Although gene expression analyses and other methods are promising tools clarifying and standardizing the pathological classification of RCC, novel innovative molecular markers for the diagnosis, prognosis, and for the monitoring of this disease during therapy as well as potential therapeutic targets are urgently needed. Using proteome-based strategies, a number of RCC-associated markers either over-expressed or down-regulated in tumor lesions in comparison to the normal epithelium have been identified which have been implicated in tumorigenesis, but never linked to the initiation and/or progression of RCC. These include members of the fatty acid binding protein family, which have the potential to serve as diagnostic or prognostic markers for the screening of RCC patients.

Proceedings of the National Academy of Sciences, 2005

A major advantage of the mouse model lies in the increasing information on its genome, transcript... more A major advantage of the mouse model lies in the increasing information on its genome, transcriptome, and proteome, as well as in the availability of a fast growing number of targeted and induced mutant alleles. However, data from comparative transcriptome and proteome analyses in this model organism are very limited. We use DNA chip-based RNA expression profiling and 2D gel electrophoresis, combined with peptide mass fingerprinting of liver and kidney, to explore the feasibility of such comprehensive gene expression analyses. Although protein analyses mostly identify known metabolic enzymes and structural proteins, transcriptome analyses reveal the differential expression of functionally diverse and not yet described genes. The comparative analysis suggests correlation between transcriptional and translational expression for the majority of genes. Significant exceptions from this correlation confirm the complementarities of both approaches. Based on RNA expression data from the 200 most differentially expressed genes, we identify chromosomal colocalization of known, as well as not yet described, gene clusters. The determination of 29 such clusters may suggest that coexpression of colocalizing genes is probably rather common. coexpression and colocalization ͉ comparative expression profiles M ost biochemical processes within and between cells are put into effect by the interaction between proteins, or between proteins and their substrates (1-3). The proteome of a cell is the result of controlled biosynthesis and, therefore, is largely (but not exclusively) regulated by gene expression (4). Vice versa, the transcriptome can be regarded as a sensitive read-out of the proteome or the biochemical state of the cell. Thus, transcriptome and proteome feed back to each other in a highly complex way. The understanding of this functional regulation is generally limited to distinct signaling or metabolic pathways. To begin to understand the mutual regulatory interactions between transcriptome and proteome, a comparative approach including the simultaneous monitoring of expression at the RNA and protein levels will be required. The basic technologies for genome-wide expression analyses at the mRNA (5-7) and protein levels (8-10) are available. Transcript profiling was used to assess normal variability in gene expression levels of mouse liver, kidney, and testis (11) and to analyze changes in expression patterns during embryonic and fetal liver development (12). So far, comparative transcriptome and proteome analyses in complex organisms are very limited and have been performed in human platelets (13) and heart tissue (14), and in the Anopheles and Culex salivary glands (15, 16). In rodents, the proteome of mouse primary islet cells was correlated with RNA expression data of purified primary rat beta cells, suggesting a close correlation between mRNA and protein expression (17). A parallel analysis of transcripts and proteins at a genomic scale in identical mouse tissue samples has not been performed. We use DNA chip-based expression profiling, 2D gel electrophoresis, and subsequent peptide mass fingerprinting (PMF) to

The Journal of Urology, 2005

ABSTRACT Renal cell carcinoma (RCC) represents the most common malignant tumor in the kidney and ... more ABSTRACT Renal cell carcinoma (RCC) represents the most common malignant tumor in the kidney and is resistant to conventional therapies. The diagnosis of RCC is often delayed leading to progression and metastatic spread of the disease. Thus, validated markers for the early detection of the disease as well as selection of patients undergoing specific therapy is urgently needed. Using treatment with the monoclonal antibody (mAb) G250 as a model, proteome-based strategies were implemented for the identification of markers which may allow the discrimination between responders and nonresponders prior to application of G250-mediated immunotherapy. Flow cytometry revealed G250 surface expression in approximately 40% of RCC cell lines, but not in the normal kidney epithelium cell lines. G250 expression levels significantly varied thereby distinguishing between low, medium and high G250 expressing cell lines. Comparisons of two-dimensional gel electrophoresis expression profiles of untreated RCC cell lines versus RCC cell lines treated with a mAb directed against G250 and the characterization of differentially expressed proteins by mass spectrometry and/or Edman sequencing led to the identification of proteins such as chaperones, antigen processing components, transporters, metabolic enzymes, cytoskeletal proteins and unknown proteins. Moreover, some of these differentially expressed proteins matched with immunoreactive proteins previously identified by proteome analysis combined with immunoblotting using sera from healthy donors and RCC patients, a technique called PROTEOMEX. Immunohistochemical analysis of a panel of surgically removed RCC lesions and corresponding normal kidney epithelium confirmed the heterogeneous expression pattern found by proteome-based technologies. In conclusion, conventional proteome analysis as well as PROTEOMEX could be successfully employed for the identification of markers which may allow the selection of patients prior to specific immunotherapy.

Journal of Dermatological Science, 1998

Luwar IgA disease (LAD) is an antibody-mediated cutaneous automumme diseme characterized by IgA a... more Luwar IgA disease (LAD) is an antibody-mediated cutaneous automumme diseme characterized by IgA autoantibodies against the epidemml basement membrane mne and by subepidmnal blisters It ba prwiowly been shown that IgA autoantibodies of LAD recogmze epidemxd protam of 97, 120, and 180 kDa These results suggest the possible heterogenaty of autoantigen

Journal of Bacteriology, 2008

The denitrifying "Aromatoleum aromaticum" strain EbN1 was demonstrated to utilize p-ethylphenol u... more The denitrifying "Aromatoleum aromaticum" strain EbN1 was demonstrated to utilize p-ethylphenol under anoxic conditions and was suggested to employ a degradation pathway which is reminiscent of known anaerobic ethylbenzene degradation in the same bacterium: initial hydroxylation of p-ethylphenol to 1-(4-hydroxyphenyl)ethanol followed by dehydrogenation to p-hydroxyacetophenone. Possibly, subsequent carboxylation and thiolytic cleavage yield p-hydroxybenzoyl-coenzyme A (CoA), which is channeled into the central benzoyl-CoA pathway. Substrate-specific formation of three of the four proposed intermediates was confirmed by gas chromatographic-mass spectrometric analysis and also by applying deuterated p-ethylphenol. Proteins suggested to be involved in this degradation pathway are encoded in a single large operon-like structure (ϳ15 kb). Among them are a p-cresol methylhydroxylase-like protein (PchCF), two predicted alcohol dehydrogenases (ChnA and EbA309), a biotin-dependent carboxylase (XccABC), and a thiolase (TioL). Proteomic analysis (two-dimensional difference gel electrophoresis) revealed their specific and coordinated upregulation in cells adapted to anaerobic growth with p-ethylphenol and p-hydroxyacetophenone (e.g., PchF up to 29-fold). Coregulated proteins of currently unknown function (e.g., EbA329) are possibly involved in p-ethylphenol-and p-hydroxyacetophenone-specific solvent stress responses and related to other aromatic solvent-induced proteins of strain EbN1.