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Burkhard Ludewig

Publications and source records attributed to Burkhard Ludewig.

At least 19 recordsLinked to original sources
PubMed2026

PMGen: from peptide-MHC structure prediction to peptide generation.

MOTIVATION: Accurate structural modeling of peptide-major histocompatibility complex (pMHC) complexes is essential for structure-driven immunotherapy design, yet current prediction tools suffer from narrow class coverage, restricted peptide lengths, insufficient accuracy, and a lack of built-in structure-aware peptide sampling. Consequently, most mimotope and altered peptide ligand designs rely solely on sequence substitution, leaving spatial and biophysical insights from pMHC structures largely unexploited. RESULTS: We introduce peptide-MHC generator (PMGen), an integrated framework for structure prediction and structure-guided design of variable-length peptides across MHC Class I and II. PMGen enforces anchor constraints within AlphaFold2 through two complementary strategies, initial guess and template engineering, achieving state-of-the-art structural fidelity without model fine-tuning. On a comprehensive benchmark, PMGen outperforms all existing methods, yielding median peptide-core Cα RMSDs of 0.62 Å for MHC-I and 0.33 Å for MHC-II. We show that PMGen can recover incorrectly predicted anchor positions and that AlphaFold pLDDT scores enable sequence-independent binding-core identification. Applied to a published neoantigen/wild-type pair, PMGen accurately captures mutation-induced conformational changes. Beyond structure prediction, we show that ProteinMPNN sampling on PMGen-predicted backbones yields higher affinity peptides while preserving the parental 3D conformation. Using PMGen to generate 63 817 high-confidence pMHC structures as training data, we further improve ProteinMPNN's peptide sequence recovery from 0.14 to 0.64 on a test set of 85 unseen MHC-I alleles, highlighting the value of accurate predicted structures for downstream machine learning tasks. AVAILABILITY AND IMPLEMENTATION: PMGen is freely available at https://github.com/soedinglab/PMGen, with an interactive Colab notebook at https://colab.research.google.com/github/soedinglab/PMGen/blob/master/colab.ipynb.

Peptides↗
PubMed2006

Control of coronavirus infection through plasmacytoid dendritic-cell-derived type I interferon.

This study demonstrates a unique and crucial role of plasmacytoid dendritic cells (pDCs) and pDC-derived type I interferons (IFNs) in the pathogenesis of mouse coronavirus infection. pDCs controlled the fast replicating mouse hepatitis virus (MHV) through the immediate production of type I IFNs. Recognition of MHV by pDCs was mediated via TLR7 ensuring a swift IFN-alpha production following encounter with this cytopathic RNA virus. Furthermore, the particular type I IFN response pattern was not restricted to the murine coronavirus, but was also found in infection with the highly cytopathic human severe acute respiratory syndrome (SARS) coronavirus. Taken together, our results suggest that rapid production of type I IFNs by pDCs is essential for the control of potentially lethal coronavirus infections.

Animals↗
PubMed2006

Dendritic cell-based multi-epitope immunotherapy of hormone-refractory prostate carcinoma.

BACKGROUND: Dendritic cell (DC)-based immunotherapy is a promising approach to augment tumor antigen-specific T cell responses in cancer patients. However, tumor escape with down-regulation or complete loss of target antigens may limit the susceptibility of tumor cells to the immune attack. Concomitant generation of T cell responses against several immunodominant antigens may circumvent this potential drawback. In this trial, we determined the immunostimulatory capacity of autologous DC pulsed with multiple T cell epitopes derived from four different prostate-specific antigens in patients with advanced hormone-refractory prostate cancer. PATIENTS AND METHODS: Autologous DC of HLA-A*0201(+) patients with hormone-refractory prostate cancer were loaded with antigenic peptides derived from prostate stem cell antigen (PSCA(14-22)), prostatic acid phosphatase (PAP(299-307)), prostate-specific membrane antigen (PSMA(4-12)), and prostate-specific antigen (PSA(154-163)). DC were intradermally applied six times at biweekly intervals followed-in the case of an enhanced immune response-by monthly booster injections. Immune monitoring during the time of ongoing vaccinations (12-59 weeks) included ex vivo ELISPOT measurements, MHC tetramer analysis and in vitro cytotoxicity assays. RESULTS: Of the initial six patients, three qualified for long-term multi-epitope DC vaccination. This regime was tolerated well by all three patients. The vaccination elicited significant cytotoxic T cell responses against all prostate-specific antigens tested. In addition, memory T cell responses against the control peptides derived from influenza matrix protein and tetanus toxoid were efficiently boosted. Clinically, the long-term DC vaccination was associated with an increase in PSA doubling time. CONCLUSIONS: DC-based multi-epitope immunotherapy with repeated boosting in men with hormone-refractory prostate carcinoma is feasible and generates efficient cellular antitumor responses.

Acid Phosphatase↗
PubMed2006

Rapid molecular dissection of viral and bacterial immunomes.

The development of preventive or therapeutic recombinant vaccines and the generation of serodiagnostic assays for infectious diseases depend essentially on the availability of molecularly defined antigens. A major bottleneck for the identification of suitable target antigens for many pathogens is the isolation of sufficient amounts of material for subsequent genomic or proteomic screening. Applying a highly efficient expression cloning strategy to the human pathogens vaccinia virus (VV) and Chlamydia pneumoniae (CP), we demonstrate that sub-nanogram amounts of isolated nucleic acids can be utilized to determine comprehensive sets of immunodominant antigens. Remarkably, the approach not only confirmed the immunogenicity of previously reported antigens but also disclosed novel vaccine candidates conserved in orthopoxviruses, including antigenic envelope proteins and immunodominant CTL epitopes. Moreover, as illustrated for CP infection, we show that a panel of novel antigens can be readily selected from the initially discovered pool to build up pathogen-specific seroassays. The established approach is rapid, making it an attractive procedure for the comprehensive dissection of immunomes of known human pathogens and newly emerging infectious agents.

Animals↗
PubMed2006

Expression of lymphotoxin beta governs immunity at two distinct levels.

Interaction of lymphotoxin alpha(1)beta(2) (LTalpha(1)beta(2)) with its receptor is key for the generation and maintenance of secondary lymphoid organ microstructure. We used mice conditionally deficient for LTbeta on different lymphocyte subsets to determine how the LTbeta-dependent lymphoid structure influences immune reactivity. All conditionally LTbeta-deficient mice mounted normal immune responses against vesicular stomatitis virus (VSV), and were protected against lymphocytic choriomeningitis virus (LCMV). In contrast, they exhibited reduced immune responses against non-replicating antigens. Completely LTbeta-deficient mice failed to retain VSV in the marginal zone and died from VSV infections, and they became virus carriers following infection with the non-cytopathic LCMV, which was correlated with defective virus replication in dendritic cells. It was ruled out that LTbeta expression on lymphocytes influenced their activation, homing capacity, or maturation. We therefore conclude that LTbeta expression influences immune reactivity at two distinct levels: (i) Expression of LTbeta on lymphocytes enhances the induction of immune responses against limiting amounts of antigen. (ii) Expression of LTbeta on non-lymphocytes governs antiviral immunity by enhancing antigen presentation on antigen-presenting cells. This prevents cytotoxic T lymphocytes exhaustion or death of the host by uncontrolled virus spread.

Animals↗
PubMed2006

Microchimerism maintains deletion of the donor cell-specific CD8+ T cell repertoire.

Rare cases of stable allograft acceptance after discontinuation of immunosuppression are often accompanied by macrochimerism (> 1% donor cells in blood) or microchimerism (< 1% donor cells in blood). Here, we have investigated whether persistence of donor cells is the cause or the consequence of long-lasting CTL unresponsiveness. We found that engraftment of splenocytes bearing a single foreign MHC class I-restricted epitope resulted in lifelong donor cell microchimerism and specific CTL unresponsiveness. This status was reversed in a strictly time- and thymus-dependent fashion when the engrafted cells were experimentally removed. The results presented herein show that microchimerism actively maintains CTL unresponsiveness toward a minor histocompatibility antigen by deleting the specific repertoire and thus excluding dominant, T cell extrinsic mechanisms of CTL unresponsiveness independent of systemically persisting donor cell antigen.

Adoptive Transfer↗
PubMed2005

CXCR5-dependent seeding of follicular niches by B and Th cells augments antiviral B cell responses.

The chemokine receptor CXCR5 and its ligand CXCL13 define the structure of B cell follicles within secondary lymphoid organs. Here, we examined the impact of CXCR5 on antiviral B cell responses in vivo. CXCR5-/- mice showed a normal production of IgM and IgG acutely after infection with vesicular stomatitis virus (VSV) and developed VSV-specific germinal centers. However, impaired Ig class switch and Ab production were observed under conditions of limited availability of Ag (i.e., after immunization with nonreplicating viral particles or soluble Ag). Adoptive transfer of CXCR5-deficient, VSV-specific B and Th cells demonstrated that CXCR5 expression on both B and Th cells is required for an efficient Ig class switch. These experiments revealed that CXCR5 is critical for the coordinated interaction of antiviral T and B cells through its impact on initial B cell expansion and the recruitment of Ag-specific B and Th cells to germinal centers.

Adoptive Transfer↗
PubMed2005

Dendritic cells generated from patients with androgen-independent prostate cancer are not impaired in migration and T-cell stimulation.

BACKGROUND: Dendritic cell (DC)-based vaccination has been investigated as immunotherapy for several types of cancer. A potential drawback to vaccination with autologous monocyte-derived DCs (MoDCs) could be that MoDCs from patients are functionally impaired. In case of androgen-independent prostate cancer (CaP), the cancer itself, diverse prior therapies, and the hormone manipulation may affect the immune system. METHODS: MoDCs from patients suffering from androgen-independent CaP were generated according to a clinically applicable protocol to evaluate the phenotype, maturation capacity, migration, and T-cell stimulation of these cells compared with those generated from tumor-free donors. RESULTS: MoDCs generated from CaP patients could be fully matured and efficiently migrated towards the chemokine CCL21. They had a strong potency to activate allogeneic CD4+ and CD8+ T-cells and to present antigens to specific CTL. CONCLUSIONS: Our data suggest that MoDCs from patients with androgen-independent CaP are functionally intact and hence qualify as cellular vaccines for immunotherapy of advanced stage CaP.

Aged↗
PubMed2005

Rapid functional exhaustion and deletion of CTL following immunization with recombinant adenovirus.

Replication-deficient adenoviruses (recombinant adenovirus (rec-AdV)) expressing different transgenes are widely used vectors for gene therapy and vaccination. In this study, we describe the tolerization of transgene-specific CTL following administration of beta-galactosidase (beta gal)-recombinant adenovirus (Ad-LacZ). Using MHC class I tetramers to track beta gal-specific CTL, we found that a significant expansion of beta gal-specific CTL was restricted to a very narrow dose range. Functional analysis revealed that adenovirus-induced beta gal-specific CTL produced only very low amounts of effector cytokines and were unable to exhibit cytolytic activity in a 51Cr release assay. Furthermore, Ad-LacZ vaccination failed to efficiently clear established beta gal-positive tumors. The impaired function of Ad-LacZ-induced CTL correlated with the presence of persisting beta gal Ag in the liver. A further increase in the peripheral Ag load by injection of Ad-LacZ into SM-LacZ transgenic mice which express beta gal as self-Ag exclusively in peripheral nonlymphoid organs, resulted in the physical deletion of beta gal-specific CTL. Our results indicate first that CTL deletion in the course of adenoviral vaccination is preceded by their functional impairment and second, that the outcome of rec-AdV vaccination depends critically on the Ag load in peripheral tissues.

Adenoviridae↗
PubMed2005

Quantification and characterization of myosin peptide-specific CD4+ T cells in autoimmune myocarditis.

Characterization of autoantigen-specific CD4+ T cells at the single cell level is crucial for understanding the immunopathological mechanisms underlying autoimmune diseases. Cardiac myosin heavy chain (myhca) is the major autoantigen associated with autoimmune myocarditis both in humans and in experimental autoimmune myocarditis (EAM) in mice. In the current study, we evaluated two methods for the enumeration and phenotypic characterization of myhca-specific CD4+ T cells during the course of EAM. Both enzyme-linked immunospot (ELISPOT) and cytokine flow cytometry (CFC) assays were suitable for the detection and characterization of myhca-specific Th cells during acute myocardial inflammation and the late healing phase of the disease. Cytokine production of myhca-specific Th cells was restricted to interferon-gamma (IFNgamma). Only trace amounts of the Th2 cytokines IL-4 and IL-5 could be detected. Concomitant surface marker analysis in the CFC assay revealed the prototypical effector phenotype of myhca-specific Th1 cells during the acute phase of the disease. Taken together, the combination of both methods appears to be most appropriate for a comprehensive ex vivo single cell analysis of Th cells in heart-specific autoimmune disorders.

Animals↗
PubMed2005

Selective replication of coronavirus genomes that express nucleocapsid protein.

The coronavirus nucleocapsid (N) protein is a structural protein that forms a ribonucleoprotein complex with genomic RNA. In addition to its structural role, it has been described as an RNA-binding protein that might be involved in coronavirus RNA synthesis. Here, we report a reverse genetic approach to elucidate the role of N in coronavirus replication and transcription. We found that human coronavirus 229E (HCoV-229E) vector RNAs that lack the N gene were greatly impaired in their ability to replicate, whereas the transcription of subgenomic mRNA from these vectors was easily detectable. In contrast, vector RNAs encoding a functional N protein were able to carry out both replication and transcription. Furthermore, modification of the transcription signal required for the synthesis of N protein mRNAs in the HCoV-229E genome resulted in the selective replication of genomes that are able to express the N protein. This genetic evidence leads us to conclude that at least one coronavirus structural protein, the N protein, is involved in coronavirus replication.

Animals↗
PubMed2005

Cinanserin is an inhibitor of the 3C-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro.

The 3C-like proteinase (3CLpro) of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is one of the most promising targets for anti-SARS-CoV drugs due to its crucial role in the viral life cycle. In this study, a database containing structural information of more than 8,000 existing drugs was virtually screened by a docking approach to identify potential binding molecules of SARS-CoV 3CLpro. As a target for screening, both a homology model and the crystallographic structure of the binding pocket of the enzyme were used. Cinanserin (SQ 10,643), a well-characterized serotonin antagonist that has undergone preliminary clinical testing in humans in the 1960s, showed a high score in the screening and was chosen for further experimental evaluation. Binding of both cinanserin and its hydrochloride to bacterially expressed 3CLpro of SARS-CoV and the related human coronavirus 229E (HCoV-229E) was demonstrated by surface plasmon resonance technology. The catalytic activity of both enzymes was inhibited with 50% inhibitory concentration (IC50) values of 5 microM, as tested with a fluorogenic substrate. The antiviral activity of cinanserin was further evaluated in tissue culture assays, namely, a replicon system based on HCoV-229E and quantitative test assays with infectious SARS-CoV and HCoV-229E. All assays revealed a strong inhibition of coronavirus replication at nontoxic drug concentrations. The level of virus RNA and infectious particles was reduced by up to 4 log units, with IC50 values ranging from 19 to 34 microM. These findings demonstrate that the old drug cinanserin is an inhibitor of SARS-CoV replication, acting most likely via inhibition of the 3CL proteinase.

Animals↗
PubMed2005

A mathematical approach for optimizing dendritic cell-based immunotherapy.

Adoptive dendritic cell (DC)-based immunotherapy represents a promising approach to overcome peripheral tolerance against autologous tumor antigens and to maintain protective antitumor immunity. The translation of successful preclinical studies, however, appears to be hampered by new complexities associated with the clinical situation. Mathematical modeling provides the means for qualitative and quantitative analysis, predictions for complex dynamic systems in immunology, and for the design and improvement of therapeutic approaches. We present here a workable computational methodology for developing meaningful data- and hypothesis-driven mathematical models for DC-based immunotherapy with a particular focus on numerical parameter estimation and sensitivity analysis.

CD8-Positive T-Lymphocytes↗
PubMed2004

Impact of CCR7 on priming and distribution of antiviral effector and memory CTL.

The chemokine receptor CCR7 is a key factor in the coordinate migration of T cells and dendritic cells (DC) into and their localization within secondary lymphoid organs. In this study we investigated the impact of CCR7 on CD8(+) T cell responses by infecting CCR7(-/-) mice with lymphocytic choriomeningitis virus (LCMV). We found that the absence of CCR7 affects the magnitude of an antiviral CTL response during the acute phase, with reduced numbers of virus-specific CTL in all lymphoid and nonlymphoid organs tested. On the single cell level, CCR7-deficient CTL gained full effector function, such that antiviral protection in CCR7-deficient mice was complete, but delayed. Similarly, adoptive transfer experiments using DC from CCR7-deficient or competent mice for the priming of CCR7-positive or CCR7-negative CD8(+) T cells, respectively, revealed that ectopic positioning of DC and CTL outside organized T cell zones results in reduced priming efficacy. In the memory phase, CCR7-deficient mice maintained a stable LCMV-specific CTL population, predominantly in nonlymphoid organs, and rapidly mounted protective CTL responses against a challenge infection with a vaccinia virus recombinant for the gp33 epitope of LCMV. Taken together, the CCR7-dependent organization of the T cell zone does not appear to be a prerequisite for antiviral effector CTL differentiation and the sustenance of antiviral memory responses in lymphoid or peripheral tissues.

Adoptive Transfer↗