Leon Bichmann

Leon Bichmann
University of Tuebingen | EKU Tübingen · Center for Bioinformatics

About

31
Publications
4,244
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456
Citations
Citations since 2016
29 Research Items
451 Citations
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2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120

Publications

Publications (31)
Article
Glioblastoma is known as the most aggressive and most common malignant primary tumor in the central nervous system. Current treatment options comprise maximal surgical resection followed by radiation and/or chemotherapy with temozolomide. However, these therapies are not able to eliminate all tumor cells, which in turn inevitably leads to disease r...
Article
Full-text available
Understanding the molecular principles that govern the composition of the MHC-I immunopeptidome across different primary tissues is fundamentally important to predict how T cell respond in different contexts in vivo. Here, we performed a global analysis of the MHC-I immunopeptidome from 29 and 19 primary human and mouse tissues, respectively. First...
Article
Full-text available
Data-independent acquisition (DIA) is becoming a leading analysis method in biomedical mass spectrometry. The main advantages include greater reproducibility and sensitivity and a greater dynamic range compared with data-dependent acquisition (DDA). However, the data analysis is complex and often requires expert knowledge when dealing with large-sc...
Article
Here, we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison (https://www.proteomicsdb.org/use/). Mass spectra under investigation can be either provided manually by the user (table format) or automatically retrieved from online repositories supporting acce...
Article
Full-text available
Background The human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding the benign HLA ligand repertoire is a prerequisite to define safe T-cell-based immunotherapies against cancer. Due to the poor availability of benign ti...
Article
Full-text available
Biomaterials play an increasing role in clinical applications and regenerative medicine. A perfectly designed biomaterial should restore the function of damaged tissue without triggering an undesirable immune response, initiate self-regeneration of the surrounding tissue and gradually degrade after implantation. The immune system is well recognized...
Preprint
Full-text available
Data-independent acquisition (DIA) is becoming a leading analysis method in biomedical mass spectrometry. Main advantages include greater reproducibility, sensitivity and dynamic range compared to data-dependent acquisition (DDA). However, data analysis is complex and often requires expert knowledge when dealing with large-scale data sets. Here we...
Preprint
Full-text available
Understanding the molecular principles that govern the composition of the mammalian MHC-I immunopeptidome (MHC-Ii) across different primary tissues is fundamentally important to predict how T cell respond in different contexts in vivo . Here, we performed a global analysis of the mammalian MHC-Ii from 29 and 19 primary human and mouse tissues, resp...
Preprint
Full-text available
Here we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison (https://www.proteomicsdb.org/use/). Mass spectra under investigation can either be provided manually by the user (table format), or automatically retrieved from online repositories supporting acce...
Conference Paper
3128 Background: The human leukocyte antigen (HLA) complex regulates the adaptive immune response by showcasing the intracellular and extracellular protein content to the immune system, which is the basis for T cell-dependent tumor rejection. Therefore, a comprehensive map of the entirety of both HLA class I- and class II-presented peptides from va...
Chapter
Computational mass spectrometry is plagued by a multitude of issues, including a heterogeneous software environment, complex workflows and proprietary tools. OpenMS addresses these challenges by providing robust open-source software for users and an open, well-designed software environment for developers. OpenMS is an open-source software C++ libra...
Article
Full-text available
In healthy individuals, immune control of persistent human cytomegalovirus (HCMV) infection is effectively mediated by virus-specific CD4+ and CD8+ T cells. However, identifying the repertoire of T cell specificities for HCMV is hampered by the immense protein coding capacity of this betaherpesvirus. Here, we present a novel approach that employs H...
Article
We provide a comprehensive analysis of the antigenic landscape of glioblastoma using a multi-omics approach including ligandome mapping of the Human Leukocyte Antigen (HLA) ligandome, next generation sequencing (NGS) as well as an in-depth characterization of tumor-infiltrating lymphocytes (TIL) using mass cytometry and ultra-deep sequencing of the...
Article
Personalized multi-peptide vaccines are currently discussed intensively for tumor immunotherapy. In order to identify epitopes - short, immunogenic peptides - suitable for eliciting a tumor-specific immune response, human leukocyte antigen (HLA)-presented peptides are isolated by immunoaffinity purification from cancer tissue samples and analyzed b...
Article
Background In Germany, approximately 30-50% of Oropharyngeal squamous-cell carcinoma (OPSCC) are related to human papillomaviruses (HPV), of which 90% are caused by HPV-16. The analysis of cancer-associated antigens is needed to develop antigen-specific immunotherapy and to determine the level of personalization required for therapeutic cancer vacc...
Preprint
The Human Leukocyte Antigen (HLA) regulates the adaptive immune response by showcasing the intracellular and extracellular protein content to the immune system, where T cells, in particular, are able to distinguish between self and foreign. Therefore, a comprehensive mapping of the entirety of both HLA class I- and class II-presented peptides is a...
Article
Full-text available
Background Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in...
Article
Antileukemia immunity plays an important role in disease control and maintenance of tyrosine kinase inhibitor (TKI)-free remission in chronic myeloid leukemia (CML). Thus, antigen-specific immunotherapy holds promise for strengthening immune control in CML but requires the identification of CML-associated targets. In this study, we used a mass spec...
Article
Chronic myeloid leukemia (CML) is characterized by the translocation t(9;22), which leads to the formation of the BCR-ABL fusion transcript. Several approved tyrosine kinase inhibitors (TKIs) target the resulting fusion protein, leading to an improved prognosis of CML patients. Currently, the main treatment goal is the achievement of a deep molecul...
Article
In recent years, therapeutic approaches for acute myeloid leukemia (AML) have been improved, however the disease is still characterized by high relapse rates and a poor overall survival mainly in elderly patients aged 60 years and older. The standard therapy for these AML patients involves hypomethylating agents (HMAs) such as decitabine. With this...
Article
Many proteins have small-molecule binding pockets that are not easily detectable in the ligand-free structures. These cryptic sites require a conformational change to become apparent; a cryptic site can therefore be defined as a site that forms a pocket in a holo structure, but not in the apo structure. Because many proteins appear to lack druggabl...
Article
Glycosaminoglycans (GAGs) represent a class of anionic periodic linear polysaccharides, which mediate cell communication processes by interactions with their protein targets in the extracellular matrix. Due to their high flexibility, charged nature, periodicity, and polymeric nature GAGs are challenging systems for computational approaches. To deal...

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Projects

Project (1)
Project
A resource of natural HLA ligands presented on benign tissues. The Human Leukocyte Antigens (HLA) are the showcase of a cell's protein content and regulate the adaptive immune response by presenting HLA class I and HLA class II peptides to T cells. This project aims at a comprehensive tissue-specific mapping of natural HLA ligands of the human body. This atlas will be relevant not only for basic research in fields such as systems biology, molecular biology and general immunology, but also for translational purposes such as the design of effective tumor vaccines. The HLA Ligand Atlas is publicly available as raw data, but also as a user-friendly web interface at www.hla-ligand-atlas.org First project preprint available at bioRxiv.org! The HLA Ligand Atlas. A resource of natural HLA ligands presented on benign tissues. Ana Marcu, Leon Bichmann, Leon Kuchenbecker, Linus Backert, Daniel J. Kowalewski, Lena Katharina Freudenmann, Markus W. Löffler, Maren Lübke, Juliane S. Walz, Julia Velz, Holger Moch, Luca Regli, Manuela Silginer, Michael Weller, Andreas Schlosser, Oliver Kohlbacher, Stefan Stevanović, Hans-Georg Rammensee, Marian C. Neidert bioRxiv 778944 doi: https://doi.org/10.1101/778944.