Biology subjects

Rammensee, H.-G.

Publications and source records attributed to Rammensee, H.-G..

8 recordsLinked to original sources

bioRxiv2026

Deep learning enables direct HLA typing from immunopeptidomics data

The immune system eliminates malignant and infected cells through T-cell-mediated recognition of peptides presented by human leukocyte antigen molecules. Mass spectrometry-based immunopeptidomics enables unbiased identification of naturally presented HLA-restricted peptides and has become central to the development of T-cell-based immunotherapies. However, immunopeptidomics data reflects the combined peptide presentation of multiple HLA alleles, and determining which allotypes are represented in this multi-allelic complexity remains an unmet computational challenge. Here, we introduce immunotype, a deep learning-based ensemble predictor for HLA class I allotyping directly from immunopeptidomics data. Immunotype integrates peptide and HLA protein sequence information through transformer encoders and a graph neural network, complemented by a curated mono-allelic reference of known peptide-HLA binding preferences. Immunotype achieves an overall accuracy of 87.2% at protein-level resolution across diverse tissues and thereby enables rapid, cost-effective HLA typing of large-scale immunopeptidomics datasets.

bioinformatics↗

bioRxiv2026

A targetable dependency on nonsense-mediated decay for proteostasis and immune control in small cell lung cancer

Small cell lung cancer (SCLC) is among the deadliest cancers with excessive somatic alterations, expectedly resulting in immunogenic epitopes. However, patient benefit from immunotherapy is limited. We found abundant frameshift mutations in SCLC, regarded as highly immunogenic, counterbalanced by a hyperactive nonsense-mediated decay (NMD) pathway, responsible for frameshift-mRNA degradation. NMD activity correlated with tumor mutational burden (TMB) across cancers, suggesting that SCLC depends on NMD for cellular homeostasis and immune evasion. NMD inhibition impaired SCLC proliferation and induced ER stress-dependent apoptosis in a TMB-dependent manner, thereby enabling pharmacological inhibition in vivo which effectively controlled tumor growth. By integrating genome and transcriptome sequencing with MHC-I immunopeptidomics and functional in vitro and in vivo assays, we identified that NMD inhibition boosted neoantigen expression and presentation by tumor cells and increased T cell recognition, thus enhancing overall tumor immunogenicity and further improving immunotherapy efficacy in vivo. Our work shows that SCLC - as a TMBhigh cancer - relies on NMD for survival and immune escape, uncovering a novel TMB-dependent tractable vulnerability for this devastating disease.

cancer biology↗

bioRxiv2020

Differential host response to a herpesvirus: Mareks disease virus peptides on chicken MHC class II molecules are derived from only a few genes and illustrate a new mode of peptide binding

Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Mareks disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Mareks disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the two class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Mareks disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only four viral genes, nearly all having the peptide motif for BL2, the dominantly-expressed class II molecule in chickens. We expressed BL2 linked to several MDV peptides, and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to core binding peptide of ten amino acids, compared to the nine amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.

immunology↗

bioRxiv2020

An innovative approach for HLA typing, molecular tumor testing and the validation of tumor exclusive antigens

DisclaimerThis manuscript has been withdrawn by the corresponding author, as it was submitted and made public in bioRxiv without knowledge and the full consent of all the authors listed. The co-authors are therefore not responsible for the contents of this manuscript. For this reason, the submitting author has chosen to withdraw this preprint as a precautionary measure and would like to state that this work should not be cited as a reference. For any related questions that may arise, please contact the corresponding author.Competing Interest StatementThe authors have declared no competing interest.

immunology↗

bioRxiv2020

Antigens in water-in-oil emulsion: a simple antigen extraction method for analysis and proof of equal antigen distribution in vaccination syringe after mixture

Therapeutic vaccination of antigens in oil emulsions is an approach becoming increasingly popular. Water-in-oil emulsions enable the formation of a depot, a slow passive antigen release and a decelerated antigen degradation. Furthermore, particularly advantageous for peptide vaccinations with a low clinical response rate is the increased immunogenicity and activation of CD8+ and CD4+ T-cells. Therefore, the use of personalized peptide vaccination cocktails in oil emulsions are tested in the treatment of cancer patients. An equal peptide distribution in the emulsion is striking for a successful depot effect to ensure the optimal efficacy and additionally, to enable reliable drug release analytics. First, the stability of the generated peptide-Montanide ISA51 emulsion was demonstrated with a cocktail of heterogeneous peptides for 24 h in room temperature. Furthermore, we developed a simple peptide extraction method to investigate the equal peptide distribution in a Montanide ISA51 emulsion in the syringe after mixing. Peptides were successfully extracted from a peptide-Montanide ISA51 vaccination cocktail in sufficient volume for analysis and an equal peptide distribution in the syringe was verified via HPLC.

pharmacology and toxicology↗

bioRxiv2019

Validation of a high-performance liquid chromatography-tandem mass spectrometry immunopeptidomics assay for the identification of HLA class I ligands suitable for pharmaceutical therapies

For more than two decades naturally presented, human leukocyte antigen (HLA)-restricted peptides (immunopeptidome) have been eluted and sequenced using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since, identified disease-associated HLA ligands have been characterized and evaluated as potential active substances. Treatments based on HLA-presented peptides have shown promising results in clinical application as personalized T cell-based immunotherapy. Peptide vaccination cocktails are produced as investigational medicinal products under GMP conditions. In order to support clinical trials based on HLA-presented tumor-associated antigens, in this study the sensitive LC-MS/MS HLA class I antigen identification pipeline was fully validated for our technical equipment according to the current US Food and Drug Administration (FDA) and European Medicines Agency (EMA) guidelines.\n\nThe immunopeptidomes of JY cells with or without spiked-in, isotope labeled peptides, of peripheral blood mononuclear cells of healthy volunteers as well as a chronic lymphocytic leukemia and a bladder cancer sample were reliably identified using a data-dependent acquisition method. As the LC-MS/MS pipeline is used for identification purposes, the validation parameters include accuracy, precision, specificity, limit of detection and robustness.

immunology↗

bioRxiv2019

The HLA Ligand Atlas. A resource of natural HLA ligands presented on benign tissues.

The human leukocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Here, we describe the HLA Ligand Atlas, an extensive collection of mostly matched HLA-I and -II ligandomes from 225 benign samples (29 tissues, 21 subjects). The initial release covers 51 HLA-I and 86 HLA-II allotypes presenting 89,853 HLA-I- and 140,861 HLA-II ligands. We observe that the immunopeptidomes differ considerably between tissues and individuals on both source protein and HLA-ligand level. 1,407 HLA-I ligands stem from non-canonical genomic regions. We highlight the importance of comparatively analyzing both benign and malignant tissues to inform tumor association, based on a case study in three glioblastoma patients. The resource provides insights into applied and basic immune-associated questions in the context of cancer immunotherapy, infection, transplantation, allergy, and autoimmunity. It is publicly available at www.hla-ligand-atlas.org.

immunology↗

bioRxiv2019

Short-term oxaliplatin exposure according to established hyperthermic intraperitoneal chemotherapy (HIPEC) protocols lacks effectiveness in vitro and ex vivo

Cytotoxicity of oxaliplatin-containing solutions (OCS), sampled during patient treatment with hyperthermic intraperitoneal chemotherapy (HIPEC), was assessed by well-established continuous impedance-based real-time cell analysis (RTCA) ex vivo. HIPEC treatment was replicated by exposing OAW-42 cancer cells to OCS for 30 or 60 minutes at 42 {degrees}C. In contrast to previous observations with continuous exposure, where cytotoxicity was proven, identical OCS obtained during HIPEC did not induce cell death reproducibly and showed strongly attenuated effects after only 30 minutes of application. Based on these unexpected findings, spike-ins of oxaliplatin (OX) into peritoneal dialysis solution (PDS) or dextrose 5 % in water (D5W) were used to replicate HIPEC conditions, as used in either our own protocols or the recently presented randomized controlled PRODIGE 7 trial, where OX HIPEC for 30 minutes failed to produce survival benefits in colorectal carcinoma patients. With OX-spiked into D5W or PDS at identical concentrations as used for PRODIGE 7 or conforming with own HIPEC protocols, we did not observe the expectable cytotoxic effects in RTCA, after replicating OX HIPEC for 30 minutes. These results were corroborated for both solvents at relevant drug concentrations by classical end-point assays for cytotoxicity in two cancer cell lines. Further results suggest that penetration depth, drug dosage, exposure time and drug solvents may constitute critical factors for HIPEC effectiveness. Accordingly, we witnessed substantial cell shrinkage with both PDS and D5W, potentially contributing to reduced drug effects. Based on these results, intensified pharmacological research seems warranted to establish effective HIPEC protocols.\n\nKey PointsO_LIOxaliplatin (OX)-containing solutions obtained during patient treatment with Hyperthermic intraperitoneal chemotherapy (HIPEC) unexpectedly showed low cytotoxicity in an impedance-based ex vivo cytotoxicity cell assay.\nC_LIO_LIOX cytotoxicity under HIPEC conditions could be enhanced by extending drug exposure to one hour by an impedance-based ex vivo cytotoxicity cell assay.\nC_LIO_LIHIPEC failed to show survival benefits in the randomized controlled PRODIGE 7 trial and was questioned in the aftermath.\nC_LIO_LIClinically relevant OX concentrations applied in conjunction with hyperthermia (42 {degrees}C) for 30 minutes, as used either at our own medical center or according to the PRODIGE 7 trial, proved predominantly ineffective, when used according to HIPEC routines in an impedance-based in vitro cytotoxicity cell assay.\nC_LIO_LIRespective findings were corroborated in two different cell lines and by two established end-point assays, showing that 50 % cell death could not be reached by the same HIPEC treatment with OX, in contrast to continuous drug exposure.\nC_LIO_LIAs potentially relevant factor, the thickness of the exposed cell layer was identified, requiring at least ~100 {micro}m penetration depth for our model to indicate effectiveness.\nC_LIO_LIAdditionally, we show relevant cell shrinkage by two drug diluents used either at our own medical center or according to the PRODIGE 7 trial, potentially associated with fluid shifts out of the cell and impaired drug effects.\nC_LIO_LIOur own as well as recent findings by Ubink et al. (Br J Surg. 2019. doi: 10.1002/bjs.11206) support the notion that lacking effectiveness of OX HIPEC may explain the negative PRODIGE 7 trial results.\nC_LI

pharmacology and toxicology↗