Daniel J. Kowalewski
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View article: Immunopeptidome analysis reveals SERPINB3 as an autoantigen driving eczematized psoriasis
Immunopeptidome analysis reveals SERPINB3 as an autoantigen driving eczematized psoriasis Open
Psoriasis (Pso) is a chronic inflammatory skin disease driven by T helper 17 (T H 17) cells, with several clinical subtypes. While self-reactive immune responses have been observed, the role of autoantigens in Pso remains unclear. Using im…
View article: HLA Ligand Atlas DIA: extending the benign immunopeptidomics resource with increased sensitivity through data-independent acquisition mass spectrometry
HLA Ligand Atlas DIA: extending the benign immunopeptidomics resource with increased sensitivity through data-independent acquisition mass spectrometry Open
The human leukocyte antigen (HLA)-presented peptide repertoire, termed immunopeptidome, plays a crucial role for T-cell mediated immune reactions. Previously, the human immunopeptidome of non-malignant tissues has been mapped in a large-sc…
View article: Mapping naturally presented T cell antigens in medulloblastoma based on integrative multi-omics
Mapping naturally presented T cell antigens in medulloblastoma based on integrative multi-omics Open
Medulloblastoma is the most frequent malignant primary brain tumor in children. Despite recent advances in integrated genomics, the prognosis in children with high-risk medulloblastoma remains devastating, and new tumor-specific therapeuti…
View article: A T-cell antigen atlas for meningioma: novel options for immunotherapy
A T-cell antigen atlas for meningioma: novel options for immunotherapy Open
View article: Supplementary Table 6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Supplementary Table 6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation Open
Statistics over-represented peptides HLA class I
View article: Supplementary Figures 1-6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Supplementary Figures 1-6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation Open
Complete supplementary figures containing: Suppl. Fig. 1: HLA-coverage (Caucasian); Suppl. Fig. 2: Maximum attainable quantities of source proteins; Suppl. Fig. 3: Comparsion with complete benign dataset; Suppl. Fig. 4: Legend PANTHER anal…
View article: Supplementary Table 8 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Supplementary Table 8 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation Open
Statistics over-represented peptides HLA class II
View article: Supplementary Figures 1-6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Supplementary Figures 1-6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation Open
Complete supplementary figures containing: Suppl. Fig. 1: HLA-coverage (Caucasian); Suppl. Fig. 2: Maximum attainable quantities of source proteins; Suppl. Fig. 3: Comparsion with complete benign dataset; Suppl. Fig. 4: Legend PANTHER anal…
View article: Supplementary Tables 1-5, 7, 9-12 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Supplementary Tables 1-5, 7, 9-12 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation Open
Supplementary Tables 1-5, 7, 9-12 containing: Suppl. Table 1: Sample characteristics; Suppl. Table 2: Patient characteristics; Suppl. Table 3: Control peptides Suppl. Table 4: Peptide-specific properties Suppl. Table 5: Over-represented Pe…
View article: Data from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Data from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation Open
Immune cell infiltrates have proven highly relevant for colorectal carcinoma prognosis, making colorectal cancer a promising candidate for immunotherapy. Because tumors interact with the immune system via HLA-presented peptide ligands, exa…
View article: Supplementary Table 6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Supplementary Table 6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation Open
Statistics over-represented peptides HLA class I
View article: Supplementary Tables 1-5, 7, 9-12 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Supplementary Tables 1-5, 7, 9-12 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation Open
Supplementary Tables 1-5, 7, 9-12 containing: Suppl. Table 1: Sample characteristics; Suppl. Table 2: Patient characteristics; Suppl. Table 3: Control peptides Suppl. Table 4: Peptide-specific properties Suppl. Table 5: Over-represented Pe…
View article: Data from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Data from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation Open
Immune cell infiltrates have proven highly relevant for colorectal carcinoma prognosis, making colorectal cancer a promising candidate for immunotherapy. Because tumors interact with the immune system via HLA-presented peptide ligands, exa…
View article: Supplementary Table 8 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Supplementary Table 8 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation Open
Statistics over-represented peptides HLA class II
View article: 713 The PRAME opportunity – high peptide copy numbers, homogenous expression and high prevalence to address a broad patient population across different solid cancers with TCR-based therapeutics
713 The PRAME opportunity – high peptide copy numbers, homogenous expression and high prevalence to address a broad patient population across different solid cancers with TCR-based therapeutics Open
Background Several peptide-HLA targets for T cell receptor (TCR)-based immunotherapies are currently being evaluated in the field, however, many are limited by their overall low prevalence, low copy numbers or relevant expression in health…
View article: Quantitative immunopeptidomics reveals a tumor stroma–specific target for T cell therapy
Quantitative immunopeptidomics reveals a tumor stroma–specific target for T cell therapy Open
T cell receptor (TCR)–based immunotherapy has emerged as a promising therapeutic approach for the treatment of patients with solid cancers. Identifying peptide–human leukocyte antigen (pHLA) complexes highly presented on tumors and rarely …
View article: HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy
HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy Open
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 pre…
View article: Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand
Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand Open
Knowledge about the peptide repertoire presented by human leukocyte antigens (HLA) holds the key to unlock target-specific cancer immunotherapies such as adoptive cell therapies or bispecific T cell engaging receptors. Therefore, comprehen…
View article: SARS-CoV-2 T-cell epitopes define heterologous and COVID-19-induced T-cell recognition
SARS-CoV-2 T-cell epitopes define heterologous and COVID-19-induced T-cell recognition Open
The SARS-CoV-2 pandemic calls for the rapid development of diagnostic, preventive, and therapeutic approaches. CD4+ and CD8+ T cell-mediated immunity is central for control of and protection from viral infections…
View article: Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy
Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy Open
View article: Additional file 1 of Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy
Additional file 1 of Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy Open
Additional file 1. Contains supplementary table Tab. S1: HLA class I and II restricted peptides from the 113 candidate genes identified by HLA ligandomics in patient cohort 1 (n = 55).
View article: Identification of HCMV-derived T cell epitopes in seropositive individuals through viral deletion models
Identification of HCMV-derived T cell epitopes in seropositive individuals through viral deletion models Open
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 b…
View article: A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer
A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer Open
Background: Radiofrequency ablation (RFA) is an established treatment option for malignancies located in the liver. RFA-induced irreversible coagulation necrosis leads to the release of danger signals and cellular content. Hence, RF…
View article: A new synthetic toll-like receptor 1/2 ligand is an efficient adjuvant for peptide vaccination in a human volunteer
A new synthetic toll-like receptor 1/2 ligand is an efficient adjuvant for peptide vaccination in a human volunteer Open
Thus, in one volunteer we show a granuloma forming by peptides combined with an efficient adjuvant in a water-in-oil-emulsion, inducing antigen specific T cells detectable in circulation and at the vaccination site, after one single vaccin…
View article: The HLA Ligand Atlas - A resource of natural HLA ligands presented on benign tissues
The HLA Ligand Atlas - A resource of natural HLA ligands presented on benign tissues Open
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…
View article: HLA-B locus products resist degradation by the human cytomegalovirus immunoevasin US11
HLA-B locus products resist degradation by the human cytomegalovirus immunoevasin US11 Open
To escape CD8+ T-cell immunity, human cytomegalovirus (HCMV) US11 redirects MHC-I for rapid ER-associated proteolytic degradation (ERAD). In humans, classical MHC-I molecules are encoded by the highly polymorphic HLA-A, -B and -C gene loci…
View article: Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy
Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy Open
Oncolytic viruses (OVs), known for their cancer-killing characteristics, also overturn tumor-associated defects in antigen presentation through the MHC class I pathway and induce protective neo-antitumor CD8 T cell responses. Nonetheless, …
View article: Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma
Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma Open
View article: Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin
Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin Open
MHC-I peptides are intracellular-cleaved peptides, usually 8-11 amino acids in length, which are presented on the cell surface and facilitate CD8+ T cell responses. Despite the appreciation of CD8+ T-cell antitumor im…
View article: MOESM4 of A new synthetic toll-like receptor 1/2 ligand is an efficient adjuvant for peptide vaccination in a human volunteer
MOESM4 of A new synthetic toll-like receptor 1/2 ligand is an efficient adjuvant for peptide vaccination in a human volunteer Open
Additional file 4. Transcriptome Granuloma Distal Edge (FPKM values).