Markus Ausserhofer

• University of Innsbruck

Non-canonical tumor-specific antigens (ncTSAs) can expand the pool of targets for cancer immunotherapy, but require robust and comprehensive computational pipelines for their prediction. Here, we present NovumRNA, a fully-automated Nextflow pipeline for predicting different classes of ncTSAs from patients' RNA sequencing data. We extensively valida...

Investigating tissue architecture is key to understanding tissue function in health and disease. While spatial omics technologies enable the study of cell transcriptomes within their native context, they often lack single-cell resolution. Deconvolution methods can computationally infer tissue composition from spatial transcriptomics data, but diffe...

The cellular and molecular heterogeneity of tumors is a major obstacle to cancer immunotherapy. Here, we use a systems biology approach to derive a signature of the main sources of heterogeneity in the tumor microenvironment (TME) from lung cancer transcriptomics. We demonstrate that this signature, which we called iHet, is conserved in different c...

An important challenge in the real-world management of patients with advanced clear-cell renal cell carcinoma (aRCC) is determining who might benefit from immune checkpoint blockade (ICB). Here we performed a comprehensive multiomics mapping of aRCC in the context of ICB treatment, involving discovery analyses in a real-world data cohort followed b...

Background Tumor-targeted therapy causes impressive tumor regression, but the emergence of resistance limits long-term survival benefits in patients. Little information is available on the role of the myeloid cell network, especially dendritic cells (DC) during tumor-targeted therapy. Methods Here, we investigated therapy-mediated immunological al...

The cellular and molecular heterogeneity of tumors is a major obstacle to cancer immunotherapy. Here, we use a systems biology approach to derive a signature of the main sources of heterogeneity in the tumor microenvironment (TME) from lung cancer transcriptomic data. We demonstrate that this signature, which we called iHet, is conserved in differe...

CD8 ⁺ T cell activation via immune checkpoint blockade (ICB) is successful in microsatellite instable (MSI) colorectal cancer (CRC) patients. By comparison, the success of immunotherapy against microsatellite stable (MSS) CRC is limited. Little is known about the most critical features of CRC CD8 ⁺ T cells that together determine the diverse immune...

Somatic mutations and gene fusions can produce immunogenic neoantigens mediating anticancer immune responses. However, their computational prediction from sequencing data requires complex computational workflows to identify tumor-specific aberrations, derive the resulting peptides, infer patients' Human Leukocyte Antigen (HLA) types, and predict ne...