A5084751312- Cancer Immunotherapy and Biomarkers
- Gene expression and cancer classification
- Immune Cell Function and Interaction
- Bioinformatics and Genomic Networks
- Single-cell and spatial transcriptomics
- Immunotherapy and Immune Responses
- Colorectal Cancer Treatments and Studies
- Diabetes Management and Research
- Cancer Genomics and Diagnostics
- Immune cells in cancer
- CAR-T cell therapy research
- Cytokine Signaling Pathways and Interactions
- RNA modifications and cancer
- Adipose Tissue and Metabolism
- Inflammatory mediators and NSAID effects
- Cancer, Lipids, and Metabolism
- Genetic factors in colorectal cancer
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Cancer Cells and Metastasis
- Microbial Metabolic Engineering and Bioproduction
- Ferroptosis and cancer prognosis
- Advanced Proteomics Techniques and Applications
- Microfluidic and Capillary Electrophoresis Applications
- RNA Research and Splicing
Innsbruck Medical University
2016-2025
Universität Innsbruck
2016-2025
Institute of Bioinformatics
2021-2025
Austrian Drug Screening Institute (Austria)
2019
St. Jude Children's Research Hospital
2019
Institute for Molecular Medicine
2019
University Medical Center of the Johannes Gutenberg University Mainz
2019
Johannes Gutenberg University Mainz
2019
Rutgers, The State University of New Jersey
2019
Tyrolean Cancer Research Institute
2017-2018
The role of the adaptive immune response in controlling growth and recurrence human tumors has been controversial. We characterized tumor-infiltrating cells large cohorts colorectal cancers by gene expression profiling situ immunohistochemical staining. Collectively, immunological data (the type, density, location within tumor samples) were found to be a better predictor patient survival than histopathological methods currently used stage cancer. results validated two additional populations....
Abstract Summary: We have developed ClueGO, an easy to use Cytoscape plug-in that strongly improves biological interpretation of large lists genes. ClueGO integrates Gene Ontology (GO) terms as well KEGG/BioCarta pathways and creates a functionally organized GO/pathway term network. It can analyze one or compare two genes comprehensively visualizes grouped terms. A one-click update option allows automatically download the most recent GO/KEGG release at any time. provides intuitive...
The Cancer Genome Atlas revealed the genomic landscapes of human cancers. In parallel, immunotherapy is transforming treatment advanced Unfortunately, majority patients do not respond to immunotherapy, making identification predictive markers and mechanisms resistance an area intense research. To increase our understanding tumor-immune cell interactions, we characterized intratumoral immune cancer antigenomes from 20 solid cancers created Immunome (https://tcia.at/). Cellular...
The role of tumor-infiltrating immune cells in the early metastatic invasion colorectal cancer is unknown.
Abstract Summary: A versatile, platform independent and easy to use Java suite for large-scale gene expression analysis was developed. Genesis integrates various tools microarray data such as filters, normalization visualization tools, distance measures well common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, support vector machines. The results of the are transparent across all implemented methods enable outcome...
We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry, immunohistochemistry data.quanTIseq analysis 8000 revealed that cytotoxic T infiltration is more strongly associated with activation CXCR3/CXCL9 axis than mutational load deconvolution-based scores have prognostic value several solid cancers. Finally, we used show how kinase...
Purpose The prognosis of patients with colorectal cancer has sometimes proved uncertain; thus, the prognostic significance immune criteria was compared that tumor extension using American Joint Committee on Cancer/International Union Against Cancer–TNM (AJCC/UICC-TNM) staging system. Patients and Methods We studied intratumoral infiltrates in center invasive margin 599 specimens stage I to IV cancers from two independent cohorts. analyzed these findings relation degree frequency recurrence....
Many patients who present with early-stage colorectal cancer (International Union Against Cancer TNM stages I and II) are nevertheless at high risk of relapse. We hypothesized that intratumoral immune reaction could influence their prognosis.The was investigated in 29 tumors by large-scale real-time polymerase chain reaction. Cytotoxic (CD8) memory (CD45RO) T cells were quantified immunohistochemical analyses tissue microarrays from the center (CT) invasive margin (IM) 602 two independent...
Insulin resistance, a major factor in the pathogenesis of type 2 diabetes mellitus, is due mostly to decreased stimulation glycogen synthesis muscle by insulin. The primary rate-controlling step responsible for decrease not known, although hexokinase activity and glucose transport have been implicated.
Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis therapy. Specifically, whole-exome using next-generation (NGS) is gaining popularity the human genetics community due moderate costs, manageable data amounts straightforward interpretation of analysis results. While and, near future, whole-genome are becoming commodities, still poses significant challenges led...
Background After the 2002/2003 severe acute respiratory syndrome outbreak, 30% of survivors exhibited persisting structural pulmonary abnormalities. The long-term sequelae coronavirus disease 2019 (COVID-19) are yet unknown, and comprehensive clinical follow-up data lacking. Methods In this prospective, multicentre, observational study, we systematically evaluated cardiopulmonary damage in subjects recovering from COVID-19 at 60 100 days after confirmed diagnosis. We conducted a detailed...
Human mesenchymal stem cells (MSC) with the capacity to differentiate into osteoblasts provide potential for development of novel treatment strategies, such as improved healing large bone defects. However, their low frequency in marrow necessitate ex vivo expansion further clinical application. In this study we asked if MSC are developing an aberrant or unwanted way during long-term cultivation and artificial conditions exert any influence on cell maintenance. To address question first...
Aging is a multifactorial process where deterioration of body functions driven by stochastic damage while counteracted distinct genetically encoded repair systems. To better understand the genetic component aging, many studies have addressed gene and protein expression profiles various aging model systems engaging different organisms from yeast to human. The recently identified small non-coding miRNAs are potent post-transcriptional regulators that can modify up several hundred target genes...
SUMMARY The Cancer Genome Atlas revealed the genomic landscapes of common human cancers. In parallel, immunotherapy with checkpoint blockers is transforming treatment advanced As only a minority patients responsive to blockers, identification predictive markers and mechanisms resistance subject intense research. To facilitate understanding tumor-immune cell interactions, we characterized intratumoral immune cancer antigenomes from 20 solid cancers, created Immunome ( http://tcia.at )....
A role for the immune system in controlling progression of solid tumors has been established several mouse models. However, effect responses and tumor escape on patient prognosis context human cancer is poorly understood. Here, we investigate cellular molecular parameters that could describe situ colorectal according to clinical metastatic lymph node or distant organ invasion (META- META+ patients). Primary samples carcinoma were analyzed by integrating large-scale phenotypic (flow...
Abstract The cancer immunoediting hypothesis postulates a dual role of the immune system: protecting host by eliminating tumor cells, and shaping editing its genome. Here, we elucidate impact evolutionary immune-related forces on in mouse model for hypermutated microsatellite-instable colorectal cancer. Analyses wild-type immunodeficient RAG1 knockout mice transplanted with MC38 cells reveal that upregulation checkpoint molecules infiltration Tregs are major escape mechanisms. Our results...
Non-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with diverse immune infiltration patterns, which has been linked to therapy sensitivity and resistance. However, full understanding of how phenotypes vary across different patient subgroups lacking. Here, we dissect the NSCLC tumor microenvironment at high resolution integrating 1,283,972 single cells from 556 samples 318 patients 29 datasets, including our dataset capturing low mRNA content. We stratify into...