Short Description
The Core Facility Genomics integrates advanced platforms for genome-wide expression, genome and methylome analyses, and cutting-edge spatial omics. These technologies allow the study of signaling pathways and cellular communication in healthy and pathological tissues. Device infrastructure includes: Nanostring GeoMX DSP, 10x Genomics Xenium In Situ, 10x Genomics Chromium Single Cell System, Illumina NextSeq 550, Affymetrix Gene Atlas Station, PyroMark Q24 Workstation, and RotorQ qPCR machines.
Contact Person
Univ.-Prof. Dr. Fritz Aberger
Research Services
DNA methylation analyses; global and spatial gene expression analyses (bulk, single-cell, and in situ); exome and genome sequencing; signal transduction analyses; multi-omic integration across genomic, epigenetic, and spatially resolved data.
Methods & Expertise for Research Infrastructure
The Core Facility Genomics supports national and international cooperation projects on molecular genetic, epigenetic, and cellular/biochemical analysis of diverse biological samples, including heterogeneous cancer and inflammatory tissues. The focus is on genome-wide and spatial profiling of mRNA expression at single-cell and subcellular resolution, epigenetic modifications such as DNA methylation in cancer cells, and DNA sequence analyses in biomedical research.
Equipment
Salzburg Cancer Research Institute
Department of Life Sciences
University Hospital Salzburg
Cancer Cluster Salzburg
University of Erlangen
University of Göttingen
German Cancer Research Center Heidelberg
University of Vienna
University of Ghent
Ludwig-Maximillian-University (LMU) Munich
University of Linz
Paracelsus Medical University (PMU), Salzburg
2014-2017
Fritz Aberger
Fonds zur Förderung der wissenschaftlichen Forschung: FWF P25629
https://www.fwf.ac.at
Hedgehog-EGFR Signaltransduktion im Basaliom
2008-2011
Fritz Aberger
Fonds zur Förderung der wissenschaftlichen Forschung: FWF P20652
https://www.fwf.ac.at
Targeting E-cadherin - Functional role of E-cadherin shedding in Helicobacter pylori-associated carcinogenesis
2012-2017
Silja Wessler
Fonds zur Förderung der wissenschaftlichen Forschung: FWF P_24074
https://www.fwf.ac.at
Cancer Cluster Salzburg
2017-2020
F. Aberger, J. Horejs-Hoeck, A. Risch, S. Wessler, C. Huber, R. Greil (SALK/PMU, SCRI)
Land Salzburg
https://www.cancercluster-salzburg.at
Epigenetics of Immunity in cancer (EPIC)
2019-2022
F. Aberger, J. Horejs-Hoeck
EU
https://www.plus.ac.at/biowissenschaften/der-fachbereich/arbeitsgruppen/aberger
BIOMED CENTER SALZBURG
2020-2023
F. Aberger
Land Salzburg
https://www.plus.ac.at/biowissenschaften
2024
Lahnsteiner A, Craig SJC, Karnali K, Weissensteiner B, McGrath B, Risch A, Makova KD
Methods in Enzymology 2024:695:159-191.
https://www.sciencedirect.com/science/article/pii/S0076687923003956?via%3Dihub
Disease-related blood-based differential methylation in cystic fibrosis and its representation in lung cancer revealed a regulatory locus in PKP3 in lung epithelial cells.
2022
Schamschula, E., Lahnsteiner, A., Assenov, Y., Hagmann, W., Zaborsky, N., Wiederstein, M., Strobl, A., Stanke, F., Muley, T., Plass, C., Tümmler, B., Risch, A.
Epigenetics. 2022 Aug;17(8):837-860.
https://www.tandfonline.com/doi/full/10.1080/15592294.2021.1959976
Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium.
2017
Feng Y, Wang Y, Liu H, Liu Z, Mills C, Han Y, Hung RJ, Brhane Y, McLaughlin J, Brennan P, Bickeboeller H, Rosenberger A, Houlston RS, Caporaso NE, Teresa Landi M, Brueske I, Risch A, Ye Y, Wu X, Christiani DC, Amos CI, Wei Q.
Scientific Reports 2017 Apr 11;7(1):825
DOI: 10.1038/s41598-017-00850-0.
Helicobacter pylori Employs a Unique Basolateral Type IV Secretion Mechanism for CagA Delivery.
2017
Tegtmeyer N, Wessler S, Necchi V, Rohde M, Harrer A, Rau TT, Asche CI, Boehm M, Loessner H, Figueiredo C, Naumann M, Palmisano R, Solcia E, Ricci V, Backert S.
Cell Host & Microbe 2017 Oct 11;22(4): 552-560.e5
DOI: 10.1016/j.chom.2017.09.005.
Hedgehog-EGFR cooperation response genes determine the oncogenic phenotype of basal cell carcinoma and tumour-initiating pancreatic cancer cells
2012
Eberl M, Klingler S, Mangelberger D, Loipetzberger A, Damhofer H, Zoidl K, Schnidar H, Hache H, Bauer HC, Solca F, Hauser-Kronberger C, Ermilov AN, Verhaegen ME, Bichakjian CK, Dlugosz AA, Nietfeld W, Sibilia M, Lehrach H, Wierling C, Aberger F.
EMBO Molecular Medicine
DOI: 10.1002/emmm.201100201
Epidermal activation of Hedgehog signaling establishes an immunosuppressive microenvironment in basal cell carcinoma by modulating skin immunity
2020
Sandra Grund-Gröschke, Daniela Ortner, Antal B Szenes-Nagy, Nadja Zaborsky, Richard Weiss, Daniel Neureiter, Martin Wipplinger, Angela Risch, Peter Hammerl, Richard Greil, Maria Sibilia, Iris K Gratz, Patrizia Stoitzner, Fritz Aberger
Mol. Oncology
DOI: 10.1002/1878-0261.12758
Context-dependent modulation of aggressiveness of pediatric tumors by individual oncogenic RAS isoforms.
2021
Bauer J, Cuvelier N, Ragab N, Simon-Keller K, Nitzki F, Geyer N, Botermann DS, Elmer DP, Rosenberger A, Rando TA, Biressi S, Fagin JA, Saur D, Dullin C, Schildhaus HU, Schulz-Schaeffer W, Aberger F, Uhmann A, Hahn H.
Oncogene
DOI: 10.1038/s41388-021-01904-4
DNA Methylation Signatures Predicting Bevacizumab Efficacy in Metastatic Breast Cancer
2018
Gampenrieder SP, Rinnerthaler G, Hackl H, Pulverer W, Weinhaeusel A, Ilic S, Hufnagl C, Hauser-Kronberger C, Egle A, Risch A, Greil R..
Theranostics
doi: 10.7150/thno.23544