Our working group uses next generation sequencing (NGS) and bioinformatic analysis of single-cell transcriptome data (scRNA), whole exome sequencing (WES), genome sequencing (WGS) and metagenome sequencing (MGS) to investigate tumor plasticity and the corresponding “tumor environment”. The latter includes immune cells, blood vessels and associated microbes.


Through mutations, cancer cells not only change their gene expression profile and their cell differentiation within the entire cell complex but also influence their environment inside the stroma (immune cells and blood vessels), as well as the microbial colonisation (metagenome). Our research group examines and bioinformatically evaluates clinical samples of non-lung carcinomas (NSCLC), colorectal carcinomas (CRC) and pancreatic carcinomas (PDAC) using single-cell analyses (scRNA-sequencing). In addition, the mutation load or tumor mutation burden (TMB) and parameters for the absence of DNA repair mechanisms, the microsatellite instability (MSI) and the homologous recombination deficiency (HRD) are calculated from high-resolution tumor and respective normal data.

Another exciting project of ours deals with the microbial colonisation of tumors and the response to new immunotherapies. For this purpose, all microbes and viruses in the tissue are recorded by means of NGS metagenome analyses and afterwards evaluated bioinformatically.

Research Team Members

Gerold Untergasser, PD. PhD

Project Leader

Agnieszka Martowicz, PhD

Data Analyst

Our aim is to further comprehend the molecular factors behind the onset of cancer.


Selected Publications

  • Borjan, B., Kern, J., Steiner, N., Gunsilius, E., Wolf, D. & Untergasser, G. Spliced XBP1Levels Determine Sensitivity of Multiple Myeloma Cells to Proteasome Inhibitor Bortezomib Independent of the Unfolded Protein Response Mediator GRP78. Frontiers in oncology, 22;9:1530. (2020).
  • Steiner, N., Jöhrer, K., Plewan, S., Brunner-Véber, A., Göbel, G., Nachbaur, D., Wolf, D., Gunsilius, E. & Untergasser, G. The FMS like Tyrosine Kinase 3 (FLT3) Is Overexpressed in a Subgroup of Multiple Myeloma Patients with Inferior Prognosis. Cancers, 19;12(9):2341. (2020).
  • Pichler, R., Lindner, A. K., Compérat, E., Obrist, P., Schäfer, G., Todenhöfer, T.,Horninger, W., Culig, Z. & Untergasser, G. Amplification of 7p12 Is Associated with Pathologic Nonresponse to Neoadjuvant Chemotherapy in Muscle-Invasive Bladder Cancer. Am J Pathol, 190(2):442-452. (2020).
  • Kocher. F,, Puccini, A., Untergasser, G., Martowicz, A., Zimmer, K., Pircher, A., Baca, Y., Xiu, J., Haybaeck, J., Tymoszuk, P., Goldberg, R. M., Petrillo, A., Shields, A. F., Salem, M. E., Marshall, J. L., Hall, M., Korn, W. M., Nabhan, C., Battaglin, F., Lenz, H. J., Lou, E., Choo, S. P., Toh, C. K., Gasteiger, S., Pichler, R., Wolf, D. & Seeber, A. Multi-omic Characterization of Pancreatic Ductal Adenocarcinoma Relates CXCR4 mRNA Expression Levels to Potential Clinical Targets. Clin. Cancer Res., 14;28(22):4957-4967. (2022).

All Publications