Mission

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.

Research

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

Agnieszka Martowicz, PhD

Project Leader

Agnieszka.Martowicz@i-med.ac.at

Gerold Untergasser, PD. PhD

Cooperation partner

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

Publications

Selected Publications

  • Vidal-Calvo E. E., Martin-Salazar A., Choudhary S., Dagil R., Raghavan S. S. R., Duvnjak L., Nordmaj M. A., Clausen T. M., Skafte A., Oberkofler J., Wang K., Agerbæk M. Ø., Løppke C., Jørgensen A. M., Ropac D., Mujollari J., Willis S., Garcias López A., Miller R. L., Karlsson R. T. G., Goerdeler F., Chen Y. H., Colaço A. R., Wang Y., Lavstsen T., Martowicz, A., Nelepcu I., Marzban M., Oo H. Z., Ørum-Madsen M. S., Wang Y., Nielsen M. A., Clausen H., Wierer M., Wolf D., Gögenur I., Theander T. G., Al-Nakouzi N., Gustavsson T., Daugaard M. & Salanti A. Tumor-agnostic cance therapy using antibodies targeting oncofetal chondroitin sulfate. Nat Commun., 15(1):7553. (2024).
  • Salcher S., Heidegger I., Untergasser, G., Fotakis G., Scheiber A., Martowicz, A., Noureen A., Krogsdam A., Schatz C., Schäfer G., Trajanoski Z., Wolf D., Sopper S. & Pircher A. Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues. Heliyon, 10(7):e28358. (2024).
  • Salcher, S., Sturm, G., Horvath, L., Untergasser, G., Kuempers, C., Fotakis, G., Panizzolo, E., Martowicz, A., Trebo, M., Pall, G., Gamerith, G., Sykora, M., Augustin, F., Schmitz, K., Finotello, F., Rieder, D., Perner, S., Sopper, S., Wolf, D., Pircher, A. & Trajanoski, Z. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell, 40(12):1503-1520.e8. (2022).
  • Pichler R., Siska P. J., Tymoszuk P., Martowicz, A., Untergasser, G., Mayr R., Weber F., Seeber A., Kocher F., Barth D. A., Pichler M. & Thurnher M. A chemokine network of T cell exhaustion and metabolic reprogramming in renal cell carcinoma. Front Immunol, 14:1095195. (2023).
  • 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., 28(22):4957-4967. (2022).

All Publications

www.pubmed.ncbi.nlm.nih.gov