News of the Institute of Computer Science Polish Academy of Sciences

Researchers from the Nencki Institute PAS, the University of Warsaw, and the Institute of Computer Science PAS, have developed the first comprehensive "Atlas” of regulatory areas active in gliomas of various degrees of malignancy, which revealed deregulation of mechanisms controlling gene expression and a new mechanism driving the invasion of malignant brain tumors. The research was published in Nature Communications on June 15, 2021.

The interdisciplinary project Symphony 3 entitled "Atlas of regulatory areas specific for the human brain - a new tool for discovering the pathways causing selected brain diseases" has been carried out by the teams of prof. Bożena Kamińska (Nencki Institute of Experimental Biology of the Polish Academy of Sciences), dr. hab. Bartosz Wilczyński (Faculty of Mathematics, Informatics and Mechanics, University of Warsaw), and dr. Michał J Dąbrowski (Institute of Computer Science of the Polish Academy of Sciences). The project was financed by the National Research Center (NCN).

The most important findings:

• Revealing the mechanisms regulating gene expression in benign and malignant gliomas.
• Predicting a new pathway for regulating gene expression related to glioma malignancy, and confirming that this pathway controls cell migration and invasiveness in glioblastoma cells.
• Creating and sharing an atlas of active regulatory regions in gliomas of various degrees of malignancy and in the brain [http://regulomics.mimuw.edu.pl/].

The PASIFIC Fellowship Programme is a unique opportunity for researchers who want to undertake state-of-the-art research in a dynamic scientific environment. It will enable scholars of all nationalities and across all scientific disciplines to establish their scientific independence and conduct ground-breaking research.
For 2 years, the fellows will be hosted at one of the institutes within the Polish Academy of Sciences (PAS), which is one of the most prestigious research institutions in Poland. They will have the freedom to choose their research area, research supervisor, host institute as well as secondment organisations best suited for their research and career development.
The PASIFIC Fellows will be offered a monthly allowance of approx. €2,500 net. Those, who decide to come to Poland together with their families, may be entitled to an additional family allowance. In addition, they will be granted a research budget of up to €93,000 per project.
Deadline: June 2021

More about PASIFIC Programme: https://pasific.pan.pl/call-1/

Potential Supervisors from the Institute of Computer Science of the Polish Academy of Sciences: Łukasz Dębowski, Włodzimierz Drabent, Jan Mielniczuk, Maciej Ogrodniczuk, Piotr Przybyła. More about supervisors you can find here: pasific.pan.pl/supervisors-from-institute-of-computer-science/

The Pan-Cancer project provides a turning point for further treatment of tumours. More that one thousand scientists from the entire world built to date the most detailed picture of tumours. Their studies were published last week in two articles in the Nature journal and in 4 other articles in Nature Communications and Biology Communications and report an almost complete picture of all tumours. These studies will enable individualised treatment for every patient and an earlier discovery of the tumours.

The Pan-Cancer Consortium analysed the complete genetic code for 2.658 tumours. On average, it was found that there are four to five driver mutations that are responsible for the tumour. These mutations are likely to become the point of attack of anti-tumour treatments and be personalised for each patient. A major focus in the investigations were the non-coding elements that occur in the regulatory regions of the genomes.

It was also possible to “carbon-date” the age of mutations. About 20% of them appear years or even decades prior to the tumour and thus offer a potential for very early diagnosis even before the tumour occurs.

Our employee, Visiting Professor Jan Komorowski, participates in the Pan-Cancer project and is a co-author of the six publications. The main contribution of his team is identification of significant mutations in the regulatory regions in genomes that has been achieved using advanced bioinformatics methods, including machine learning, applied to Big Data.

Rheinbay, E., Nielsen, M.M., Abascal, F. et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 578, 102–111 (2020). doi: 10.1038/s41586-020-1965-x,
Campbell, P.J., Getz, G., Korbel, J.O. et al. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020). doi: 10.1038/s41586-020-1969-6,
Carlevaro-Fita, J., Lanzós, A., Feuerbach, L. et al. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol 3, 56 (2020). doi: 10.1038/s42003-019-0741-7,
Reyna, M.A., Haan, D., Paczkowska, M. et al. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun 11, 729 (2020). doi: 10.1038/s41467-020-14367-0,
Paczkowska, M., Barenboim, J., Sintupisut, N. et al. Integrative pathway enrichment analysis of multivariate omics data. Nat Commun 11, 735 (2020). doi: 10.1038/s41467-019-13983-9,
Shuai, S., Abascal, F., Amin, S.B. et al. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nat Commun 11, 734 (2020). doi: 10.1038/s41467-019-13929-1

Professor Wojciech Penczek, Director of ICS PAS has been elected a Corresponding Member of the Polish Academy of Sciences. The 140 sesion of General Assembly of the Polish Academy of Sciences took plase on December 5. In accordance with the Regulations on the selection of Academy members, candidates for members should be distinguished by their special scientific achievements, environmental authority and good repute.

Congratulations!

Picture 1: Private Archive
Picture 2: Jarosław Deluga-Góra / PAS