Systems Genomics - Heinäniemi lab

Research group

Our research is focused on elucidating disease mechanisms that are related to aberrant regulation of cell states. Genome-wide technologies can reveal the collective activity of the genome, even at single cell resolution. These readouts capture the repertoire of cell states in tissues. We study regulatory mechanisms that control changes in cell states, such as those active during cell differentiation or in response to cellular stress.

Based on systems biology, bioinformatics and machine learning, we aim to decipher key regulatory circuits formed by protein and RNA molecules from different genomics datasets.

Research group description

Cells represent the fundamental unit of life. Within tissues, cells are in constant interaction with their environment. Our goal is to elucidate disease mechanisms that are related to aberrant regulation of cell states. We develop computational models based on systems biology and data analysis tools with bioinformatics and machine learning methods suitable for integrating different types of genomics data or combining datasets across studies. We apply them in our own research that utilizes large omics datasets and collect new genomics data from cell models and human studies.

Childhood acute lymphoblastic leukemia: The most common type of cancer in children develops as a consequence of arrested cell differentiation of early lymphoid precursor cells. We study changes in the gene regulatory network across different leukemia subtypes. To translate genomics into clinical practice, we also develop data analysis tools that allow determining at unprecedented resolution the alterations in cancer cells.

Cell-cell interaction in disease development: In addition to regulatory networks that operate inside cells, we study how these interactions extend to tissue level. Inflammation and cellular stress influence cell states within a tissue. We are addressing the question what role changes in cell-cell-interactions have in this process. By characterizing such tissue-level regulatory circuits, we can discover new therapy targets that would enable reverting the changes in cell states at early stage during disease progression. Later at advanced disease state it would be more challenging to repair tissue damage. We are focusing on the role of endothelial cells and macrophages in context of coronary artery disease development. Cell-cell interactions have an important role also in cancer.

A central future goal in our research is to connect the molecular and cell-interaction levels together, in order to better model the dynamics of cell state changes.

Recent publications:

Nature 2020. Signalling input from divergent pathways subverts B cell transformation https://pubmed.ncbi.nlm.nih.gov/32699415/

Cancer Cell 2020. Immunogenomic Landscape of Hematological Malignancies. https://pubmed.ncbi.nlm.nih.gov/32649887/

Sci Rep 2020. Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia. https://pubmed.ncbi.nlm.nih.gov/32029838/

Keywords

Group members - UEF

Other group members

  • Aleksi Kokko, BSc
    Aleksi Kokko, BSc
  • Minna Voutilainen, BSc
    Minna Voutilainen, BSc
  • Sini Hakkola, BSc
    Sini Hakkola, BSc
  • Mikko Sipola
    Mikko Sipola
  • Sanni Moisio
    Sanni Moisio