A geneticist by training with some computational biology experience, Katja brings a wealth of experience to the role of Research Director of the FIMM Technology Centre. Here, Dr Kivinen describes her background:

I did my undergraduate degree in genetics at the University of Helsinki. My Master’s thesis focused on the characterization of mutations in the SEC1 gene which has an important role in the budding yeast protein secretion pathway. After graduation, I became really interested in an emerging field called bioinformatics and moved to Cambridge to do my PhD at EMBL-EBI. My supervisor, Dr Alvis Brazma, led a growing team that built databases and tools for gene expression analysis. My PhD focused on using the available gene expression profiles for two types of yeast to cluster genes and to identify potential regulatory signals shared between genes within each cluster. 

Following a joint PhD from EMBL-EBI and the University of Cambridge, I was highly interested in studying human genetics. To pursue this, I moved to Professor Juha Kere’s group at the Karolinska Institute in Stockholm, Sweden. Here, I led research in preeclampsia and provided general analysis support across a dozen other medical conditions. My tasks included automating repetitive data processing steps, performing linkage, association, gene expression, and sequence analysis, and training others in using software and databases. 

After two years at Karolinska, I returned to Cambridge and joined the malaria programme led by Professor Dominic Kwiatkowski at the Wellcome Sanger Institute (WSI) where I worked for eight years. I led genome-wide genotyping and sequencing of human malaria samples, and acted as a human interface between the lab and computational teams. Working at the Sanger Institute was an eye-opening experience for me. It taught me a lot about genomics technologies (genotyping and sequencing analysis of thousands of samples), malaria biology, data production, analysis and troubleshooting, and the management of large-scale projects. 

Once the human genotyping and sequencing neared completion, I began to look for new challenges and joined the University of Cambridge as a research manager for three newly founded centers in cardiovascular research led by Professor Martin Bennett and Nick Morrell. We started from scratch, with an initial sixty people interested in cardiovascular research. During my five years at the university, the network increased to over five hundred people. I was responsible for budgets and finances, recruitment of students and research fellows, communications (including mailing lists, newsletters, website and social media channels, and public engagement), and annual reports to funders. Part of my role was to identify and connect researchers with shared interests, and I organized meetings and events of all sizes.

Last year, I was looking forward to getting started with the building work for the Cambridge Heart & Lung Research Institute when I heard that Prof Janna Saarela had been appointed as the new Director of NCMM in Oslo. I showed my interest in her previous position and applied as the Head of FIMM Technology Centre - and the rest is history.   

Can you describe your research, and how you became interested in the field?

I became interested in preeclampsia during my years at the Karolinska Institute. Some of my friends had experienced complications during pregnancy and one lost a baby during preterm delivery to treat eclampsia. Professor Hannele Laivuori, who was also a postdoc at the time at Karolinska, had collected blood samples from a noteworthy set of families with early-onset and severe preeclampsia across multiple generations.  

Due to family reasons, I had to shorten my postdoctoral position, but kept my research interest in preeclampsia alive and continued to collaborate with Professor Laivuori while at WSI and the University of Cambridge. Together with an inspiring set of researchers, we founded a national preeclampsia consortium (FINNPEC) in 2007 and later joined an international effort (InterPregGen) to study preeclampsia across Europe, as well as in Uzbekistan and Kazakhstan. InterPregGen has published a landmark paper on the genetic basis of preeclampsia in children who were born through preeclamptic pregnancies. Another paper focusing on mothers is also in the pipeline. FINNPEC has completed genome-wide studies of preeclamptic mothers, alongside their partners and children. We and colleagues plan to analyse the data collected shortly. It will be exciting to see whether we can identify genetic factors in fathers that increase the risk of preeclamptic pregnancy.

Can you describe the FIMM Technology Centre and its core units? 

The FIMM Technology Centre (TC) is part of the University of Helsinki and receives partial funding and support towards salaries and equipment purchases through the Helsinki Institute of Life Science (HiLIFE). TC is open to all (both academic and commercial entities) and operates on a ‘first come-first served’ basis, however there are projects in collaboration with the hospital that include cancer-patient samples and these are prioritized. The Centre is the descendent of the Finnish Genome Center, which previously provided genomics services. Over the past years, other services have been set up to support the research conducted at FIMM, and some of these have grown into self-sustaining core units after the surrounding research community became more aware of them. 

Which biomedical research services does the Centre offer? 

The TC offers services such as genomics (sequencing, genotyping), transcriptomics (RNA-seq), metabolomics (+ lipidomics), high-throughput drug sensitivity screening, high content imaging and digital pathology. Also, the centre has a core unit focusing on the development and optimization of single cell technologies. Another unit focuses on high-quality sample preparation from challenging sources (e.g. EV, FFPE samples). Since data processing and analysis are vital to all core units, the TC has a dedicated in-house IT-team that provides expert support as well as bioinformaticians embedded in most core units. Lastly, the Centre is the proud part-owner of a national hematological biobank. Please do contact us if you study leukemia, for example! 

How does the infrastructure support FIMM’s research and its grand challenges?

Currently, FIMM has four Grand Challenge programmes: Human genomics for health & disease; Digital diagnostics for precision medicine; Functional precision medicine in cancer; Data science in population health. 

The TC’s core purpose is to provide state-of-the-art infrastructure and expert staff in support of cutting-edge research. Having a range of infrastructures available in-house allows research groups at FIMM to quickly test new ideas to see what works best. Some TC core units are closely tied to specific FIMM grand challenges and local hospital projects whilst others have a wider remit. For example, HTB is the national provider of drug sensitivity screening and HCA is the only provider of high-content imaging in Finland. 

We have regular discussions with FIMM research group leaders to ensure that TC services align with their needs. In 2019, we surveyed FIMM and local researchers on the types of metabolomics services they would be interested in. Right now, we are surveying the needs of two national initiatives – FINNGEN and iCAN – so that we can serve them better as well.

Can you describe your role at FIMM Technology Centre?

I want to provide mentorship, leadership, minimize bureaucracy, and build trust. I really want to provide growth and collaboration opportunities not just within FIMM but across the University of Helsinki. Also, I want to identify synergies and develop partnerships across the University of Helsinki and with other universities. I want to hire the best and give them space, time, and resources to succeed in their profession. Finally, I want to make FIMM TC the best workplace it can be.

Can you tell me about some of the actual projects taking place at the FIMM Technology Centre?

The TC has recently started a project for a Finnish hospital to help them dissect how different combinations of mutations affect the sensitivity of cancer cells to available drugs. 

The pilot phase will focus on leukemia and we hope to expand the project to cover other types of cancer. Also, the Centre is continuously developing new methods and is currently involved in several international benchmarking exercises. These do not usually cover full costs but are important to give their research teams opportunities to test that their protocols produce high-quality data and to raise awareness of the TC’s services.

Does the Centre collaborate with other infrastructures in Finland and in other countries? 

The TC core units collaborate closely with similar units across Helsinki, as well as with other Universities in Finland. Local collaboration brings clear benefits through, for example, purchasing equipment service contracts together at a discounted price, exchanging best practices, sharing software for project management and invoicing, and by providing complementary services and expanding the shared user base. Biocenter Finland (BF) provides national coordination of research infrastructures. Most TC core units are members of BF and some act as national leaders of their infrastructure network. At the European level, TC core units are members in several ESFRIs: BBMRI, EATRIS, Elixir, EU-Openscreen, and Euro-bioimaging. FIMM also acts as the national node for EU-LIFE, and TC staff are active in relevant workgroups, for example IT and core facilities. Finally, TC core units are active in several Nordic frameworks. 

We are of course a member of the Nordic EMBL Partnership for Molecular Medicine and have recently applied for funding towards joint activities, which we have recently been awarded by NordForsk. Our genomics and single cell analytics units have also become active in the Nordic Alliance in Clinical Genomics (NACG). 

Which future projects are there in the pipeline at FIMM Technology Centre and what are the goals of the Centre in terms of development (from a technical and translational perspective)?

The TC focuses widely on cancer and plans to expand in cancer research in the near future. In addition, genomics is a very important research area in Finland and also connects the different centres in the Nordic countries. Future projects also include studying gender differences in health and disease as well as sex-specific transcription. The TC strives for stronger clinical partnerships, accreditation of some services and translating research to patient benefits.  

Dr Kivinen was also appointed as HiLIFE Deputy Director for Research Infrastructures (RI) in June 2020. 

The role will involve supporting the HiLIFE Director in further development of the HiLIFE infrastructure strategy and programme. Tasks here will include developing operations, communication and collaboration of HiLIFE infrastructure platforms and Life Science Research Infrastructures (LSRIs). The Deputy Director for RIs is a member of the HiLIFE management team and also represents HiLIFE in infrastructure related committees at the University and in Biocenter Finland and other national RI collaboration forums.

Learn more about the FIMM Technology Centre and its core units. 

Visit Dr Kivinen's page on the FIMM website to learn more about her research activities.