FIMM received significant infrastructure funding for developing single cell analytics services and eSISU
FIMM researchers together with their collaborators have received significant infrastructure funding from the Academy of Finland. Three separate projects were funded, two of them in the category of new initiatives and non-roadmap infrastructures. These two novel infrastructure projects are called “Infrastructure for Single Cell Capture and Processing (SC-infra)” and “eSISu – eInfrastructure of Finnish Sequence Data”. In addition, FIMM received 44 000 € for coordination activities of BBMRI.fi, Finland’s biobank roadmap infrastructure.
Single cell analytics have huge scientific potential
The Infrastructure for Single Cell Capture and Processing (SC-infra) received funding for three years. Total investment to this novel infrastructure, including the share of the host universities, is 1 million €. Molecular profiling of individual cells is one of the key emerging fields of research. With the support of this funding, FIMM will purchase an equipment needed for capturing hundreds of single cells and processing them for subsequent sequencing-based analyses. Currently, averages of a large group of cells are typically measured, which can mask the unique characteristics that each cell has. Thus single cell analysis approaches are needed for detecting variation between seemingly similar cells originating from the same tissue or tumor.
Depending on the scientific question, genetic variation, expression levels (transcriptomics), methylation levels (epigenomics) and protein levels can all be of great interest. However, core units providing such services have been lacking in Finland.
There are many potential applications for single cell analysis. Overall, analysis of individual cells may provide valuable information on various diseases and developmental processes and also facilitate the discovery of novel cell subtypes. From the FIMM perspective, characterization of individual cancer cells is perhaps the most exciting application. Understanding better the tremendous tumour heterogeneity and the emerging subclones may give crucial clues to developing more efficient therapeutic strategies for a given patient.
The successful infrastructure application was done in collaboration with several partners from the Universities of Helsinki (Institute of Biotechnology, Research Programs Unit) and Turku. Services will be available both in the Meilahti and Viikki campuses and in Turku but each node will profile their services based on the existing expertise and local needs. It is important to provide the services locally since long deliveries of living cells compromises the quality of the results.
– We were extremely pleased when we heard that our application as a new initiative was prioritized as number one by the University of Helsinki, tells Pirkko Mattila, Senior Researcher at FIMM Techonology Centre who was the coordinator of the application.
With the help of the Academy of Finland funding FIMM can purchase an equipment needed for capturing single cells and processing their DNA or RNA for subsequent analysis. The institute will also hire a post- doctoral researcher for developing methodology and setting up services. The aim is to be able to serve customers already this spring.
– There seems to be great need and interest towards single cell analytics in the Finnish research community, and we are very eager to answer to this need, continues Janna Saarela, the director of the FIMM Technology Centre.
Infrastructure for Single Cell Capture and Processing aims to respond to this demand by developing methods and setting up national services for medium to high throughput capture, processing and analysis of individual cells. The services will be open for all researchers and will be provided in collaboration with existing national infrastructures of the Biocenter Finland infrastructure networks.
– To be able to develop single cell services further, our network has applied for the service to be included among the Biocenter Finland activities. The application is currently being evaluated by the Scientific Advisory Board of Biocenter Finland and the decision expected in a month, Pirkko Mattila continues.
– We at FIMM will concentrate on developing sequencing-based single cell analytics as well as bioinformatics needed to analyze the results. Our newest group leader Simon Anders is the chair of the proposed Biocenter Finland Single Cell Network and he will also be responsible for developing new bioinformatics methods for single cell analysis.
eSISU – storing valuable Finnish genomic data
SISu (Sequencing Initiative Suomi) is a data resource of Finnish genome sequences for researchers and clinicians. The current version of eSISu contains allele frequency data from more than 6000 individual’s exomes. The data are freely available at www.sisuproject.fi.
FIMM received nearly 300 000 € for further development of the eSISu infrastructure. The aim is to increase the total number of sequenced individuals to 35 000 and of sequence variants to 30 million. This would significantly improve the SISu database for the benefit of patients, clinicians and researchers.
– No international entity will have interest to integrate and harmonize all Finnish sequence data. The funding helps us to commit to store the valuable Finnish genomic data in Finland, says Aarno Palotie, the Principal Investigator behind the project.