Research Community Programs


SciLifeLab Research Community Programs (RCPs)

To facilitate internationally competitive, cutting-edge collaborative research across Sweden, SciLifeLab supports seven Research Community Programs (RCPs) – networks that connect top researchers with each other and with the SciLifeLab infrastructure.

The aims of the RCPs are:

  • to bring together a critical mass of scientific expertise across several departments and universities in Sweden on a particular theme or topic,
  • to form new links between infrastructures and researchers,
  • to engage established and young PIs to combine forces and work together in multidisciplinary and national collaborations.

The seven RCPs have been selected through an open call process and are granted three-year funding from SciLifeLab for coordination, scientific interaction and community building around their respective research areas. During this time, all RCPs will remain as open communities for including new qualified members and new technologies. PIs from any Swedish university are eligible to participate in one or more SciLifeLab RCP relevant to their research focus.

Starting date: 2019-01-01

 

Biology of Molecular Interactions

Coordinating PI: Alexey Amunts
Co-coordinating PI:
Ilaria Testa
Number of participating PI’s at start:
8
Affiliation of key participants:
Stockholm University; KTH Royal Institute of Technology; Gothenburg University; Karolinska Institute; Lund University; Umeå University; Uppsala University
Contact: molecular.interactions@scilifelab.se; Twitter account: @SciLifeLab_BMI

The program for Molecular Interactions is established to account for the complex dynamics of the cellular phenomena and to explore a therapeutic potential of studied macromolecules. The program brings together 23 research groups complemented by molecular biology orientated facilities including cryo-EM, super-resolution imaging, protein production, proteomics and drug discovery that set up to provide the needed research infrastructure. To further develop technological innovations and support translational opportunities, the program bridges partnerships with the MAX IV laboratory and leading pharma companies AstraZeneca and Sobi. Taken together this provides a promising environment for conducting fundamentally important research and training.

 

The Human Protein Atlas

Coordinating PI: Mathias Uhlén
Co-coordinating PI: Cecilia Lindskog
Number of participating PI’s at start: 9
Affiliation of key participants:
KTH Royal Institute of Technology, Uppsala University; Chalmers University of Technology; Karolinska Institute; Lund University
Contact: mathias.uhlen@scilifelab.se

The Human Protein Atlas (HPA) program is an effort to map all human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow free exploration of the human proteome (1). HPA is part of various international initiatives (2) and it involves SciLifeLab groups at KTH, KI, SU, Uppsala University, Lund University and Chalmers. The program has contributed to several thousands of publications in the field of human biology and disease and was recently selected by the organization ELIXIR as a core database of fundamental importance for the life science community. The Protein Atlas consists of three separate parts, each focusing on a particular aspect of the genome-wide analysis of the human proteins; the Tissue Atlas (3), the Cell Atlas (4) and the Pathology Atlas (5).

References
1. Uhlen et al (2010). Towards a knowledge-based human protein atlas. Nature biotechnology. 28, 1248
2. Uhlen et al (2016). A proposal for validation of antibodies. Nature Methods. 13: 823-7
3. Uhlen et al (2015). Tissue-based map of the human proteome. Science 347: 1260419
4. Thul et al (2017). A subcellular map of the human proteome. Science 356 (6340): eaal3321
5. Uhlen et al (2017). A pathology atlas of the human cancer transcriptome. Science 357 (6352)

 

Large-scale clinical genomics and complex diseases

Coordinating PI:  Richard Rosenquist Brandell
Co-coordinating PI: To be announced soon
Number of participating PI’s at start: 11
Affiliation of key participants: Karolinska Institute; Gothenburg University; Karolinska University Hospital; KTH Royal Institute of Technology; Linköping University; Lund University; Lund University Hospital; Umeå University Hospital; Uppsala University; Uppsala University Hospital; Örebro University; Örebro University Hospital
Contact: info@genomicmedicine.se

In this SciLifeLab Research Community Program, we will bring together researchers from all over Sweden working on large-scale genomics as a way to understand the causes of complex genetic diseases (e.g. cardiovascular, metabolic, neurological, autoimmune, allergic and psychiatric diseases) as well as to help improve treatment. Our primary goal is to connect the community to take the next step for complex diseases in precision medicine. This is a joint program between the Genomic Medicine Sweden (GMS) initiative and the Genomic Aggregation Project in Sweden (GAPS). These initiatives have worked separately up to this point, but there are clear advantages to combining efforts. The goal of GMS is to develop new infrastructures within Swedish healthcare enabling clinical implementation of genomic medicine for individualized diagnosis and treatment, i.e. precision medicine. Ultimately, GMS will improve healthcare, strengthen Swedish research, and provide a foundation for innovation and collaboration with the private sector. We will build upon the infrastructures already existing within SciLifeLab for high-throughput sequencing (NGI/Clinical Genomics) and bioinformatics (NBIS). In the past 3 years, GAPS has brought together research groups from across Sweden who study the genetic basis of common diseases. We have aggregated existing genomic data from over 100,000 Swedes and have deep connections to groups doing similar work across Europe but especially in the Nordic countries. The primary focus of GMS is rare diseases, cancer, and infectious diseases. Together with GAPS and the Swedish community working on complex diseases, the next step for GMS will be to extend the scope and also include complex diseases, with the objective to bring precision medicine to the clinic.

More about Genomic Medicine Sweden (GMS)  and  Genomic Aggregation Project in Sweden (GAPS)
If you are interested to join the Large-scale clinical genomics and complex diseases community program, please contact info@genomicmedicine.se.

 

Human Cell Atlas and Spatial Omics Profiling

Coordinating PI: Joakim Lundeberg
Co-coordinating PI:
Emma Lundberg
Number of participating PI’s at start:
5
Affiliation of key participants:
KTH Royal Institute of Technology; Karolinska Institute; Stockholm University; Uppsala University
Contact: joakim.lundeberg@scilifelab.se

The RCP project is organized around Human Developmental Cell Atlas initiative, located and managed at SciLifeLab. The Human Developmental Cell Atlas procures human fetal samples and process them according to the highest ethical and technical standards; performs single cell RNA-seq and spatial analyses on these samples; performs computational analyses to discover cell types, model their activity, build the 3D atlas, and store and disseminate the data; ensure that all ethical, experimental and computational procedures are aligned and integrated with the international Human Cell Atlas. In particular this RCP focus’ on assembling expertise at Swedish Universities for analysis and annotation of developmental tissue from brain, lung and heart. The consortium aims to accelerate research into human biology and disease, and strengthen Swedish science by building on our very strong position in single-cell genomics, proteomics and infrastructures.

 

Aquatic Microbiome Research Initiative

Coordinating PI: Stefan Bertilsson
Co-coordinating PI: Rachel A Foster
Number of participating PI’s at start: 6
Affiliation of key participants: Uppsala University; Stockholm University; Chalmers University of Technology; Gothenburg University; KTH Royal Institute of Technology;  Linnaeus University; Swedish University of Agricultural Sciences; Umeå University
Contact: Stebe@ebc.uu.se

Aquatic Microbiome Research Initiative (AMRI) bring together Swedish researchers and technology competence centers in a collaborative effort to advance our understanding of one of the earth’s largest biomes: the aquatic microbial world. Activities within AMRI are focused on the following broader themes, each led by a coordinator: microbial biogeography across and within aquatic biomes (Jarone Pinhassi), functional diversity (Anders Andersson), microbial interactions and evolution (Rachel A Foster) and microbes as ecosystem engineers (Stefan Bertilsson). Planned AMRI activities include an annual ‘All Hands’ meeting, quarterly workshops on specific technologies and topics such as single cell analyses, advanced isotope analyses and imaging, envioronmental genomics and metabolomics. We will also enable short-term student/postdoc research exchanges, promote the initiation of collaborative joint pilot experiments, and build platforms for shared data analysis, protocols and best practices. The long-term goal is to coordinate research on the organization and functioning of microbial landscapes and provide an active network for expanding Swedish research beyond regions or local laboratories. AMRI is an open platform and new researchers are encouraged to contact coordinators and/or AMRI project assistant, Caroline Littlefield Karlsson (caroline.littlefieldkarlsson@lnu.se), for more information.

References
Bunse, C. and J. Pinhassi (2017). Marine bacterioplankton seasonal succession dynamics. Trends in Microbiology. 25(6):464-505
Hugerth et al (2015). Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biology 16:e279
Smith et al (2017). Microbial formation of labile organic carbon in Antarctic glacial environments. Nature Geoscience.10(5): 356-359
Bravo et al (2017). Molecular composition of organic matter controls methylmercury formation in boreal lakes. Nature Communications. 8:e14255

 

Phenotypic Drug Discovery in Human Disease

Coordinating PI: Oscar Fernández-Capetillo
Co-coordinating PI: Karin Forsberg Nilsson
Number of participating PI’s at start: 8
Affiliation of key participants: Lund University; Uppsala University; Gothenburg University; Karolinska Institute; KTH Royal Institute of Technology
Contact: oscar.fernandez-capetillo@ki.se

The low success rate of drug approvals despite the ongoing enormous technological developments calls for an urgent improvement of the drug discovery workflow. Disease-relevant models, phenotypic screening and target ID technologies, are three key aspects in this process. However, several challenges such as access to biological starting points, difficult assay development, or the high cost of target ID, often hamper the forward development of efficient drug discovery. To address these challenges, and to impact precision medicine in a collaborative and efficient manner, we have initiated the the Phenotypic Drug Discovery in Human Disease RCP. Through annual meetings, workshops and lab exchange programs, we will engage research groups and facilities in areas comprising (i) disease-relevant models, (ii) assay design and development of phenotypic screens, and (iii) chemical proteomics technologies and alternative target ID methods, to ultimately improve the state-of-the-art drug development workflow and increase the number of drugs successfully approved.

 

Swedish Tumor Microenvironment (STorM) Program

Coordinating PI: Kristian Pietras
Co-coordinating PI:
Anna Dimberg
Number of participating PI’s at start:
5
Affiliation of key participants: 
Lund University; Uppsala University; Karolinska Institute; KTH Royal Institute of Technology; Linköping University Hospital; Stockholm University; Norrlands University Hospital
Contact: kristian.pietras@med.lu.se

Cancer arises as a consequence of a series of genetic alterations in any of the more than 200 specialized cell types of our body. Through these genetic changes, cancer cells may evade the strict control of cell division and form a tumor. Recent studies highlight the importance of communication between cancer cells and their surrounding tissue (the tumor microenvironment) to enable a tumor to develop into a clinically manifested disease. Various cell types in the tumor microenvironment provide a range of factors that promote the initiation of cancer, fuel the growth of malignant cells, facilitate the spread of the disease and make tumors resistant to treatment. The Swedish Tumor Microenvironment (STorM) network leverages the power of thirty internationally leading research groups in the field spanning across the entire country. The overarching aim of the program is to identify novel communication pathways within the tumor microenvironment that can be exploited as cancer drug targets and biomarkers. The program will foster cross-disciplinary studies which optimally combines experimental studies in cell and animal models, correlative analyses of clinical samples, and cutting-edge technology.

Further details

Each RCP has been granted 1 MSEK per year for three years. The funding, including both national infrastructure support and host university / SFO funding, should cover network coordination as well as collaborative costs and not be used for actual research funding.

Members of SciLifeLab RCPs will not get priority access to national infrastructure services, but should closely interact with infrastructure scientists, engage in method development, share data, expertise etc.

 


Contact

For any questions about the SciLifeLab RCPs, please contact Alice Sollazzo, Project coordinator:
rcps@scilifelab.se