Stem Cells and Genome Editing

Stem cell research is one of the most rapidly developing areas in biomedicine. The combination of genome editing with patient derived induced pluripotent stem cells (iPS cells) provides endless possibilities for cellular modelling of disease mechanisms and a platform for drug discovery. While the generation of human iPS cell lines has become a routine technology, it still requires special expertise, experience, and facilities. At the same time, know-how and technology development for differentiating cells to true models of human cells and tissues is becoming a bottleneck for taking full advantage of human iPS cell methodology. This is especially true for brain diseases, which form the largest societal burden of human diseases, and brain is the tissue composed of the most numerous cell types in the human body. These approaches can be effectively applied to study monogenic diseases using cell types that are otherwise not available for research. Furthermore, the approach is not limited to monogenic diseases but can also be used to study the functional effects of disease-associated genetic variants and the influence of environmental factors in defined cellular systems.

Genome editing toolbox is one of the most rapidly expanding set of ubiquitous research tools for life sciences based on CRISPR genome editing technology that was awarded Nobel prize in chemistry in 2020. Stem cells and genome editing platform aims to maintain and systematically build resources and services for in vitro and in vivo genome editing purposes as well as to maintain physical facilities enabling wide use of the resources across the Finnish biocenters.

Contact details

Nodes

Services

Recent user publications

Nodes

Node/Host University	Node PI
Biomedicum Stem Cell Center (BSCC), Hi-LIFE, UH Pluripotency unit , Neural unit	Diego Balboa, UH, diego.balboa@helsinki.fi
BioMediTech (BMT/MET), TAU	Katriina Aalto-Setälä katriina.aalto-setala@tuni.fi
Biocenter Kuopio Stem Cell Center, UEF	Riikka Martikainen riikka.martikainen@uef.fi
Finnish Genome Editing Center (FinGEEC), UH	Topi Tervonen topi.tervonen@helsinki.fi
Genome Editing Core (GEC) at the Turku Bioscience Centre (TBC)	Kari Kurppa kjkurp@utu.fi

UEF: University of Eastern Finland; UH: University of Helsinki; UTU: University of Turku; TAU: Tampere University; ÅAU: Åbo Akademi University.

Contact details

Platform Chair

Diego Balboa
diego.balboa@helsinki.fi

Services

Cell and reporter lines distribution

BF network offers a large range of human embryonic (hESCs), induced pluripotent stem cell (iPS cell) and iPS cell reporter lines with a complete service package including protocols for the stem cell maintenance and expansion, characterization data documentation and highly qualified technical support. BF network can assist with the selection of the appropriate stem cell line for your specific research needs.

Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center
BioMediTech, Tampere University
iPS Cells
Biocenter Kuopio
Stem Cell Center

Derivation and characterization of human iPS cell lines

BF network offers custom iPS cell line production service. Currently the methods for iPS cell generation are based on non-integrative technologies (Sendai virus, episomal vector and CRISPR activator) for reprogramming of somatic cells transduction. Reprogramming method is selected according to customer’s needs.

Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center
Biomeditech, Tampere University
iPS Cells
Biocenter Kuopio
Stem Cell Center

Training

BF network offers hands on laboratory-based training in fundamental aspects of pluripotent stem cell culture and analysis.
- Training packages tailored for the client's needs in stem cell culture.

Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center
Biomeditech, Tampere University
iPS Cells
Biocenter Kuopio
Stem Cell Center

Cell line editing

The service enables generation of disease relevant cellular model systems including knock-outs, knock-ins, and either creation or reversion of pathogenic mutations. This service also facilitates generation of reporter cell lines with fluorescent or other kinds of tags. Cellular systems can be created to facilitate genetic screening and drug screening. Furthermore, cell line editing can be used to validate hits from genetic screens or drug screens. Much needed isogenic cell lines for isogenic disease models can be generated by cell line editing.

Target cell type and intended type of editing will determine the approach and feasibility of editing projects. The projects are initiated together with scientists requiring the services. Therefore, there will be evaluation phase when FinGEEC personnel will determine whether the project is currently doable and whether the client agrees with the price and duration of the project, and risks involved.

Note that this service is not currently provided for primary cells. For human pluripotent stem cell editing, please, contact BSCC, HiLIFE, UH.

Helsinki Institute of Life Science - HiLIFE
FinGEEC-Helsinki

Biomeditech, Tampere University
iPS Cells

Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center

Turku Bioscience Centre (TBC)
Genome Editing Core (GEC)

Pooled CRISPR screening

Pooled CRISPR screening is extremely versatile method. Practically any phenotype that allows cell separation can be queried. Essential genes in specific cell types can be determined by pooled CRISPR screening or drug resistance and sensitivity genes can be discovered. Novel genes and pathways involved in cell differentiation can be mapped. These screens can be performed in cell lines, stem cells (BSCC, HiLIFE, UH) or primary cells, however, we currently have the service setup for established cell lines only.

Pooled CRISPR screens provided by FinGEEC-Turku are highly customized and are designed, and performed in collaboration with clients. Pooled CRISPR screens currently mostly rely on lentiviral gene transfer, therefore, this service is closely coordinated together with local VGTCT nodes

Please, see Addgene plasmid repository has most of the genome-scale pooled CRISPR libraries readily available as DNA preparations for a price as low as 500 dollars per library.

Turku Bioscience Centre (TBC)
Genome Editing Core (GEC)

Continuous visualization of live cells

The IncuCyte S3 automatically acquires and analyzes images around the clock, providing an information-rich analysis. IncuCyte S3 accommodates up to six microplates at a time. Users can schedule experiments at different image acquisition frequencies and magnifications in parallel. Remote, networked access with unlimited, free licenses.

Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center

Turku Bioscience Centre (TBC)
Genome Editing Core (GEC)

Analytic genome editing services

Analytic gene editing services include 1) Guide RNA validation service in 293FT cells 2) SURVEYOR analysis for editing efficacy, 3) Edited sequence analysis by Sanger seq, 4) TOPO TA clone analysis to identify exact editing events.

Helsinki Institute of Life Science - HiLIFE
FinGEEC-Helsinki

Neural iPSC services

Differentiation of human pluripotent stem cells into different brain cell types, including neurons, microglia, astrocytes, and cerebral organoids. Differentiation protocols are selected based on customer needs.

Multiwell microelectrode array (MEA) for the functional characterization of neuronal cultures with a Axion Maestro Edge multiwell microelectrode array system with full temperature and CO2 control. The system allows for the use of Axion 24-well and 6-well plates. Simultaneous measurement of the signal in all the wells and electric stimulation are possible. The system is equipped with software for the quantification of spikes, bursts, and network bursts. Raw data can also be exported and analyzed elsewhere.

Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center

Recent user publications

Diego Balboa, Tom Barsby, Väinö Lithovius, Jonna Saarimäki-Vire, Muhmmad Omar-Hmeadi, Oleg Dyachok, Hossam Montaser, Per-Eric Lund, Mingyu Yang, Hazem Ibrahim, Anna Näätänen, Vikash Chandra, Helena Vihinen, Eija Jokitalo, Jouni Kvist, Jarkko Ustinov, Anni I Nieminen, Emilia Kuuluvainen, Ville Hietakangas, Pekka Katajisto, Joey Lau, Per-Ola Carlsson, Sebastian Barg, Anders Tengholm, Timo Otonkoski. Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells. Nat Biotechnol. 2022 Jul;40(7):1042-1055. doi: 10.1038/s41587-022-01219-z.

Le Dour C, Chatzifrangkeskou M, Macquart C, Magiera MM, Peccate C, Jouve C, Virtanen L, Heliö T, Aalto-Setälä K, Crasto S, Cadot B, Cardoso D, Mougenot N, Adesse D, Di Pasquale E, Hulot JS, Taimen P, Janke C, Muchir A. Actin-microtubule cytoskeletal interplay mediated by MRTF-A/SRF signaling promotes dilated cardiomyopathy caused by LMNA mutations. Nat Commun. 2022 Dec 22;13(1):7886. doi: 10.1038/s41467-022-35639-x. PMID: 36550158.

Ryytty S, Modi SR, Naumenko N, Shakirzyanova A, Rahman MO, Vaara M, Suomalainen A, Tavi P, Hämäläinen RH. Varied Responses to a High m.3243A>G Mutation Load and Respiratory Chain Dysfunction in Patient-Derived Cardiomyocytes. Cells. 2022 Aug 19;11(16):2593. doi: 10.3390/cells11162593.

D. Belitškin, P. Munne, S.M. Pant, J.M. Anttila, I. Suleymanova, K. Belitškina, D. Kirchhofer, J. Janetka, T. Käsper, S. Jalil, J. Pouwels, T.A. Tervonen, J. Klefström. Hepsin promotes breast tumor growth signaling via the TGFβ-EGFR axis. Mol Oncol, 2023 Oct 23. doi: 10.1002/1878-0261.13545.

Karolina Pavic, Nikhil Gupta, Judit Domènech Omella, Rita Derua, Anna Aakula, Riikka Huhtaniemi, Juha A Määttä, Nico Höfflin, Juha Okkeri, Zhizhi Wang, Otto Kauko, Roosa Varjus, Henrik Honkanen, Daniel Abankwa, Maja Köhn, Vesa P Hytönen, Wenqing Xu, Jakob Nilsson, Rebecca Page, Veerle Janssens, Alexander Leitner, Jukka Westermarck. Structural mechanism for inhibition of PP2A-B56α and oncogenicity by CIP2A. Nat Commun. 2023 Feb 28;14(1):1143. doi: 10.1038/s41467-023-36693-9.