I am Professor and Consultant in Clinical Genetics in Stockholm, Sweden. Currently I am the head of the Clinical Genetics diagnostic laboratory (Karolinska University Hospital) and group leader for Rare Diseases research group at the Department of Molecular Medicine and Surgery (Karolinska Institutet). My specific area of interest is the study of structural human genomic variation, its biological consequences and involvement in rare and common human disorders.
My group members combine conventional and next generation genetic analysis with careful clinical assessments and functional follow up in vivo (zebrafish) and in vitro (primary cells and iPS cells). To characterize the breakpoints of chromosome rearrangements we use a variety of methodologies and next generation sequencing (NGS) platforms.
This work is truly translational! Patients are initially identified in the health care system and outlined phenotypically and cytogenetically in the clinical genetic service. Then the research part takes over aiming to outline the exact genetic rearrangement down to single gene and breakpoint level in order to correlate symptoms with a specific gene defect. Finally, our findings are returned to the health care system in the form of new information about gene function.
Project 1: The role of structural genomic variation in human health and disease
Backgound: Structural genomic variation comprises 1) copy-neutral balanced events (inversions and translocations) as well as 2) unbalanced events with either loss or gain of chromosome material (deletions, duplications, triplications and multi allelic copy number variants (CNVs). The size may vary from events that are visible in a light microscope (>5-10 Mb) down to the size of a single exon (<100-200 base pairs). In the past decade structural variants have emerged as important contributors to the genetic load of both rare and common disorders especially within the area of neurodevelopmental disease and malformation syndromes. However, a specific rearrangement often affects many genes and regulatory regions and the specific disease causing factors are still poorly characterized.
Aim: These studies are focused on the detailed characterization of structural genomic rearrangements in order to identify the specific causative and modifying genes and to understand the underlying mutational mechanisms involved.
Work Plan: We use short-, linked- and long-read whole genome sequencing (WGS) to characterize and identify structural variants. Patents with structural variants are recruited through the clinical genetic diagnostic laboratory where individuals with neurodevelopmental disorders and malformation syndromes are analyzed with chromosome analysis, oligonucleotide array-based comparative genomic hybridization (aCGH) and clinical WGS. After WGS and bioinformatics analysis functional follow up studies of candidate genes and variants are done in primary patient cells (e.g. fibroblasts, lymphocytes), induced pluripotent stem cells and in zebrafish.
We have several ongoing studies:
Study I) Identification and characterization of rare disease associated structural chromosomal variants by massive parallel whole genome sequencing
The first objective is to implement WGS for the clinical diagnostic detection of structural variants. To this end, we develop novel bioinformatic analysis pipelines to identify both balanced and unbalanced structural variants from WGS data. The second objective is to study the rearrangement breakpoints and from the mutational signatures observed, infer the underlying mechanisms involved. Finally, we are interested in how the genes affected by structural variants cause disease. Our ambition is to characterize all genetic lesions in a given patient, from single base pair changes to large chromosomal rearrangements, and to follow up with functional studies. In this way, we will evaluate the relationship between structural variants and the burden of point mutations (an area that is still largely unexplored).
Study II) Identification of new disease genes by sequencing balanced chromosomal aberrations.
In this project we use WGS (described above) to study balanced chromosomal rearrangements (inversions and translocations). The hypothesis is that genes disrupted by the chromosomal breakpoints are driving the clinical symptoms seen in the rearrangement carriers. Identified candidate genes are evaluated in zebrafish.
Project 2: Computational development of bioinformatic tools and databases to interpret structural variants in individuals with rare diseases
The aim of this project is to develop novel bioinformatic tools for the discovery and interpretation of disease-causing SV, as well as to evaluate the clinical feasibility of novel OMICs technologies. The project is translational and is carried out as a collaboration with Clinical genomics at Scilifelab Solna. The project will contribute to our knowledge on the structure and diversity of the human genome, as well as to bring novel technologies to the routine diagnostic workflow.
Project 3: Zebrafish models to study genetic and disease mechanisms underlying rare human disorders
Despite recent progress in identifying the genetic cause of rare disorders we still lack the ability to interpret the pathogenic potential of rare variants identified in small families or in uncharacterized genes and assess the genetic basis of variability in clinical presentations. Due to the technical advantages, the zebrafish has become a very popular model to test and further understand the role of candidate genes in disease. Approximately 70% of the human genes have a zebrafish orthologue and many of the cellular pathways in embryonic development and tissue function are similar to those found in humans. One of the most commonly used techniques to assess the role of a specific gene is to knockdown the target protein levels using antisense oligonucleotides or morpholinos. This technique is however being replaced by the use of the genome editing technique CRISPR/Cas9. The CRISPR/Cas9 technique results in permanent changes in the genome that, given the specificity of the technique, more closely resemble the mutations found in the patients.
In this project we evaluate novel genes and mutations identified in patients with rare diseases investigated with clinical exome/whole genome sequencing or through our research studies outlined above. We use overexpression of wild type and mutated RNA, transient knock down (morpholinos) and stable knockdown (CRISPR/Cas9 mutagenesis). For select genes we also screen the mutant zebrafish for therapeutic compounds. Disorders of particular interest are neurodevelopmental diseases, ciliopathies, congenital malformation syndromes and muscle disorders.
Project 4: Cellular models to understand mechanisms underlying childhood neurodevelopmental disorders
Here we use patient specific induced pluripotent stem cells (hiPSCs), which are translationally relevant to human in comparison with other models, in order to explore mechanisms of neurodevelopmental disorders and at the same time expand our knowledge about the normal functions and development of the healthy brain. Organoid 3D culture recapitulates development of various brain regions therefore is a unique tool to model brain disorders. Samples from patients’ diagnosed with rare neurodevelopmental disorders are obtained through clinical genetics (Karolinska University Hospital). This is a unique resource as they can help us understand more about how chromosomal rearrangement or loss of encoded proteins can affect neuronal development and function in vitro. Genes/disorders of particular interest are CTNND2, NFACS and Williams syndrome.
Previous and Current Research Funding:
- 2020 KI - StratNeuro
- 2020-2021 Region Stockholm - Högre klinisk forskare
- 2018-2022 Swedish Research Council (Vetenskapsrådet)
- 2019-2021 Cancerfonden
- 2019-2022 Hjärnfonden
- 2019 Läkaresällskapet
- 2017-2022 Stockholms läns landsting, HMT
- 2017-2021 Stockholms läns landsting, ALF
- 2015-2018 Svenska Sällskapet för Medicinsk Forskning
- 2015-2017 Marianne och Marcus Wallenbergs Stiftelse
- 2015-2016 Science for Life Laboratory
- 2015-2017 Riksbankens Jubileumsfond
- 2015-2016 Jeanssons Foundation
- 2014-2016 Hjärnfonden
- 2015-2016 Kungl. Fysiografiska Sällskapet i Lund
- 2013-2015 Swedish Research Council (Vetenskapsrådet)
- 2016-2019 Karolinska Institutet
- 2013-2015 Stockholms läns landsting, ALF
- 2010-2013 Swedish Research Council (Vetenskapsrådet)
- Josephine Wincent, MD, PhD, Postdoc
- Jonas Carlsten, MD, PHD, Postdoc
- Raquel Vaz, PhD, Postdoc
- Mansoureh Shahsavani, PhD, Postdoc
- Maria Pettersson, PhD, Postdoc
- Jesper Eisfeldt, PhD, Postdoc
- Jakob Schuy, PhD student
- Marlene Ek, PhD student
- Wolfgang Hofmeister, PhD, Assistant professor
- Ameli Norling, MD, PhD, Postdoc
- Vanja Börjesson, Master student
- Miriam Armenio, Research Assistant
- Alisa Foerster, Master student
- Amel Al-Murrani, Research Assistant
Academic honours, awards and prizes
Academic honors, awards and prizes:
2016-2019 Selected for four year funding as Research Associate (forskarassistent), Karolinska Institutet