Niklas Dahl – Induced pluripotent cell models to recapitulate disorders of the human brain and identification of genetic risk factors for common traits

The overarching aim of our research is to improve treatment outcomes and prognosis for selected disease groups.

The research is divided into two separate projects:

By establishing brain models from stem cells, our goal is to identify pathophysiological mechanisms involved in epilepsy, cognitive impairment, and malformations of the brain’s blood vessels. These models can also be used for drug development.
A second goal is to identify inherited genetic factors, each one with a small effect size, that together increase the risk for common diseases. We are primarily focusing on breast cancer and cardiac hypertrophy. The knowledge may enable individual-specific risk assessments and treatments.

Project 1 – Epilepsy and cognitive impairment

Epilepsy and cognitive impairment with an early onset are global health problems. The disorders are heterogeneous, but a majority of cases are caused by genetic abnormalities leading to persistent symptoms and a severely reduced quality of life. Effective treatment options are lacking.

Today, the development of new drugs is limited by insufficient knowledge of the underlying disease mechanisms, which in turn is due to difficulties in accessing biological material and the lack of relevant model systems that can replicate disease processes.

Combining new technologies

These limitations can be partially overcome through a combination of new technologies, such as induced pluripotent stem cells (iPSC), DNA modification with CRISPR/Cas9 (gene editing), image analysis, DNA/RNA sequencing complemented with bioinformatic algorithms and analysis.

In this project, we use somatic cells, e.g., fibroblasts, from patients with genetically confirmed disease. These cells can be “reprogrammed” into stem cells (iPSC) and then differentiated into various types of brain cells in 2D or more complex 3D structures known as organoids (Fig 1).

The iPSC-derived brain cell models are analyzed for morphology, growth, molecular composition, and various functions, providing new insights into the processes contributing to each disease. Culture conditions of the iPSC disease models are adapted for exposure to various compounds and candidate drugs that may normalize abnormalities in the iPSC brain-models as a step toward drug development.

Specific aims:

Establish and develop neuronal models from iPSC for selected forms of therapy-resistant epilepsy (e.g. Dravet syndrome) and cognitive disorders (e.g. Down syndrome) caused by specific genetic abnormalities.
Analyze the development and homeostasis of neuronal disease models to identify disease-specific mechanisms and biomarkers at the cellular and molecular levels.
Monitor and normalize the expression of disease-specific biomarkers in the neuronal models. Initiate the first steps in the development and/or optimization of candidate drugs for each condition.

Two microscope images. One shows a network of cells in bright colours against a dark background. The other shows a brain organoid stained in blue and red.

Fig 1. (A) Network of GABAergic interneurons derived from iPSC. These cells are important for balancing the electrical activity in the brain. (B) Brain organoid from iPSC after 3 months of cultivation. The organoid recreates CNS structures in 3D. The cerebral cortex (blue) is partly surrounded by meningeal cells (red). Ventricular zone structures are indicated by arrows.

Project 2 – Inherited factors for breast cancer and heart muscle enlargement

The aim of this project is to identify combinations of inherited factors that influence an individual’s risk for the relatively common diseases. We will primarily focus on breast cancer and early-onset heart muscle enlargement (hypertrophic cardiomyopathy). These diseases cause significant morbidity and increase the risk of premature death. Early identification of “high-risk individuals” enables early and personalized treatment interventions.

The project is based on knowledge of each individual’s unique genetic makeup, which includes more than 4 million possible variations. Half of these variants are inherited from each parent. Individual variants may have a small-size effect on the risk for a specific disease.

Certain combinations of several small-size effect variants, randomly inherited, can lead to a markedly increased risk of breast cancer in women or early-onset heart muscle enlargement – a concept known as the polygenic risk score (PRS; Fig 2). The concept has recently been robustly validated for selected disorders and in some populations for clinical applications.

Genetic variants with high or low disease risk

By analyzing the entire genome in large groups of patients with breast cancer and hypertrophic cardiomyopathy within the Swedish population, we aim to identify “patterns” of genetic variants that can be associated with high or low risk levels of developing disease. If strong links are found in individuals with disease and PRS, we then aim to validate our findings in a clinical setting and in a prospective study. In such a study, we will also offer relatives of affected individuals to participate.

Specific aims:

Identify patients diagnosed with breast cancer or hypertrophic cardiomyopathy in the swedish population.
Identify disease risk variants through databases (e.g., UK Biobank, FinnGen, etc.), collaborations, and published association (GWAS) studies.
Genotype patients for selected risk variants using SNP array technology. Perform statistical analyses to identify specific “patterns” of gene variants associated with each disease to define PRS.
Expand the study to include relatives and newly diagnosed cases for clinical validation, genotyping, and follow-up.

Graph with two curves that illustrate how a combination of randomly inherited gene variants increases the life-time risk for disease.

Fig 2. Normal distribution of different inherited gene variants in the population related to lifetime disease risk (black curve). The specific combination of randomly inherited gene variants of an individual gives a polygenic risk score (PRS) for a disease, corresponding to an increased — or decreased — lifetime disease risk when compared to the general population.