SATB2-dependent mechanisms in human cognitive ability

The impressive cognitive abilities of human beings are unmatched in the animal kingdom. Therefore it seems reasonable to assume that during human evolution specific cellular and molecular mechanisms have emerged that underlie and support human-specific higher brain functions. Our project is designed to test whether the three-dimensional folding of DNA within the cell nucleus of cortical pyramidal neurons provides such an evolutionary optimized mechanism. To this end we will compare the 3D-structure of the genome in mouse and human nerve cells. Studies in various non-neuronal cell types have revealed that changes in the spatial organization of genomes can strongly influence gene transcription and that expression of individual genes can be either stimulated or repressed by altering DNA loops. While up until recently it was simply impossible to address such questions in human neurons, we now can generate human nerve cells in the laboratory from so called induced pluripotent stem cells. Under appropriate cell culture conditions these cells have the capacity to form cellular aggregates that resemble in certain limited aspects miniature brains. Such brain organoids form the bases of our project. In these organoids we aim to identify the functions of a particular protein which binds to specific sites in DNA and determines formation of precisely oriented DNA loops via formation of protein complexes. This protein Special AT-rich sequence binding protein 2 (SATB2) displays certain properties that render it a prime candidate of a genome organizer supporting cognitive abilities. For example, human genetic studies have demonstrated that variants of the SATB2 gene are associated with variation in intelligence in the general human population. Our own previous work supports that genetic variants of genes regulated by SATB2, variants of SATB2 interacting proteins as well as variants of binding sites in DNA are associated with cognitive abilities. Furthermore SATB2 was identified as a schizophrenia risk gene and human patients with defects in one copy of the SATB2 gene suffer from SATB2-associated syndrome, a disease which is characterized by severe cognitive deficits. In order to establish the precise functions of SATB2 in 3D-folding of neuronal DNA we will perform a series of complex molecular biology experiments. Next generation sequencing- methods in combination with bioinformatics analyses will enable us to generate 3D-models of DNA in the nucleus of human cortical neurons in the presence or absence of SATB2. The evolution of SATB2-dependent mechanism will be studied by comparing mouse and human 3D genome organization. From our studies we expect not only novel insights into molecular evolution of cognition. The project should also indicate new avenues to therapies of neuropsychiatric diseases which are frequently characterized by cognitive dysfunction.

The exceptional cognitive abilities of humans are unparalleled in the animal kingdom. Conversely, cognitive impairments are symptoms of numerous neurological and psychiatric disorders. Therefore, it is of great importance to investigate the molecular and cellular mechanisms that enable these advanced functions of the human brain. We explored the hypothesis that the three-dimensional structure of DNA in cortical neurons influences cognitive abilities. Our focus was on the "Special AT-rich sequence binding protein 2" (SATB2), which binds to specific DNA sequences and organizes them into precisely aligned loops through complex formation. Genetic studies in humans have shown that variants of the SATB2 gene are associated with intelligence. Patients with mutations in one of the two copies of the SATB2 gene suffer from "SATB2-associated syndrome," characterized by severe cognitive impairments. To understand the role of SATB2 in DNA folding, we first conducted molecular biological studies on genetically modified mice. Using functional genomics and bioinformatics analyses, we determined the 3D structure of DNA in neurons with and without SATB2. We found that SATB2 influences the 3D structure of more than half of all genes associated with cognitive performance, including many with highly specialized neuronal functions. In the human genome, these genes are not only crucial for cognitive abilities but also contribute to the risk of neuropsychiatric and neurodevelopmental disorders. Our results also show that SATB2 affects chromatin loops between enhancers and promoters of neuronal, activity-regulated genes, thereby controlling their expression. Non-coding DNA regions whose 3D structure is regulated by SATB2 in mice are genetically associated with educational attainment, intelligence, and schizophrenia in humans. These findings, which establish SATB2 as a genome regulator for cognitive functions in mice, highlight the need to conduct similar experiments in human cells to identify specific functions of SATB2 related to human cognitive abilities. Thanks to the ability to generate human neurons from induced pluripotent stem cells in the laboratory, we developed a human cell culture model and compared neurons from mice and humans in parallel molecular biological experiments. These studies are still ongoing. In the long term, we aim to develop approaches for new therapies to support the cognitive performance of patients with neuropsychiatric disorders. By developing human models, we also contribute to the reduction of animal testing in neuroscience research