Regulation and function of ciliary dyslexia candidate genes

Dyslexia is defined as an unexpected difficulty in reading despite normal intelligence, senses and instruction. It is the most common learning disability with estimated 5-10% of the population affected. Its heredity is estimated to about 40-60%. Despite the established heredity of the condition, it has been very challenging to pinpoint the underlying genes. In the past 15 years, a number of dyslexia candidate genes have been suggested. A handful of them have been replicated in several studies, including DYX1C1, DCDC2 and KIAA0319. More recently, the very same genes have been independently associated to functions of the cilium. Cilia are microtubule-based organelles present on the surface of most eukaryotic cells. The aim of this thesis was to investigate the molecular functions of ciliary dyslexia candidate genes and their role at the cilium.

In paper I, we found X-box motifs in the promoter regions of DYX1C1, DCDC2 and KIAA0319 and showed that they are functional and able to bind ciliogenic RFX transcription factors. Knockdown of certain RFX transcription factors altered the expression of DYX1C1 and DCDC2, but not KIAA0319. Overall, we strengthened the evidence for DYX1C1 and DCDC2 as ciliary genes. In paper II, we identified DCDC2 as a causative gene for nephronophthisis-related ciliopathy (NPHP-RC) with loss-of function mutations present in two affected families. We observed localization of DCDC2 to the ciliary axoneme of affected organs and demonstrated a crucial role of the Wnt pathway in the pathogenesis of NPHP-RC. 3D modeling in spheroids and in vivo modeling in zebrafish confirmed these observations. In paper III, we identified CPAP as an interacting partner of both DYX1C1 and DCDC2. In addition, we observed genetic pathway synergy between DYX1C1 and DCDC2 using zebrafish and a human ciliated cell model. In paper IV, we performed transcriptomics on differentiating human neuroepithelial stem cells and characterized the expression of dyslexia candidate genes. We found that some dyslexia candidate genes are upregulated during human neuronal differentiation. Remarkably, we identified the group of ciliary genes as the major group of upregulated genes. In addition, we showed that cilia are present on the surface of neuronal cells throughout differentiation. In paper V, we asked whether dyslexia and ciliopathies might have a common genetic origin by investigating the genome of two individuals with situs inversus and dyslexia. We identified rare variants in dynein heavy chain genes likely causing their situs inversus phenotype. Their involvement in dyslexia remains to be determined.

In conclusion, the work conducted within this thesis strengthened and expanded on the role of DYX1C1 and DCDC2 at the cilium and in ciliopathies and identified the group of ciliary genes as a major gene class in human neuronal differentiation. A link between cilia and dyslexia remains elusive.

List of scientific papers

I. Kristiina Tammimies, Andrea Bieder, Gilbert Lauter, Debora Sugiaman-Trapman, Rachel Torchet, Marie-Estelle Hokkanen, Jan Burghoorn, Eero Castrén, Juha Kere, Isabel Tapia-Páez, Peter Swoboda. Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor (RF)X transcription factors through X-box promoter motifs. The FASEB Journal. 2016 Oct;30(10):3578-3587.
https://doi.org/10.1096/fj.201500124RR

II. Markus Schueler, Daniela A. Braun, Gayathri Chandrasekar, Heon Yung Gee,Timothy D. Klasson, Jan Halbritter, Andrea Bieder, Jonathan D. Porath, Rannar Airik, Weibin Zhou, Joseph J. LoTurco, Alicia Che, Edgar A. Otto, Detlef Böckenhauer, Neil J. Sebire, Tomas Honzik, Peter C. Harris, Sarah J. Koon, Meral Gunay-Aygun, Sophie Saunier, Klaus Zerres, Nadina Ortiz Bruechle, Joost P.H. Drenth, Laurence Pelletier, Isabel Tapia-Páez, Richard P. Lifton, Rachel H. Giles, Juha Kere, Friedhelm Hildebrandt. DCDC2 mutations cause a renal-hepatic ciliopathy by disrupting Wnt signaling. American Journal of Human Genetics. 2015 Jan 8;96(1):81-92.
https://doi.org/10.1016/j.ajhg.2014.12.002

III. Andrea Bieder, Gayathri Chandrasekar, Arpit Wason, Jay Gopalakrishnan, Juha Kere, Isabel Tapia-Páez. Genetic and protein interaction studies reveal pathway synergy between the ciliary dyslexia candidate genes DYX1C1 and DCDC2. [Manuscript]

IV. Andrea Bieder, Masahito Yoshihara, Shintaro Katayama, Kaarel Krjutškov, Anna Falk, Juha Kere, Isabel Tapia-Páez. Expression of dyslexia candidate genes and ciliary genes during human neuronal differentiation. [Manuscript]

V. Andrea Bieder, Elisabet Einarsdottir, Hans Matsson, Harriet E. Nilsson, Jesper Eisfeldt, Anca Dragomir, Martin Paucar, Tobias Granberg, Tie-Qiang Li, Anna Lindstrand, Juha Kere, Isabel Tapia-Páez. Rare variants in dynein heavy chain genes in two individuals with situs inversus and developmental dyslexia. [Manuscript]