Cilia are conserved cellular organelles that are nearly ubiquitous in the vertebrate body plan. Although cilia were first observed by van Leeuwenhoek in the 17th century, it was not until the turn of 21st century, that the myriad roles of these complex structures emerged [Davis et al, 2012, Oh et al, 2015, Heydeck et al, 2018]. Through collaborative efforts of many laboratories worldwide, we and others have established cilia as key mediators of extracellular cues such as morphogenetic signaling that are critical to proper development and homeostasis. We now know that cells have a repertoire ~1000 proteins, the ciliary proteome, that are required for correct ciliogenesis and ciliary function. Not surprisingly, the disruption of any of these components can give rise to genetic disorders called ciliopathies. Our researchers have a long-standing interest in understanding the genetic architecture of these clinically distinct but overlapping disorders; in the mechanistic dissection of ciliary function in discrete spatiotemporal contexts [Boldt et al, 2016; Heydeck et al, 2018]; and our long-term goal is to develop novel therapeutic strategies aimed to ameliorate or at least prolong the onset of symptoms.
Our ciliopathy research employs a multidisciplinary approach involving genetic analysis of humans with either rare Mendelian or common complex traits underscored by a ciliary defect. We use mouse and zebrafish models coupled to robust cell-based assays to quantitatively assess ciliary output. Through interactions and collaborations with academic colleagues, patient support groups, and partners from the pharmaceutical industry, we recruit and study the genetic architecture and pathomechanisms of individuals with ciliopathies. Clinical features of the rare ciliopathies, such as psychiatric illness and obesity, are common in the general population. We and others have hypothesized that increased mutational burden in ciliary genes can increase the risk for such disorders [Oh et al, 2015]. To investigate this possibility, our researchers used a combination of targeted resequencing of ciliary genes in human cohorts combined with animal models and cell-based assays to establish how specific genetic lesions can lead to neuroanatomical and behavioral alterations that may be relevant to schizophrenia, autism, and obesity [Kamiya et al, 2008; Lim et al, 2014; Migliavacca et al, 2015].
Genetic Architecture of Rare Ciliopathies
Consistent with the broad roles of cilia in the vertebrate body plan, ciliary and basal body defects have been causally linked with at least 35 discrete disorders in humans, caused by mutations in >190 causal genes. Although each disorder, such as Bardet-Biedl syndrome, Meckel-Gruber syndrome, Joubert syndrome, Nephronopthisis, or Primary Ciliary Dyskinesia are individually rare (~1/100,000 to 1/200,000) as many as 100 additional independent clinical entities have been proposed as ciliopathies [Davis et al, 2012]. The advancement of next generation sequencing in recent years has propelled causal gene discovery [Hjeij et al, 2013, Lindstrand et al, 2014, Roberson et al, 2015, and Lindstrand et al 2016] and has also provided a platform to uncover genetic modifiers [Khanna et al, 2009]. Using sequencing or copy number variant analysis of research participant samples coupled to in vivo studies in zebrafish, the ACT-GeM aims to understand the genetic architecture of disease by mapping mutational burden to ciliary functional modules such as the BBSome, transition zone, and intraflagellar transport complexes [Zaghloul et al, 2010, Davis et al, 2011; Lindstrand, et al 2016; Kousi et al, 2018 BioRxIV]. Furthermore, our ciliary toolkit has offered the opportunity to investigate cis-compensatory effects predicted by comparative genomics; these events are not unique to ciliary genes but likely impact at least 3-12% of human disease variants [Jordan et al 2015].
Cilia and Cell Signaling
A major role of the cilium is to act as a chemo-, mechano- and photosensor. Cilia also mediate communication between extra- and intra-cellular signaling effectors not only during development, but also during regenerative and homeostatic processes. Comprehensive study of ciliary mutants ranging from mouse to zebrafish have implicated a prominent role for cilia in signaling paradigms including Shh, Wnt, and Notch. Coupled to robust in vitro assays, we have demonstrated that signaling effectors function at the cilium in response to certain environmental cues [Gerdes et al, 2007 and [Liu et al, 2014]. Our ongoing research goals are to understand the detailed molecular mechanisms by which ciliary proteins interact in signaling transduction, and to understand the tissue-specific and context-dependent phenomena that result in variable disease phenotypes [Garcia-Gonzalo et al, 2011].
Recent technological improvements have empowered the efficient manipulation of gene expression and the genome itself. Using a combination of RNAi and CRISPR in cells and zebrafish embryos, our researchers are leading the search for the identification of suppressors of ciliopathies, in other words, genes whose ablation or attenuation might have therapeutic benefit to the phenotypes driven by ciliary dysfunction. Our work shows early promise with the identification of suppressors for a subset of ciliopathies, which have in turn opened possibilities for the testing of lead therapeutic compounds [Tsai et al In Press]. We aspire to systematize this approach for numerous disorders for which we might have the opportunity to provide ameliorating or therapeutic leads.