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Modeling Human Disease in Humans: The Ciliopathies

2011; Cell Press; Volume: 147; Issue: 1 Linguagem: Inglês

10.1016/j.cell.2011.09.014

1097-4172

Gaia Novarino, Naiara Akizu, Joseph G. Gleeson,

Microtubule and mitosis dynamics

Soon, the genetic basis of most human Mendelian diseases will be solved. The next challenge will be to leverage this information to uncover basic mechanisms of disease and develop new therapies. To understand how this transformation is already beginning to unfold, we focus on the ciliopathies, a class of multi-organ diseases caused by disruption of the primary cilium. Through a convergence of data involving mutant gene discovery, proteomics, and cell biology, more than a dozen phenotypically distinguishable conditions are now united as ciliopathies. Sitting at the interface between simple and complex genetic conditions, these diseases provide clues to the future direction of human genetics. Soon, the genetic basis of most human Mendelian diseases will be solved. The next challenge will be to leverage this information to uncover basic mechanisms of disease and develop new therapies. To understand how this transformation is already beginning to unfold, we focus on the ciliopathies, a class of multi-organ diseases caused by disruption of the primary cilium. Through a convergence of data involving mutant gene discovery, proteomics, and cell biology, more than a dozen phenotypically distinguishable conditions are now united as ciliopathies. Sitting at the interface between simple and complex genetic conditions, these diseases provide clues to the future direction of human genetics. Until a few years ago, identifying the genetic basis of an inherited human disease was an arduous undertaking, requiring potentially a decade or more of work in ascertainment of families for linkage analysis, followed by endless fine mapping of the locus and, finally, sequencing of candidate genes one by one until that “eureka” moment when the likely causative gene was identified. The newly discovered disease gene was often entirely novel, without recognizable domains or a path to understand the disease mechanism. A mouse model was then generated, in which the disease gene was inactivated. The mouse faithfully recapitulated the human phenotype in some cases but, more often, showed no phenotype or phenotypes not clearly related to the human disease. Once established, the model was studied from multiple perspectives to understand the cell biological and biochemical basis of disease, culminating in attempts to test potential therapies. Although successful in a few instances such as losartan treatment for Marfan syndrome (Habashi et al., 2006Habashi J.P. Judge D.P. Holm T.M. Cohn R.D. Loeys B.L. Cooper T.K. Myers L. Klein E.C. Liu G. Calvi C. et al.Losartan, an AT1 antagonist, prevents aortic aneurysm in a mouse model of Marfan syndrome.Science. 2006; 312: 117-121Crossref PubMed Scopus (1274) Google Scholar), this path has not fulfilled the promises of genomic medicine. This strategy has begun to change over the past 10 years due to increased knowledge of human genetic diseases, annotation of the human genome, and an amazing suite of tools to explore disease mechanisms. It is not uncommon now to open up a journal to find that geneticists have solved the molecular basis of a dozen or more conditions. And since we now know a lot more about the function of genes, protein domains, and networks, frequently just the discovery of the molecular cause of a disease can partially explain its mechanism. For instance, the discovery that the Rett syndrome gene encodes a methyl-CpG-binding protein (Amir et al., 1999Amir R.E. Van den Veyver I.B. Wan M. Tran C.Q. Francke U. Zoghbi H.Y. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2.Nat. Genet. 1999; 23: 185-188Crossref PubMed Scopus (3519) Google Scholar) immediately set the stage for a host of important discoveries in epigenetics related to brain function. The types of mutations displayed by patients, known as allelic diversity (Figure 1), can tell us something about the effect of these disease-causing variants on protein function. By identifying patients with different phenotypes due to specific types of mutations in the same gene (i.e., genocopies), we can understand human disease as a network of related signs and symptoms. For example, specific types of mutations in the gene encoding p53 predispose to very different types of cancers. By comparing the genes mutated in phenotypically related human diseases, we can learn about the disturbed protein networks that underlie them. Finally, by exploring gene-gene and gene-environment interactions, we can begin to characterize genetic and epigenetic modifiers of disease. Perhaps the best example is age-related macular degeneration, in which a substantial part of the risk of disease can be quantified based on gene-environment interactions (Chen et al., 2010Chen Y. Bedell M. Zhang K. Age-related macular degeneration: genetic and environmental factors of disease.Mol. Interv. 2010; 10: 271-281Crossref PubMed Scopus (89) Google Scholar). Although they are individually rare conditions, the ciliopathies have emerged as a dynamic new field of biology that exemplifies how genetics can be employed to drive research in basic cell biology and vice versa. The primary cilium is structured with a basal body at its base and a 9-paired microtubule axoneme, surrounded by plasma membrane but lacking the central pair of microtubules and outer dynein arms that define its cousin, the motile cilium. Primary cilia were first observed more than a century ago and were initially thought to be evolutionary remnants. How is it that biologists missed their importance for so long? More than a dozen disorders are now considered to be within the ciliopathy spectrum, including Joubert syndrome (JBTS), nephronophthisis (NPHP), Senior-Loken syndrome (SLS), orofaciodigital (OFD), Jeune syndrome, autosomal dominant and recessive polycystic kidney disease (ADPKD and ARPKD), Leber congenital amaurosis (LCA), Meckel-Gruber syndrome (MKS), Bardet-Biedl syndrome (BBS), Usher syndrome (US), and some forms of retinal dystrophy (RD). Between them, these conditions involve nearly every major body organ, including kidney, brain, limb, retina, liver, and bone (Figure 2A ), highlighting the important role of the primary cilium in development and homeostasis. These conditions were largely defined by clinical geneticists in the middle of the last century, who did their best to ascribe syndromes to unique combinations of clinical features. Individual diseases are known for the most commonly involved or diseased organ: BBS patients display the triad of obesity, polydactyly, and retinopathy but can display a host of other pathologies. MKS is a lethal condition at birth, with occipital encephalocele, PKD, and polydactyly. JBTS is characterized by a very peculiar radiographic finding known as the “molar tooth sign,” characterized by elongated superior cerebellar peduncles, deepened interpeduncular fossa, and cerebellar vermis hypoplasia. For each of these conditions, significant phenotypic variability has been observed even between members of the same family, making clinical diagnosis a challenge. Now that these conditions have been united by their underlying cell biology, we can begin to see commonalities between individual syndromes (Figure 2A). For instance, low muscle tone, cystic kidney disease, agenesis of the brain's corpus callosum, mental retardation, and hyperpnea/apnea are additional clinical features often present in ciliopathy patients. Individuals affected by BBS can have several clinical features common to JBTS such as mental retardation, hypotonia, and apnea. However, they also share other symptoms that are usually not present in JBTS but are common to other ciliopathies, such as polydactyly and retinal dystrophy (RD). Moreover, BBS patients are usually obese, a unique trait that is absent among the other ciliopathies. The first few genes identified from positional cloning of human or mouse phenotypes for what would eventually become the ciliopathies initially did not point in an obvious way to the cilium as the site of action. It was not until evidence began to accumulate that the encoded proteins localize specifically near the cilium that the field was born (Ansley et al., 2003Ansley S.J. Badano J.L. Blacque O.E. Hill J. Hoskins B.E. Leitch C.C. Kim J.C. Ross A.J. Eichers E.R. Teslovich T.M. et al.Basal body dysfunction is a likely cause of pleiotropic Bardet-Biedl syndrome.Nature. 2003; 425: 628-633Crossref PubMed Scopus (501) Google Scholar, Barr and Sternberg, 1999Barr M.M. Sternberg P.W. A polycystic kidney-disease gene homologue required for male mating behaviour in C. elegans.Nature. 1999; 401: 386-389Crossref PubMed Scopus (392) Google Scholar, Kim et al., 2004Kim J.C. Badano J.L. Sibold S. Esmail M.A. Hill J. Hoskins B.E. Leitch C.C. Venner K. Ansley S.J. Ross A.J. et al.The Bardet-Biedl protein BBS4 targets cargo to the pericentriolar region and is required for microtubule anchoring and cell cycle progression.Nat. Genet. 2004; 36: 462-470Crossref PubMed Scopus (324) Google Scholar, Otto et al., 2003Otto E.A. Schermer B. Obara T. O'Toole J.F. Hiller K.S. Mueller A.M. Ruf R.G. Hoefele J. Beekmann F. Landau D. et al.Mutations in INVS encoding inversin cause nephronophthisis type 2, linking renal cystic disease to the function of primary cilia and left-right axis determination.Nat. Genet. 2003; 34: 413-420Crossref PubMed Scopus (478) Google Scholar, Taulman et al., 2001Taulman P.D. Haycraft C.J. Balkovetz D.F. Yoder B.K. Polaris, a protein involved in left-right axis patterning, localizes to basal bodies and cilia.Mol. Biol. Cell. 2001; 12: 589-599Crossref PubMed Scopus (252) Google Scholar). Although the localization data is now incontrovertible, the functions of the encoded proteins at the cilium for the most part still remain a mystery, and some of the effects of these proteins do not seem to have direct relevance to ciliary function (Yen et al., 2006Yen H.J. Tayeh M.K. Mullins R.F. Stone E.M. Sheffield V.C. Slusarski D.C. Bardet-Biedl syndrome genes are important in retrograde intracellular trafficking and Kupffer's vesicle cilia function.Hum. Mol. Genet. 2006; 15: 667-677Crossref PubMed Scopus (145) Google Scholar). The question that emerges is how a single subcellular organelle can mediate such diverse clinical features. About 50 genes encoding predominantly ciliary-localized proteins have now been identified that are mutated in these partially overlapping syndromes (Figure 2B). In a series of positional cloning studies, each of these ciliopathy genes was initially found as causative for a restricted phenotype. Surprisingly, in most instances, this gene identification was followed by reports of mutations in the same gene in a different ciliopathy category (Baala et al., 2007aBaala L. Audollent S. Martinovic J. Ozilou C. Babron M.C. Sivanandamoorthy S. Saunier S. Salomon R. Gonzales M. Rattenberry E. et al.Pleiotropic effects of CEP290 (NPHP6) mutations extend to Meckel syndrome.Am. J. Hum. Genet. 2007; 81: 170-179Abstract Full Text Full Text PDF PubMed Scopus (191) Google Scholar, Baala et al., 2007bBaala L. Romano S. Khaddour R. Saunier S. Smith U.M. Audollent S. Ozilou C. Faivre L. Laurent N. Foliguet B. et al.The Meckel-Gruber syndrome gene, MKS3, is mutated in Joubert syndrome.Am. J. Hum. Genet. 2007; 80: 186-194Abstract Full Text Full Text PDF PubMed Scopus (173) Google Scholar, den Hollander et al., 2006den Hollander A.I. Koenekoop R.K. Yzer S. Lopez I. Arends M.L. Voesenek K.E. Zonneveld M.N. Strom T.M. Meitinger T. Brunner H.G. et al.Mutations in the CEP290 (NPHP6) gene are a frequent cause of Leber congenital amaurosis.Am. J. Hum. Genet. 2006; 79: 556-561Abstract Full Text Full Text PDF PubMed Scopus (444) Google Scholar). This occurred with such regularity that the field began to wonder whether any genotype-phenotype correlations would stand the test of time. How could mutations in a single gene produce such pleiotropic phenotypic effects in patients? Were these observations exceptions to the rule of strict genotype-phenotype correlation, or were they the exception that proves the rule of widespread phenotypic pleiotropy? The primary cilium is a hair-like, immotile cellular organelle protruding from almost all eukaryotic cells, frequently described as the cell's “antenna” for transducing extracellular signals. For the purposes of this Review, we focus exclusively on diseases involving nonmotile cilia and do not include diseases like primary cilia dyskinesia that involve motile cilia, as there is little phenotypic or genetic overlap. Cilia are generated during interphase from the mother centriole by coalescence of vesicles at its distal end that fuse with the plasma membrane. After this docking of the mother centriole, the microtubule axoneme protrudes out of the cell, concurrent with recruitment of a host of ciliary-specific proteins. The basal body (i.e., the docked mother centriole) possesses several specialized accessory structures termed transition fibers, basal feet, and ciliary rootlets and is surrounded by the pericentriolar matrix. But for many years, the molecular determinants of these structures were unknown. Recent work has begun to hint at the molecular architecture of these anatomically defined structures. The 9+0 microtubule arrangement of the axoneme emerges from the basal body in a triplet configuration and shifts to a doublet configuration at the ciliary transition zone (TZ). The Y-shaped microtubule extensions that define the TZ require the Cep290 protein for their formation in Chlamydamonas (Craige et al., 2010Craige B. Tsao C.C. Diener D.R. Hou Y. Lechtreck K.F. Rosenbaum J.L. Witman G.B. CEP290 tethers flagellar transition zone microtubules to the membrane and regulates flagellar protein content.J. Cell Biol. 2010; 190: 927-940Crossref PubMed Scopus (266) Google Scholar), although it is not clear whether Cep290 constitutes or otherwise contributes to these structures or whether this function is conserved in vertebrates. The location of the TZ marks the ciliary diffusion barrier: a septin-2 cytoskeleton that separates the ciliary and cytoplasmic compartments (Hu et al., 2010Hu Q. Milenkovic L. Jin H. Scott M.P. Nachury M.V. Spiliotis E.T. Nelson W.J. A septin diffusion barrier at the base of the primary cilium maintains ciliary membrane protein distribution.Science. 2010; 329: 436-439Crossref PubMed Scopus (352) Google Scholar). Attention has shifted to the TZ as the site of action of proteins mutated in several ciliopathies (Garcia-Gonzalo et al., 2011Garcia-Gonzalo F.R. Corbit K.C. Sirerol-Piquer M.S. Ramaswami G. Otto E.A. Noriega T.R. Seol A.D. Robinson J.F. Bennett C.L. Josifova D.J. et al.A transition zone complex regulates mammalian ciliogenesis and ciliary membrane composition.Nat. Genet. 2011; 43: 776-784Crossref PubMed Scopus (397) Google Scholar), but clear structure-function relationships are still lacking. Protein synthesis and vesicular transport do not occur inside cilia, so the assembly of this organelle, its maintenance, and its function are totally dependent upon an intraflagellar transport system by which proteins track bidirectionally along the polarized microtubules of the axoneme (Kozminski et al., 1993Kozminski K.G. Johnson K.A. Forscher P. Rosenbaum J.L. A motility in the eukaryotic flagellum unrelated to flagellar beating.Proc. Natl. Acad. Sci. USA. 1993; 90: 5519-5523Crossref PubMed Scopus (666) Google Scholar). Although the involvement of primary cilia in human diseases is now well established, many questions about its function remain. The current paradigm describes the primary cilium as an organelle for detecting and modulating the response to extracellular signaling molecules and as a location for organizing their cytoplasmic effectors. It is well poised to mediate both effects, as cilia typically protrude in a polarized fashion, which can help the cell interpret the context of extracellular signals. Many cellular receptors are localized to the primary cilium, and the basal body is itself a signaling hub, probably serving as an efficient transit point to transmit signals into the nucleus. In fact, a number of transcription factors undergo processing within or near the cilium prior to nuclear entry. Numerous critical developmental signaling pathways have been directly linked to primary cilia, such as Hedgehog (Hh), canonical and noncanonical Wnt, and some forms of PDGF signaling, highlighting cilia's role as a signaling hub (Huangfu et al., 2003Huangfu D. Liu A. Rakeman A.S. Murcia N.S. Niswander L. Anderson K.V. Hedgehog signalling in the mouse requires intraflagellar transport proteins.Nature. 2003; 426: 83-87Crossref PubMed Scopus (975) Google Scholar, Schneider et al., 2005Schneider L. Clement C.A. Teilmann S.C. Pazour G.J. Hoffmann E.K. Satir P. Christensen S.T. PDGFRalphaalpha signaling is regulated through the primary cilium in fibroblasts.Curr. Biol. 2005; 15: 1861-1866Abstract Full Text Full Text PDF PubMed Scopus (431) Google Scholar, Simons et al., 2005Simons M. Gloy J. Ganner A. Bullerkotte A. Bashkurov M. Krönig C. Schermer B. Benzing T. Cabello O.A. Jenny A. et al.Inversin, the gene product mutated in nephronophthisis type II, functions as a molecular switch between Wnt signaling pathways.Nat. Genet. 2005; 37: 537-543Crossref PubMed Scopus (573) Google Scholar). In addition to the modulation of these signaling pathways, primary cilia are essential for mechanical, odor, and photo reception. The interpretation of the ciliopathies as a unique group of disorders associated with defects in a single organelle gave a new direction to the investigation of these human diseases. The marriage of proteomics with genomics in the area of ciliary biology can be traced to an influential paper showing that the RFX-type transcription factor DAF-19 is essential for assembly of cilia in C. elegans sensory neurons and regulates several genes encoding intraflagellar transport proteins (Swoboda et al., 2000Swoboda P. Adler H.T. Thomas J.H. The RFX-type transcription factor DAF-19 regulates sensory neuron cilium formation in C. elegans.Mol. Cell. 2000; 5: 411-421Abstract Full Text Full Text PDF PubMed Scopus (237) Google Scholar). The RFX transcription factor family emerged in ciliated proto-eukaryotes, but it was only later that the RFX genes were co-opted to regulate expression of cilia-specific genes based upon the presence of an X box in their promoter (Piasecki et al., 2010Piasecki B.P. Burghoorn J. Swoboda P. Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals.Proc. Natl. Acad. Sci. USA. 2010; 107: 12969-12974Crossref PubMed Scopus (57) Google Scholar). This work set the stage for a comparative genomics approach to search for X-box-containing genes that were likely to encode proteins relevant to primary cilia. Two follow-up studies demonstrated the potential of this approach in identifying important components of the primary cilium (Avidor-Reiss et al., 2004Avidor-Reiss T. Maer A.M. Koundakjian E. Polyanovsky A. Keil T. Subramaniam S. Zuker C.S. Decoding cilia function: defining specialized genes required for compartmentalized cilia biogenesis.Cell. 2004; 117: 527-539Abstract Full Text Full Text PDF PubMed Scopus (404) Google Scholar, Li et al., 2004Li J.B. Gerdes J.M. Haycraft C.J. Fan Y. Teslovich T.M. May-Simera H. Li H. Blacque O.E. Li L. Leitch C.C. et al.Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene.Cell. 2004; 117: 541-552Abstract Full Text Full Text PDF PubMed Scopus (581) Google Scholar) and raised the idea of building a ciliary protein database. The ciliome (Gherman et al., 2006Gherman A. Davis E.E. Katsanis N. The ciliary proteome database: an integrated community resource for the genetic and functional dissection of cilia.Nat. Genet. 2006; 38: 961-962Crossref PubMed Scopus (227) Google Scholar, Inglis et al., 2006Inglis P.N. Boroevich K.A. Leroux M.R. Piecing together a ciliome.Trends Genet. 2006; 22: 491-500Abstract Full Text Full Text PDF PubMed Scopus (167) Google Scholar) now consists of more than 3000 genes encoding proteins either localized to cilia or essential for their assembly or function (Arnaiz et al., 2009Arnaiz O. Malinowska A. Klotz C. Sperling L. Dadlez M. Koll F. Cohen J. Cildb: a knowledgebase for centrosomes and cilia.Database (Oxford). 2009; 2009: bap022Crossref PubMed Scopus (77) Google Scholar). The ciliary proteome has already proved to be a powerful resource, accelerating the identification of candidate human ciliopathy genes by short-listing positional candidates. For example, the cloning of MKS1, BBS3, BBS5, and the BBS modifier MGC1203 was achieved by sequencing a reduced set of candidate genes (Badano et al., 2006Badano J.L. Leitch C.C. Ansley S.J. May-Simera H. Lawson S. Lewis R.A. Beales P.L. Dietz H.C. Fisher S. Katsanis N. Dissection of epistasis in oligogenic Bardet-Biedl syndrome.Nature. 2006; 439: 326-330Crossref PubMed Scopus (206) Google Scholar, Chiang et al., 2004Chiang A.P. Nishimura D. Searby C. Elbedour K. Carmi R. Ferguson A.L. Secrist J. Braun T. Casavant T. Stone E.M. Sheffield V.C. Comparative genomic analysis identifies an ADP-ribosylation factor-like gene as the cause of Bardet-Biedl syndrome (BBS3).Am. J. Hum. Genet. 2004; 75: 475-484Abstract Full Text Full Text PDF PubMed Scopus (182) Google Scholar, Kyttälä et al., 2006Kyttälä M. Tallila J. Salonen R. Kopra O. Kohlschmidt N. Paavola-Sakki P. Peltonen L. Kestilä M. MKS1, encoding a component of the flagellar apparatus basal body proteome, is mutated in Meckel syndrome.Nat. Genet. 2006; 38: 155-157Crossref PubMed Scopus (189) Google Scholar, Li et al., 2004Li J.B. Gerdes J.M. Haycraft C.J. Fan Y. Teslovich T.M. May-Simera H. Li H. Blacque O.E. Li L. Leitch C.C. et al.Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene.Cell. 2004; 117: 541-552Abstract Full Text Full Text PDF PubMed Scopus (581) Google Scholar). Extending the idea of a ciliary proteome to a ciliary “interactome” was the natural extension of this work through the identification of proteins that physically interact as part of specific complexes (Eley et al., 2008Eley L. Gabrielides C. Adams M. Johnson C.A. Hildebrandt F. Sayer J.A. Jouberin localizes to collecting ducts and interacts with nephrocystin-1.Kidney Int. 2008; 74: 1139-1149Crossref PubMed Scopus (39) Google Scholar, Gorden et al., 2008Gorden N.T. Arts H.H. Parisi M.A. Coene K.L. Letteboer S.J. van Beersum S.E. Mans D.A. Hikida A. Eckert M. Knutzen D. et al.CC2D2A is mutated in Joubert syndrome and interacts with the ciliopathy-associated basal body protein CEP290.Am. J. Hum. Genet. 2008; 83: 559-571Abstract Full Text Full Text PDF PubMed Scopus (157) Google Scholar). Through pair-wise testing of potential yeast two-hybrid interactions (Otto et al., 2005Otto E.A. Loeys B. Khanna H. Hellemans J. Sudbrak R. Fan S. Muerb U. O'Toole J.F. Helou J. Attanasio M. et al.Nephrocystin-5, a ciliary IQ domain protein, is mutated in Senior-Loken syndrome and interacts with RPGR and calmodulin.Nat. Genet. 2005; 37: 282-288Crossref PubMed Scopus (282) Google Scholar) and identification of binding partners by serial mass spectrometry (Nachury et al., 2007Nachury M.V. Loktev A.V. Zhang Q. Westlake C.J. Peränen J. Merdes A. Slusarski D.C. Scheller R.H. Bazan J.F. Sheffield V.C. Jackson P.K. A core complex of BBS proteins cooperates with the GTPase Rab8 to promote ciliary membrane biogenesis.Cell. 2007; 129: 1201-1213Abstract Full Text Full Text PDF PubMed Scopus (947) Google Scholar, Sang et al., 2011Sang L. Miller J.J. Corbit K.C. Giles R.H. Brauer M.J. Otto E.A. Baye L.M. Wen X. Scales S.J. Kwong M. et al.Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways.Cell. 2011; 145: 513-528Abstract Full Text Full Text PDF PubMed Scopus (391) Google Scholar), a number of discrete, functionally relevant complexes have now emerged as the likely minimal disease-causing modules (Figure 2C). An important observation, which has stood the test of time, is that the composition of these specific protein modules could have been predicted based upon the phenotype observed in patients. Specifically, the proteins from seven of the eight most conserved genes mutated in BBS form a core complex termed the BBSome (Nachury et al., 2007Nachury M.V. Loktev A.V. Zhang Q. Westlake C.J. Peränen J. Merdes A. Slusarski D.C. Scheller R.H. Bazan J.F. Sheffield V.C. Jackson P.K. A core complex of BBS proteins cooperates with the GTPase Rab8 to promote ciliary membrane biogenesis.Cell. 2007; 129: 1201-1213Abstract Full Text Full Text PDF PubMed Scopus (947) Google Scholar), found to play important roles in ciliary protein and vesicular transport. Importantly, this complex does not contain proteins encoded by other ciliopathy diseases genes such as NPHP, JBTS, or MKS. This is perhaps surprising considering that mutations in MKS genes can cause BBS (Leitch et al., 2008Leitch C.C. Zaghloul N.A. Davis E.E. Stoetzel C. Diaz-Font A. Rix S. Alfadhel M. Lewis R.A. Eyaid W. Banin E. et al.Hypomorphic mutations in syndromic encephalocele genes are associated with Bardet-Biedl syndrome.Nat. Genet. 2008; 40: 443-448Crossref PubMed Scopus (292) Google Scholar). Three separate complexes containing many of the proteins mutated in NPHP, JBTS, and MKS were recently identified, and although their function is still under investigation, genes for two of the copurifying proteins, ATXN10 and TCTN2, were found to be mutated in patients matching the same “module” phenotype (Sang et al., 2011Sang L. Miller J.J. Corbit K.C. Giles R.H. Brauer M.J. Otto E.A. Baye L.M. Wen X. Scales S.J. Kwong M. et al.Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways.Cell. 2011; 145: 513-528Abstract Full Text Full Text PDF PubMed Scopus (391) Google Scholar). In general, the complexes also display specificity in subcellular localization and function: the MKS/JBTS complex transduces hedgehog signaling and localizes to the ciliary transition zone, whereas the BBS complex forms a coat complex to target vesicles to the cilium and localizes to ciliary membrane (Jin et al., 2010Jin H. White S.R. Shida T. Schulz S. Aguiar M. Gygi S.P. Bazan J.F. Nachury M.V. The conserved Bardet-Biedl syndrome proteins assemble a coat that traffics membrane proteins to cilia.Cell. 2010; 141: 1208-1219Abstract Full Text Full Text PDF PubMed Scopus (401) Google Scholar). Proteins have nonredundant function within a given module and do not associate or function in other modules. This work has been further corroborated by analyzing a series of C. elegans double mutants, which demonstrate worsened synthetic phenotypes (i.e., functional interactions) only when mutations occur in two different modules (Williams et al., 2011Williams C.L. Li C. Kida K. Inglis P.N. Mohan S. Semenec L. Bialas N.J. Stupay R.M. Chen N. Blacque O.E. et al.MKS and NPHP modules cooperate to establish basal body/transition zone membrane associations and ciliary gate function during ciliogenesis.J. Cell Biol. 2011; 192: 1023-1041Crossref PubMed Scopus (305) Google Scholar), but not with two different mutations in the same module. For instance, the B9 domain proteins of the MKS module functionally interact with the NPHP module (Williams et al., 2008Williams C.L. Winkelbauer M.E. Schafer J.C. Michaud E.J. Yoder B.K. Functional redundancy of the B9 proteins and nephrocystins in Caenorhabditis elegans ciliogenesis.Mol. Biol. Cell. 2008; 19: 2154-2168Crossref PubMed Scopus (79) Google Scholar), but not with most other genes in the MKS module. The conclusion is that each module probably mediates partially separate ciliary functions. Inactivating one component in a module is probably sufficient to fully inactivate the module, so functional interaction is only observed by inactivating a component in a different module. Taken together, these examples show that the availability of various disease proteomes in combination with the explosion of currently available genomic and transcriptomic data sets are driving forward biological network analysis in human disease (Figure 3). What can the study of the ciliopathies teach us about the future direction of human genetic disease? Most obviously, that human genetics will be a lot more complex than many of us would have predicted. One obvious example is in the degree of multiple allelism at particular genetic loci. Although some of the ciliopathy genes are associated with only a single phenotypic class to date, other gene mutations can result in phenotypes along the entire ciliopathy clinical spectrum. For instance, mutations in CEP290 are reported in MKS, JBTS, NPHP, BBS, and LCA, spanning the full breadth of severity (Coppieters et al., 2010bCoppieters F. Lefever S. Leroy B.P. De Baere E. CEP290, a gene with many faces: mutation overview and presentation of CEP290base.Hum. Mutat. 2010; 31: 1097-1108Crossref PubMed Scopus (178) Google Scholar), whereas ARL13B mutations are restricted to patients with JBTS. For ARL13B, it is not clear whether this gene is only capable of causing a restricted phenotype or whether there are additional mutations to be identified in other ciliopathy class disorders. Current data would suggest the latter, as only hypomorphic mutations in ARL13B gene were identified in humans, whereas comparably more severe phenotypes were observed in mouse and zebrafish (Caspary et al., 2007Caspary T. Larkins C.E. Anderson K.V. The graded response to Sonic Hedgehog depends on cilia architecture.Dev. Cell. 2007; 12: 767-778Abstract Full Text Full Text PDF PubMed Scopus (488) Google Scholar, Sun et al., 2004Sun Z. Amsterdam A. Pazour G.J. Cole D.G. Miller M.S. Hopkins N. A genetic screen in zebrafish identifies cilia genes as a principal cause of cystic kidney.Development. 2004; 131: 4085-4093Crossref PubMed Scopus (404) Google Scholar), suggesting