Two key questions thematically underscore my research in the Center for Human Disease Modeling at Duke University: First of all, how can variation at the DNA level be functionally interpreted beyond the resolution of genetics arguments alone? Secondly, once empowered with functional information about genetic variants, how can pathogenic alleles be mapped back to disease phenotypes? Using the ciliary disease module as a model system of investigation, we are using multidisciplinary tactics to address these questions and continue to harness these approaches toward the further dissection of the architecture of human genetic disease. Moreover, we have applied the in vivo tools and lessons learned from ciliary phenotypes affecting the renal, craniofacial, and central nervous systems to interrogate rare pediatric disorders characterized by these phenotypic hallmarks.
Associate Professor of Pediatrics
School of Medicine
Assistant Professor of Cell Biology
School of Medicine
Associate Professor of Cell Biology
School of Medicine
Member of the Duke Cancer Institute
Duke Cancer Institute
School of Medicine
University of Liege (Belgium)
Postdoctoral Research Fellow, Institute Of Genetic Medicine
Johns Hopkins University
Postdoctoral Research Fellow, Cell Biology
Epigenetic Control of Intestinal Inflammation
Epigenetic control of intestinal inflammation
Bridge Funding Plan with Ann & Robert H Lurie Children's Hospital of Chicago
Institutes and Centers
Ann & Robert H. Lurie Children's Hospital of Chicago
Genetic and Functional Dissection of Congenital Anomalies of the Brain
Institutes and Centers
University of North Carolina - Chapel Hill
Functional Dissection of CNVs in Neurodevelopmental Traits
Institutes and Centers
National Institutes of Health
Dual Molecular Effects of Dominant RORA Mutations Cause Two Variants of Syndromic Intellectual Disability with Either Autism or Cerebellar Ataxia.
RORα, the RAR-related orphan nuclear receptor alpha, is essential for cerebellar development. The spontaneous mutant mouse staggerer, with an ataxic gait caused by neurodegeneration of cerebellar Purkinje cells, was discovered two decades ago to result from homozygous intragenic Rora deletions. However, RORA mutations were hitherto undocumented in humans. Through a multi-centric collaboration, we identified three copy-number variant deletions (two de novo and one dominantly inherited in three generations), one de novo disrupting duplication, and nine de novo point mutations (three truncating, one canonical splice site, and five missense mutations) involving RORA in 16 individuals from 13 families with variable neurodevelopmental delay and intellectual disability (ID)-associated autistic features, cerebellar ataxia, and epilepsy. Consistent with the human and mouse data, disruption of the D. rerio ortholog, roraa, causes significant reduction in the size of the developing cerebellum. Systematic in vivo complementation studies showed that, whereas wild-type human RORA mRNA could complement the cerebellar pathology, missense variants had two distinct pathogenic mechanisms of either haploinsufficiency or a dominant toxic effect according to their localization in the ligand-binding or DNA-binding domains, respectively. This dichotomous direction of effect is likely relevant to the phenotype in humans: individuals with loss-of-function variants leading to haploinsufficiency show ID with autistic features, while individuals with de novo dominant toxic variants present with ID, ataxia, and cerebellar atrophy. Our combined genetic and functional data highlight the complex mutational landscape at the human RORA locus and suggest that dual mutational effects likely determine phenotypic outcome.
Guissart, C; Latypova, X; Rollier, P; Khan, TN; Stamberger, H; McWalter, K; Cho, MT; Kjaergaard, S; Weckhuysen, S; Lesca, G; Besnard, T; Õunap, K; Schema, L; Chiocchetti, AG; McDonald, M; de Bellescize, J; Vincent, M; Van Esch, H; Sattler, S; Forghani, I; Thiffault, I; Freitag, CM; Barbouth, DS; Cadieux-Dion, M; Willaert, R; Guillen Sacoto, MJ; Safina, NP; Dubourg, C; Grote, L; Carré, W; Saunders, C; Pajusalu, S; Farrow, E; Boland, A; Karlowicz, DH; Deleuze, J-F; Wojcik, MH; Pressman, R; Isidor, B; Vogels, A; Van Paesschen, W; Al-Gazali, L; Al Shamsi, AM; Claustres, M; Pujol, A; Sanders, SJ; Rivier, F; Leboucq, N; Cogné, B; Sasorith, S; Sanlaville, D; Retterer, K; Odent, S; Katsanis, N; Bézieau, S; Koenig, M; Davis, EE; Pasquier, L; Küry, S
Guissart, Claire, et al. “Dual Molecular Effects of Dominant RORA Mutations Cause Two Variants of Syndromic Intellectual Disability with Either Autism or Cerebellar Ataxia..” Am J Hum Genet, vol. 102, no. 5, May 2018, pp. 744–59. Pubmed, doi:10.1016/j.ajhg.2018.02.021.
Am J Hum Genet
Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network.
Ocular developmental anomalies (ODA) such as anophthalmia/microphthalmia (AM) or anterior segment dysgenesis (ASD) have an estimated combined prevalence of 3.7 in 10,000 births. Mutations in SOX2 are the most frequent contributors to severe ODA, yet account for a minority of the genetic drivers. To identify novel ODA loci, we conducted targeted high-throughput sequencing of 407 candidate genes in an initial cohort of 22 sporadic ODA patients. Patched 1 (PTCH1), an inhibitor of sonic hedgehog (SHH) signaling, harbored an enrichment of rare heterozygous variants in comparison to either controls, or to the other candidate genes (four missense and one frameshift); targeted resequencing of PTCH1 in a second cohort of 48 ODA patients identified two additional rare nonsynonymous changes. Using multiple transient models and a CRISPR/Cas9-generated mutant, we show physiologically relevant phenotypes altering SHH signaling and eye development upon abrogation of ptch1 in zebrafish for which in vivo complementation assays using these models showed that all six patient missense mutations affect SHH signaling. Finally, through transcriptomic and ChIP analyses, we show that SOX2 binds to an intronic domain of the PTCH1 locus to regulate PTCH1 expression, findings that were validated both in vitro and in vivo. Together, these results demonstrate that PTCH1 mutations contribute to as much as 10% of ODA, identify the SHH signaling pathway as a novel effector of SOX2 activity during human ocular development, and indicate that ODA is likely the result of overactive SHH signaling in humans harboring mutations in either PTCH1 or SOX2.
Chassaing, N; Davis, EE; McKnight, KL; Niederriter, AR; Causse, A; David, V; Desmaison, A; Lamarre, S; Vincent-Delorme, C; Pasquier, L; Coubes, C; Lacombe, D; Rossi, M; Dufier, J-L; Dollfus, H; Kaplan, J; Katsanis, N; Etchevers, HC; Faguer, S; Calvas, P
Chassaing, Nicolas, et al. “Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network..” Genome Res, vol. 26, no. 4, Apr. 2016, pp. 474–85. Pubmed, doi:10.1101/gr.196048.115.
Ectopic Expression of Retrotransposon-Derived PEG11/RTL1 Contributes to the Callipyge Muscular Hypertrophy.
The callipyge phenotype is an ovine muscular hypertrophy characterized by polar overdominance: only heterozygous +Mat/CLPGPat animals receiving the CLPG mutation from their father express the phenotype. +Mat/CLPGPat animals are characterized by postnatal, ectopic expression of Delta-like 1 homologue (DLK1) and Paternally expressed gene 11/Retrotransposon-like 1 (PEG11/RTL1) proteins in skeletal muscle. We showed previously in transgenic mice that ectopic expression of DLK1 alone induces a muscular hypertrophy, hence demonstrating a role for DLK1 in determining the callipyge hypertrophy. We herein describe newly generated transgenic mice that ectopically express PEG11 in skeletal muscle, and show that they also exhibit a muscular hypertrophy phenotype. Our data suggest that both DLK1 and PEG11 act together in causing the muscular hypertrophy of callipyge sheep.
Xu, Xuewen, et al. “Ectopic Expression of Retrotransposon-Derived PEG11/RTL1 Contributes to the Callipyge Muscular Hypertrophy..” Plos One, vol. 10, no. 10, 2015. Pubmed, doi:10.1371/journal.pone.0140594.
Whole-exome resequencing distinguishes cystic kidney diseases from phenocopies in renal ciliopathies
Rare single-gene disorders cause chronic disease. However, half of the 6000 recessive single gene causes of disease are still unknown. Because recessive disease genes can illuminate, at least in part, disease pathomechanism, their identification offers direct opportunities for improved clinical management and potentially treatment. Rare diseases comprise the majority of chronic kidney disease (CKD) in children but are notoriously difficult to diagnose. Whole-exome resequencing facilitates identification of recessive disease genes. However, its utility is impeded by the large number of genetic variants detected. We here overcome this limitation by combining homozygosity mapping with whole-exome resequencing in 10 sib pairs with a nephronophthisis-related ciliopathy, which represents the most frequent genetic cause of CKD in the first three decades of life. In 7 of 10 sibships with a histologic or ultrasonographic diagnosis of nephronophthisis-related ciliopathy, we detect the causative gene. In six sibships, we identify mutations of known nephronophthisis-related ciliopathy genes, while in two additional sibships we found mutations in the known CKD-causing genes SLC4A1 and AGXT as phenocopies of nephronophthisis-related ciliopathy. Thus, whole-exome resequencing establishes an efficient, noninvasive approach towards early detection and causation-based diagnosis of rare kidney diseases. This approach can be extended to other rare recessive disorders, thereby providing accurate diagnosis and facilitating the study of disease mechanisms. © 2013 International Society of Nephrology.
Gee, HY; Otto, EA; Hurd, TW; Ashraf, S; Chaki, M; Cluckey, A; Vega-Warner, V; Saisawat, P; Diaz, KA; Fang, H; Kohl, S; Allen, SJ; Airik, R; Zhou, W; Ramaswami, G; Janssen, S; Fu, C; Innis, JL; Weber, S; Vester, U; Davis, EE; Katsanis, N; Fathy, HM; Jeck, N; Klaus, G; Nayir, A; Rahim, KA; Attrach, IA; Hassoun, IA; Ozturk, S; Drozdz, D; Helmchen, U; O'toole, JF; Attanasio, M; Lewis, RA; Nürnberg, G; Nürnberg, P; Washburn, J; Macdonald, J; Innis, JW; Levy, S; Hildebrandt, F
Gee, H. Y., et al. “Whole-exome resequencing distinguishes cystic kidney diseases from phenocopies in renal ciliopathies.” Kidney International, vol. 85, no. 4, Jan. 2014, pp. 880–87. Scopus, doi:10.1038/ki.2013.450.
KIF7 mutations cause fetal hydrolethalus and acrocallosal syndromes.
KIF7, the human ortholog of Drosophila Costal2, is a key component of the Hedgehog signaling pathway. Here we report mutations in KIF7 in individuals with hydrolethalus and acrocallosal syndromes, two multiple malformation disorders with overlapping features that include polydactyly, brain abnormalities and cleft palate. Consistent with a role of KIF7 in Hedgehog signaling, we show deregulation of most GLI transcription factor targets and impaired GLI3 processing in tissues from individuals with KIF7 mutations. KIF7 is also a likely contributor of alleles across the ciliopathy spectrum, as sequencing of a diverse cohort identified several missense mutations detrimental to protein function. In addition, in vivo genetic interaction studies indicated that knockdown of KIF7 could exacerbate the phenotype induced by knockdown of other ciliopathy transcripts. Our data show the role of KIF7 in human primary cilia, especially in the Hedgehog pathway through the regulation of GLI targets, and expand the clinical spectrum of ciliopathies.
Putoux, A; Thomas, S; Coene, KLM; Davis, EE; Alanay, Y; Ogur, G; Uz, E; Buzas, D; Gomes, C; Patrier, S; Bennett, CL; Elkhartoufi, N; Frison, M-HS; Rigonnot, L; Joyé, N; Pruvost, S; Utine, GE; Boduroglu, K; Nitschke, P; Fertitta, L; Thauvin-Robinet, C; Munnich, A; Cormier-Daire, V; Hennekam, R; Colin, E; Akarsu, NA; Bole-Feysot, C; Cagnard, N; Schmitt, A; Goudin, N; Lyonnet, S; Encha-Razavi, F; Siffroi, J-P; Winey, M; Katsanis, N; Gonzales, M; Vekemans, M; Beales, PL; Attié-Bitach, T
Putoux, Audrey, et al. “KIF7 mutations cause fetal hydrolethalus and acrocallosal syndromes..” Nat Genet, vol. 43, no. 6, June 2011, pp. 601–06. Pubmed, doi:10.1038/ng.826.
Animals, Genetically Modified
Bone and Bones
Chromatography, High Pressure Liquid
Ciliary Motility Disorders
DNA Copy Number Variations
DNA Mutational Analysis
Disease Models, Animal
Gene Expression Profiling
Gene Expression Regulation
Gene Expression Regulation, Developmental
Gene Knockdown Techniques
Genetic Association Studies
Genetic Diseases, Inborn
Genetic Predisposition to Disease
Green Fluorescent Proteins
Hand Deformities, Congenital
Heart Defects, Congenital
Intracellular Signaling Peptides and Proteins
Kidney Diseases, Cystic
Microscopy, Electron, Transmission
Molecular Sequence Data
Oligonucleotide Array Sequence Analysis
Otx Transcription Factors
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Sequence Homology, Amino Acid
Associate Professor of Pediatrics
300 North Duke Street, DUMC, Durham, NC 27701
Box 104775 Med Ctr, DUMC, Durham, NC 27701