Homozygous Mutations in TBC1D23 Lead to a Non-degenerative Form of Pontocerebellar Hypoplasia
2017; Elsevier BV; Volume: 101; Issue: 3 Linguagem: Inglês
10.1016/j.ajhg.2017.07.015
ISSN1537-6605
AutoresIsaac Marin‐Valencia, Andreas Gerondopoulos, Maha S. Zaki, Tawfeg Ben‐Omran, Mariam Almureikhi, Ercan Demir, Alicia Guemez‐Gamboa, Anne Gregor, Mahmoud Y. Issa, Bart Appelhof, Susanne Roosing, Damir Musaev, Başak Rosti, Sara A. Wirth, Valentina Stanley, Frank Baas, Francis A. Barr, Joseph G. Gleeson,
Tópico(s)Genetics and Neurodevelopmental Disorders
ResumoPontocerebellar hypoplasia (PCH) represents a group of recessive developmental disorders characterized by impaired growth of the pons and cerebellum, which frequently follows a degenerative course. Currently, there are 10 partially overlapping clinical subtypes and 13 genes known mutated in PCH. Here, we report biallelic TBC1D23 mutations in six individuals from four unrelated families manifesting a non-degenerative form of PCH. In addition to reduced volume of pons and cerebellum, affected individuals had microcephaly, psychomotor delay, and ataxia. In zebrafish, tbc1d23 morphants replicated the human phenotype showing hindbrain volume loss. TBC1D23 localized at the trans-Golgi and was regulated by the small GTPases Arl1 and Arl8, suggesting a role in trans-Golgi membrane trafficking. Altogether, this study provides a causative link between TBC1D23 mutations and PCH and suggests a less severe clinical course than other PCH subtypes. Pontocerebellar hypoplasia (PCH) represents a group of recessive developmental disorders characterized by impaired growth of the pons and cerebellum, which frequently follows a degenerative course. Currently, there are 10 partially overlapping clinical subtypes and 13 genes known mutated in PCH. Here, we report biallelic TBC1D23 mutations in six individuals from four unrelated families manifesting a non-degenerative form of PCH. In addition to reduced volume of pons and cerebellum, affected individuals had microcephaly, psychomotor delay, and ataxia. In zebrafish, tbc1d23 morphants replicated the human phenotype showing hindbrain volume loss. TBC1D23 localized at the trans-Golgi and was regulated by the small GTPases Arl1 and Arl8, suggesting a role in trans-Golgi membrane trafficking. Altogether, this study provides a causative link between TBC1D23 mutations and PCH and suggests a less severe clinical course than other PCH subtypes. Originally named by Brun in 1917,1Brun R. Zur Kenntnis der Bildungsfehler des Kleinhirns. Epikritische Bemerkungen zur Entwicklungspathologie, Morphologie und Klinik der umschriebenen Entwicklungshemmungen des Neozerebellums.Schweiz. Arch. Neurol. Psychiatr. 1917; 1: 48-105Google Scholar pontocerebellar hypoplasia (PCH) is a devastating neurological disorder characterized by impaired growth and/or degeneration of cerebral structures, primarily the pons and cerebellum. To date, ten different clinical subtypes of PCH have been described, the majority leading to a neurodegenerative course, manifesting with progressive intellectual and motor decline.2Rudnik-Schöneborn S. Barth P.G. Zerres K. Pontocerebellar hypoplasia.Am. J. Med. Genet. C. Semin. Med. Genet. 2014; 166C: 173-183Crossref PubMed Scopus (61) Google Scholar, 3Namavar Y. Barth P.G. Poll-The B.T. Baas F. Classification, diagnosis and potential mechanisms in pontocerebellar hypoplasia.Orphanet J. Rare Dis. 2011; 6: 50Crossref PubMed Scopus (136) Google Scholar Treatments are only palliative and the prognosis is poor, as most affected individuals die during infancy or childhood. Despite the expansion of known genes associated with PCH, most individuals remain without genetic diagnosis, suggesting that additional causes remain to be identified. We recruited a cohort of 75 families with likely autosomal-recessive PCH, of which 53 (70.6%) documented parental consanguinity and 19 (25.3%) had two or more affected individuals. All affected members were clinically evaluated by a pediatric neurologist and geneticist, blood and/or saliva samples and skin biopsies were collected from participating individuals after obtaining proper informed consent, and DNA for whole-exome sequencing (WES) was extracted from at least one affected member of each family as described.4Dixon-Salazar T.J. Silhavy J.L. Udpa N. Schroth J. Bielas S. Schaffer A.E. Olvera J. Bafna V. Zaki M.S. Abdel-Salam G.H. et al.Exome sequencing can improve diagnosis and alter patient management.Sci. Transl. Med. 2012; 4: 138ra78Crossref PubMed Scopus (197) Google Scholar The study followed the IRB guidelines and was approved by the ethical committees of UC San Diego, The Rockefeller University, and other participating institutions. In consanguineous families, we emphasized homozygous, rare ( 4 or phastCons > 0.9).5Akizu N. Cantagrel V. Zaki M.S. Al-Gazali L. Wang X. Rosti R.O. Dikoglu E. Gelot A.B. Rosti B. Vaux K.K. et al.Biallelic mutations in SNX14 cause a syndromic form of cerebellar atrophy and lysosome-autophagosome dysfunction.Nat. Genet. 2015; 47: 528-534Crossref PubMed Scopus (88) Google Scholar Likely causative mutations were identified in 47 families (62.6% of the total) (Figure 1A). Seven families (9.3%) had a likely causative variant in a gene not previously implicated in PCH. A total of 34 families (45.3%) carried mutations in genes previously associated with degenerative forms of PCH, encoding proteins involved in tRNA splicing, mRNA processing, and protein synthesis.5Akizu N. Cantagrel V. Zaki M.S. Al-Gazali L. Wang X. Rosti R.O. Dikoglu E. Gelot A.B. Rosti B. Vaux K.K. et al.Biallelic mutations in SNX14 cause a syndromic form of cerebellar atrophy and lysosome-autophagosome dysfunction.Nat. Genet. 2015; 47: 528-534Crossref PubMed Scopus (88) Google Scholar, 6Schaffer A.E. Eggens V.R. Caglayan A.O. Reuter M.S. Scott E. Coufal N.G. Silhavy J.L. Xue Y. Kayserili H. Yasuno K. et al.CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration.Cell. 2014; 157: 651-663Abstract Full Text Full Text PDF PubMed Scopus (170) Google Scholar, 7Namavar Y. Barth P.G. Kasher P.R. van Ruissen F. Brockmann K. Bernert G. Writzl K. Ventura K. Cheng E.Y. Ferriero D.M. et al.PCH ConsortiumClinical, neuroradiological and genetic findings in pontocerebellar hypoplasia.Brain. 2011; 134: 143-156Crossref PubMed Scopus (164) Google Scholar, 8Budde B.S. Namavar Y. Barth P.G. Poll-The B.T. Nürnberg G. Becker C. van Ruissen F. Weterman M.A. Fluiter K. te Beek E.T. et al.tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia.Nat. Genet. 2008; 40: 1113-1118Crossref PubMed Scopus (181) Google Scholar Six families (8%) demonstrated a non-degenerative course of PCH, and among these, TBC1D23 mutations were identified as a cause for this condition. TBC1D23 has been recently linked also with autosomal-recessive intellectual disability.9Harripaul R. Vasli N. Mikhailov A. Rafiq M.A. Mittal K. Windpassinger C. Sheikh T.I. Noor A. Mahmood H. Downey S. et al.Mapping autosomal recessive intellectual disability: combined microarray and exome sequencing identifies 26 novel candidate genes in 192 consanguineous families.Mol. Psychiatry. 2017; (Published online April 11, 2017)https://doi.org/10.1038/mp.2017.60Crossref PubMed Scopus (99) Google Scholar We found six affected individuals with mutations in TBC1D23 from four unrelated families from Egypt (families I and II), Turkey (family III), and Lebanon (family IV) (Figures 1B and S1). Family I presented with two affected boys of 16 years (I-IV-1) and 2 years (I-IV-5) of age, family II presented with two non-identical girl twins of 4 years of age (II-III-1 and II-III-2), family III presented with one boy of 14 months of age (III-IV-1), and family IV presented with a girl of 6 months of age (IV-II-1) (Figure 1B). Some of these individuals manifested reduced head circumference at birth (≥−2 SD standard deviations [SD] below the mean) and all showed signs of global psychomotor deficits since early infancy, involving gross and fine motor skills, language (expressive > receptive), and social interaction due to communication impairment (Table 1). In the most recent clinical evaluation, all subjects were microcephalic (≥−3 SD), and height and weight ranged from normal to −5 SD. Neurological exam was remarkable for generalized weakness (6/6 affected subjects), global hypotonia (5/6), and cerebellar deficits such as uncoordinated limb movements (4/6), hyporeflexia (3/6), and impaired or no ambulation (6/6). Brainstem symptoms including dysphagia and dysarthria were present in subjects from family I. None of the six individuals manifested clinical signs of neurological deterioration and, hitherto, they are all alive. Brain MRI showed pontocerebellar hypoplasia in all subjects, along with thin corpus callosum (I-IV-5, II-III-1, II-III-2, IV-II-1) and cortical hypoplasia (I-IV-5, II-III-1, II-III-2) (Figure 1C). The radiological findings of subject III-IV-1 did not change appreciably over a 3-year interval (Figure S2), which is consistent with the non-progressive course of this form of PCH.Table 1Description of Clinical Findings of Individuals with TBC1D23 MutationsI-IV-1I-IV-5II-III-1II-III-2III-VI-1IV-II-1Mutation (genomic hg19)chr3:g.100029386G>Achr3:g.100029386G>Achr3:g.100035033T>Achr3:g.100035033T>Achr3:g.100035032G>Achr3:g.100014144A>GMutation (cDNA) (NM_001199198.2)c.1553G>Ac.1553G>Ac.1687+2T>Ac.1687+2T>Ac.1687+1G>Ac.726−2A>GMutation (protein)p.[Arg518Gln;?]p.[Arg518Gln;?]p.His534Trpfs∗36p.His534Trpfs∗36p.His534Trpfs∗36p.?Gestational age40383737N/AN/AWeight at birth (kg)3 (−0.90 SD)2.8 (−1.22 SD)1.6 (−3.47 SD)1.5 (−3.66 SD)3.8 (+0.49 SD)8.8 at age 2 years (−3 SD)Length at birth (cm)50 (−0.06 SD)48 (−0.81 SD)48 (−0.65 SD)47 (−1.10 SD)N/AN/AHC at birth (cm)32.2 (−1.62 SD)32 (−1.71 SD)32 (−1.90 SD)31.5 (−2.24 SD)42 at 14 months (−3.84 SD)41.2 at 2 years (−4.4 SD)Age at diagnosisdelayed since infancy, but first seen at 16 years of age2 yearsdelayed since infancy, but first seen at 4 years of agedelayed since infancy, but first seen at 4 years of age14 months6 monthsWeight (kg), age at last examination38, 16 years (−2.65 SD)14, 6 years (−2.96 SD)14.5, 4 years (−0.79 SD)11.5, 4 years (−2.62 SD)N/A11.9, 7.5 years (−4.11 SD)Height (cm), age at last examination143, 16 years (−3.56 SD)103, 6 years (−2.44 SD)103, 4 years (+0.50 SD)97, 4 years (−0.89 SD)N/A98, 7.5 years (−4.89 SD)HC (cm), age at last examination48, 16 years (−4.77 SD)44.5, 6 years (−5.27 SD)43.5, 4 years (−3.96 SD)41.5, 4 years (−5.25 SD)50, 16 years (−3.4 SD)42, 7.5 years (−7.77 SD)Psychomotor DevelopmentGross motordelayed; can walk alonedelayed; sits onlydelayed; can walk alonedelayed; walks supporteddelayeddelayedFine motordelayeddelayeddelayeddelayedabsentdelayedLanguagedelayeddelayeddelayeddelayedabsentdelayed (babbling at 7 years of age)SocialdelayeddelayeddelayeddelayedabsentdelayedRegression of acquired milestones––––––Neurological FindingsBrainstem findingsdysarthria. no history of apnea, hearing deficit, dizziness, or dysphagiaminimal dysphagia. no history of apnea, hearing deficit, or dizziness.––N/A–Cerebellar deficitstruncal and appendicular ataxiatruncal and appendicular ataxiatruncal and appendicular ataxiatruncal and appendicular ataxia––Muscle strength (scale 0->5 in upper and lower extremities)grade 4/5grade 4/5grade 4/5grade 4/5grade 5/5grade 3/5Muscle tonehypotoniahypotoniahypotoniahypotonianormal muscle tonehypotonia; reduced muscle tone at 2 years, but developed spasticity especially in lower limbs at 7 years.Deep tendon reflexesnormalnormalhyporeflexiahyporeflexianormalhyporeflexia; last examined at 2 years of ageGaitwide base unsteady gait, ataxiacan sit and only stand supported with wide base gaitwide base gait, ataxianon-ambulatorywide base gaitcrawling, unsupported sitting, and cannot bear weight in left limb.SeizuresOnset––––11 years2 yearsType––––focal seizures with secondary generalizationmyoclonic seizuresOther Systemic Findingsrecurrent respiratory infections, sepsis, muscle atrophyrecurrent respiratory infections, sepsisstrabismus, recurrent respiratory infections, hypoplasia of labia minorastrabismus, recurrent respiratory infections, muscle atrophy, hypoplasia of labia minoraesotropia of left eye, proximal interphalangeal joint contractures–Abbreviations are as follows: plus sign (+), present; minus sign (-) absent, (N/A) not assessed. SD, standard deviation; HC, head circumference. Mutations in brackets have a presumed effect on splicing. Open table in a new tab Abbreviations are as follows: plus sign (+), present; minus sign (-) absent, (N/A) not assessed. SD, standard deviation; HC, head circumference. Mutations in brackets have a presumed effect on splicing. All six affected individuals carried mutations predicted to result in altered splicing, occurring at or near canonical splice sites (Figure 1D; Table 1), so we used genome build hg19 and transcript GenBank: NM_001199198.2 (transcript 1) to annotate splicing effects. We found that both TBC1D23 transcripts were differently expressed in human tissues, with transcript 1 primarily expressed in the fetal and adult brain and spinal cord (Figure 2A). To study potential effects of the variants on splicing, we used RT-PCR to amplify annotated transcripts from fibroblasts of families II and III, who carried mutations c.1687+2T>A and c.1687+1G>A, respectively (primers are available upon request). Affected individuals had shorter transcripts relative to control individuals (Figure 2B), and sequencing of the amplified PCR products confirmed that shorter transcripts had skipped exon 16 (Figure 2C), leading to a shift in the reading frame and truncated protein (p.His534Trpfs∗36) (Figures 1D and 2D). Fibroblasts from families I and IV were not available to assess splicing. Family IV carried a variant in a canonical splice site (c.726−2A>G) and family I carried a missense mutation at the last base of exon 14 (c.1553G>A), both of which were also expected to compromise splicing. Cellular localization of endogenous TBC1D23 was examined in control, carrier, and affected individuals’ fibroblasts using specific antibodies. In control fibroblasts, TBC1D23 overlapped with the trans-Golgi marker TGN46 and showed signal adjacent to the cis-Golgi marker GM130 (Figure 2E). This trans-Golgi staining pattern of TBC1D23 was absent in cells from affected individuals, whereas cells from carriers showed reduced staining intensity. Despite the loss of detectable TBC1D23 in affected subjects (Figures 2D and 2E), there was no obvious alteration in the relative positions of the cis/trans-Golgi markers or the ribbon-like structure of the Golgi (Figure 2E). TBC1D23 belongs to a family of Tre2-Bub2-Cdc16 (TBC) domain-containing Rab-specific GTPase-activating proteins (TBC/RabGAPs) that regulate membrane trafficking by inactivating Rabs.10Bernards A. GAPs galore! A survey of putative Ras superfamily GTPase activating proteins in man and Drosophila.Biochim. Biophys. Acta. 2003; 1603: 47-82PubMed Google Scholar, 11Fukuda M. TBC proteins: GAPs for mammalian small GTPase Rab?.Biosci. Rep. 2011; 31: 159-168Crossref PubMed Scopus (143) Google Scholar, 12Stenmark H. Rab GTPases as coordinators of vesicle traffic.Nat. Rev. Mol. Cell Biol. 2009; 10: 513-525Crossref PubMed Scopus (2283) Google Scholar Most TBC/RabGAPs contain two catalytic residues, Arg and Gln, to stimulate the hydrolysis of GTP in Rab proteins.13Pan X. Eathiraj S. Munson M. Lambright D.G. TBC-domain GAPs for Rab GTPases accelerate GTP hydrolysis by a dual-finger mechanism.Nature. 2006; 442: 303-306Crossref PubMed Scopus (259) Google Scholar, 14Frasa M.A. Koessmeier K.T. Ahmadian M.R. Braga V.M. Illuminating the functional and structural repertoire of human TBC/RABGAPs.Nat. Rev. Mol. Cell Biol. 2012; 13: 67-73Crossref PubMed Scopus (24) Google Scholar TBC1D23 falls in the category of unconventional TBC/RabGAPs since it lacks the catalytic Arg-Gln residues and it might, a priori, work through a different mechanism to induce GTP hydrolysis14Frasa M.A. Koessmeier K.T. Ahmadian M.R. Braga V.M. Illuminating the functional and structural repertoire of human TBC/RABGAPs.Nat. Rev. Mol. Cell Biol. 2012; 13: 67-73Crossref PubMed Scopus (24) Google Scholar or it might have a Rab-independent function. When compared to TBC1D20, which acts on Rab1, none of the 55 Rabs tested showed robust activation of GTP hydrolysis in the presence of purified TBC1D2315Haas A.K. Fuchs E. Kopajtich R. Barr F.A. A GTPase-activating protein controls Rab5 function in endocytic trafficking.Nat. Cell Biol. 2005; 7: 887-893Crossref PubMed Scopus (166) Google Scholar (Figure S3). This raised the possibility that TBC1D23 is a Rab-binding protein, or effector, rather than a Rab regulator and it may target to the Golgi via this means. However, two lines of evidence argue against this. First, a region in TBC1D23 (469–570 aa), C-terminal to the TBC1 and Rhodanese domains, is responsible for its targeting to the trans-Golgi (Figures 3A and 3B ). Second, TBC1D23 remains associated with trans-Golgi membranes when Rabs are depleted, with just a subset (Rab1a/b, Rab2a/b, Rab6a/b, Rab7a, Rab14a/b) giving rise to altered TBC1D23 localization due to their effects on Golgi structure or trafficking to and from the Golgi (Figure S3). This suggested a Rab-independent targeting mechanism. Like Rabs, Ras superfamily GTPases of the Arl and Arf group are known to be involved in recruitment of cytosolic proteins to membrane surfaces. Strikingly, depletion of Arl1, but not ArfRP1 or other Arfs or Arls, resulted in the complete loss of TBC1D23 from the trans-Golgi (Figure 3C). Conversely, knocking down Arl8 resulted in elevated staining for TBC1D23 at the trans-Golgi (Figure 3C). These findings connect TBC1D23 to an Arl1-dependent trafficking process at the trans-Golgi16Panic B. Perisic O. Veprintsev D.B. Williams R.L. Munro S. Structural basis for Arl1-dependent targeting of homodimeric GRIP domains to the Golgi apparatus.Mol. Cell. 2003; 12: 863-874Abstract Full Text Full Text PDF PubMed Scopus (116) Google Scholar, 17Wu M. Lu L. Hong W. Song H. Structural basis for recruitment of GRIP domain golgin-245 by small GTPase Arl1.Nat. Struct. Mol. Biol. 2004; 11: 86-94Crossref PubMed Scopus (88) Google Scholar, 18Lu L. Horstmann H. Ng C. Hong W. Regulation of Golgi structure and function by ARF-like protein 1 (Arl1).J. Cell Sci. 2001; 114: 4543-4555Crossref PubMed Google Scholar, 19Lu L. Tai G. Hong W. Autoantigen Golgin-97, an effector of Arl1 GTPase, participates in traffic from the endosome to the trans-golgi network.Mol. Biol. Cell. 2004; 15: 4426-4443Crossref PubMed Scopus (149) Google Scholar and to Arl8 function in the endosome-lysosome system.20Donaldson J.G. Jackson C.L. ARF family G proteins and their regulators: roles in membrane transport, development and disease.Nat. Rev. Mol. Cell Biol. 2011; 12: 362-375Crossref PubMed Scopus (594) Google Scholar, 21Nakae I. Fujino T. Kobayashi T. Sasaki A. Kikko Y. Fukuyama M. Gengyo-Ando K. Mitani S. Kontani K. Katada T. The arf-like GTPase Arl8 mediates delivery of endocytosed macromolecules to lysosomes in Caenorhabditis elegans.Mol. Biol. Cell. 2010; 21: 2434-2442Crossref PubMed Scopus (44) Google Scholar, 22Pu J. Schindler C. Jia R. Jarnik M. Backlund P. Bonifacino J.S. BORC, a multisubunit complex that regulates lysosome positioning.Dev. Cell. 2015; 33: 176-188Abstract Full Text Full Text PDF PubMed Scopus (208) Google Scholar Thus far, these two Arls have not been associated with human disease and the impact of their interaction with TBC1D23 on brain development requires additional studies. To investigate the role of TBC1D23 in brain development, we designed a zebrafish model of disease. A single tbc1d23 ortholog (GenBank: NM_200487) encodes a protein with 77% identity with the human TBC1D23 amino acid sequence. tbc1d23 transcript was detected as early as the first hours post-fertilization (hpf) by RT-PCR, and by in situ RNA hybridization tbc1d23 was primarily localized in the head at 48 hpf (Figures 4A and 4B ), suggesting a role in brain development. To test whether knockdown tbc1d23 in zebrafish replicates the human phenotype, we knocked down tbc1d23 using a translation blocking morpholino targeting the ATG start codon (tbc1d23-ATG MO; 5′-CTTCCCCTACAGCATCCGCCATTGC-3′) and a splice blocking morpholino targeting intron 4 to exon 5 (tbc1d23-splice MO; 5′-GCAGTCTCTGCAAAAGGCAATATGC-3′). In contrast to scramble MO, both ATG and splice MO-injected embryos (3 ng each) had reduced brain and eye size and manifested curved tails at 48 hpf (more severe in ATG MO embryos), and this phenotype was partially rescued with injection of zebrafish tbc1d23 mRNA (Figures 4C and 4D). These findings were corroborated in Tg(HuC:Kaede) transgenic zebrafish line, which expresses the fluorescent protein Kaede in neurons. The ATG MO injected Tg(HuC:Kaede) zebrafish showed reduced signal in the neural axis and manifested altered morphology of forebrain, brainstem, and cerebellum relative to scramble MO embryos (Figure 4E). Altogether, tbc1d23 disruption in zebrafish replicates the human phenotype by impairing brain growth and development. This study enhances the genetic diagnosis and expands the phenotypic spectrum of PCH. In contrast to most subtypes, individuals with TBC1D23-associated PCH did not show clinical neurological deterioration and MRI findings did not worsen over time. None of the affected individuals have died so far and the oldest are currently 16 years old (I-IV-1 and III-IV-1). This distinctive clinical course is therefore highly valuable for family counseling and prognostication since most individuals with other PCH subtypes show progressive worsening and typically succumb during infancy or early childhood.2Rudnik-Schöneborn S. Barth P.G. Zerres K. Pontocerebellar hypoplasia.Am. J. Med. Genet. C. Semin. Med. Genet. 2014; 166C: 173-183Crossref PubMed Scopus (61) Google Scholar TBC1D23 individuals shared some neurological manifestations with other forms of PCH, such as psychomotor impairment, microcephaly, brainstem deficits, and ataxia.2Rudnik-Schöneborn S. Barth P.G. Zerres K. Pontocerebellar hypoplasia.Am. J. Med. Genet. C. Semin. Med. Genet. 2014; 166C: 173-183Crossref PubMed Scopus (61) Google Scholar In addition to severe volume loss of pons and cerebellum, TBC1D23 individuals manifested hypoplasia of cortex and of corpus callosum as seen in other forms of PCH3Namavar Y. Barth P.G. Poll-The B.T. Baas F. Classification, diagnosis and potential mechanisms in pontocerebellar hypoplasia.Orphanet J. Rare Dis. 2011; 6: 50Crossref PubMed Scopus (136) Google Scholar (Figure 1C). At the systemic level, the most common findings in all affected subjects were recurrent respiratory infections and even sepsis (Table 1). This could relate to the essential role of the brainstem to swallowing function and handling respiratory secretions. However, it has been reported that TBC1D23 may have inhibitory effects on innate immunity and on LPS-induced cytokine release in mice,24De Arras L. Yang I.V. Lackford B. Riches D.W. Prekeris R. Freedman J.H. Schwartz D.A. Alper S. Spatiotemporal inhibition of innate immunity signaling by the Tbc1d23 RAB-GAP.J. Immunol. 2012; 188: 2905-2913Crossref PubMed Scopus (21) Google Scholar and we cannot exclude the possibility that loss of TBC1D23 could exacerbate the inflammatory response against bacterial infections and lead to more severe clinical manifestations. At baseline, affected individuals did not show significant increase of inflammatory markers and cytokine levels compared to control subjects (Table S1). Thus, more studies are necessary to evaluate the immune system of these individuals in order to determine their inflammatory response to infections. Thus far, deleterious mutations in two TBC/RabGAPs genes have been implicated in disorders of brain development: TBC1D24 (MIM: 613577), which causes focal and familial infantile myoclonic epilepsy,25Corbett M.A. Bahlo M. Jolly L. Afawi Z. Gardner A.E. Oliver K.L. Tan S. Coffey A. Mulley J.C. Dibbens L.M. et al.A focal epilepsy and intellectual disability syndrome is due to a mutation in TBC1D24.Am. J. Hum. Genet. 2010; 87: 371-375Abstract Full Text Full Text PDF PubMed Scopus (101) Google Scholar, 26Falace A. Buhler E. Fadda M. Watrin F. Lippiello P. Pallesi-Pocachard E. Baldelli P. Benfenati F. Zara F. Represa A. et al.TBC1D24 regulates neuronal migration and maturation through modulation of the ARF6-dependent pathway.Proc. Natl. Acad. Sci. USA. 2014; 111: 2337-2342Crossref PubMed Scopus (78) Google Scholar, 27Falace A. Filipello F. La Padula V. Vanni N. Madia F. De Pietri Tonelli D. de Falco F.A. Striano P. Dagna Bricarelli F. Minetti C. et al.TBC1D24, an ARF6-interacting protein, is mutated in familial infantile myoclonic epilepsy.Am. J. Hum. Genet. 2010; 87: 365-370Abstract Full Text Full Text PDF PubMed Scopus (120) Google Scholar and TBCK (MIM: 616899), which has been associated with severe infantile syndromic encephalopathy.28Chong J.X. Caputo V. Phelps I.G. Stella L. Worgan L. Dempsey J.C. Nguyen A. Leuzzi V. Webster R. Pizzuti A. et al.University of Washington Center for Mendelian GenomicsRecessive inactivating mutations in TBCK, encoding a Rab GTPase-activating protein, cause severe infantile syndromic encephalopathy.Am. J. Hum. Genet. 2016; 98: 772-781Abstract Full Text Full Text PDF PubMed Scopus (27) Google Scholar, 29Bhoj E.J. Li D. Harr M. Edvardson S. Elpeleg O. Chisholm E. Juusola J. Douglas G. Guillen Sacoto M.J. Siquier-Pernet K. et al.Mutations in TBCK, encoding TBC1-domain-containing kinase, lead to a recognizable syndrome of intellectual disability and hypotonia.Am. J. Hum. Genet. 2016; 98: 782-788Abstract Full Text Full Text PDF PubMed Scopus (34) Google Scholar, 30Liu Y. Yan X. Zhou T. TBCK influences cell proliferation, cell size and mTOR signaling pathway.PLoS ONE. 2013; 8: e71349Crossref PubMed Scopus (34) Google Scholar Like TBC1D23, both TBC1D24 and TBCK are part of the unconventional group of TBC/RabGAPs since they lack the Arg and/or Gln fingers of the TBC domain. TBC1D24 regulates neuronal migration and maturation by inactivating ADP ribosylation factor (ARF) 6, a small GTPase involved in vesicle trafficking.26Falace A. Buhler E. Fadda M. Watrin F. Lippiello P. Pallesi-Pocachard E. Baldelli P. Benfenati F. Zara F. Represa A. et al.TBC1D24 regulates neuronal migration and maturation through modulation of the ARF6-dependent pathway.Proc. Natl. Acad. Sci. USA. 2014; 111: 2337-2342Crossref PubMed Scopus (78) Google Scholar Whether ARF6 inactivation occurs by direct or indirect induction of GTP hydrolysis is still unknown. On the other hand, the target GTPase of TBCK has not been yet identified. TBCK regulates cell growth and proliferation by modulating transcription of several constituents of the mTOR pathway.30Liu Y. Yan X. Zhou T. TBCK influences cell proliferation, cell size and mTOR signaling pathway.PLoS ONE. 2013; 8: e71349Crossref PubMed Scopus (34) Google Scholar Structural and molecular modeling analyses of mutations in the TBC domain suggests that TBCK may also have Rab GAP activity and that the loss of GAP function is associated with disease.28Chong J.X. Caputo V. Phelps I.G. Stella L. Worgan L. Dempsey J.C. Nguyen A. Leuzzi V. Webster R. Pizzuti A. et al.University of Washington Center for Mendelian GenomicsRecessive inactivating mutations in TBCK, encoding a Rab GTPase-activating protein, cause severe infantile syndromic encephalopathy.Am. J. Hum. Genet. 2016; 98: 772-781Abstract Full Text Full Text PDF PubMed Scopus (27) Google Scholar Our results point toward a Rab-independent trafficking role of TBC1D23 that may be critical during hindbrain formation, but not contributory to degeneration. Ivanova et al.31Ivanova E.L. Mau-Them F.T. Riazuddin S. Kahrizi K. Laugel V. Schaefer E. de Saint Martin A. Runge K. Iqbal Z. Marie-Aude S. et al.Homozygous truncating variants in TBC1D23 cause pontocerebellar hypoplasia and alter cortical development.Am. J. Hum. Genet. 2017; 101 (this issue): 428-440Abstract Full Text Full Text PDF PubMed Scopus (33) Google Scholar showed that vesicle trafficking in fibroblasts from affected individuals lacking TBC1D23 is significantly slower than control subjects. 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Ferriero D.M. et al.PCH ConsortiumClinical, neuroradiological and genetic findings in pontocerebellar hypoplasia.Brain. 2011; 134: 143-156Crossref PubMed Scopus (164) Google Scholar In PCH, how mutations in genes that regulate protein synthesis cause neurodegeneration whereas genes involved in trafficking and signaling impairs primarily brain development, and why all these genes preferentially involve the hindbrain are questions that remain unsolved. Whether there are key molecular pathways involved in hindbrain formation where these genes converge and lead to a pontocerebellar phenotype is a matter that needs further investigation. The authors thank all families for participation in this study. We thank Tessa van Dijk for coordinating data gathering from family 4572. Thanks to the Rockefeller and UCSD Microscopy Cores (P30 NS047101) for imaging support. I.M.-V. was sponsored by Pilot Grant awarded by the Center for Basic and Translational Research on Disorders of the Digestive System at The Rockefeller University through the generosity of the Leona M. and Harry B. Helmsley Charitable Trust. We thank the Broad Institute (U54HG003067 to E. Lander and UM1HG008900 to D. MacArthur) and the Yale Center for Mendelian Disorders (U54HG006504 to R. Lifton and M. Gunel). This work was supported by NIH grants P01HD070494, 1R01NS098004, R01NS048453, R01NS052455, and UL1TR001866 from the National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH) Clinical and Translational Science Award (CTSA) program, the Simons Foundation Autism Research Initiative (275275), Howard Hughes Medical Institute (to J.G.G.), Qatar National Research Foundation NPRP 6-1463-3-351 (to T.B.-O. and J.G.G.), NIH grant K99NS089943 (to A.G.-G.), American Academy of Neurology Clinical Research Training Scholarship 2017-205 (to I.M.-V.), Joshua Deeth Foundation (to F.B.), and a Wellcome Trust Senior Investigator Award 097769/Z/11/Z (to F.A.B.). The accession number for the TBC1D23 sequence reported in this paper is Genbank: NM_001199198.2. Download .pdf (25.84 MB) Help with pdf files Document S1. Figures S1–S3 and Table S1 ExAC Browser, http://exac.broadinstitute.org/GATK, https://www.broadinstitute.org/gatk/GenBank, http://www.ncbi.nlm.nih.gov/genbank/GME Variome, http://igm.ucsd.edu/gmeMutation Assessor, http://mutationassessor.org/OMIM, http://www.omim.org/PolyPhen-2, http://genetics.bwh.harvard.edu/pph2/PROVEAN, http://provean.jcvi.orgSIFT, http://sift.bii.a-star.edu.sg/UCSC Genome Browser, http://genome.ucsc.edu Homozygous Truncating Variants in TBC1D23 Cause Pontocerebellar Hypoplasia and Alter Cortical DevelopmentIvanova et al.The American Journal of Human GeneticsAugust 17, 2017In BriefPontocerebellar hypoplasia (PCH) is a heterogeneous group of rare recessive disorders with prenatal onset, characterized by hypoplasia of pons and cerebellum. Mutations in a small number of genes have been reported to cause PCH, and the vast majority of PCH cases are explained by mutations in TSEN54, which encodes a subunit of the tRNA splicing endonuclease complex. Here we report three families with homozygous truncating mutations in TBC1D23 who display moderate to severe intellectual disability and microcephaly. Full-Text PDF Open Archive
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