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Saudi Journal of Kidney Diseases and Transplantation
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Table of Contents   
CASE REPORT  
Year : 2019  |  Volume : 30  |  Issue : 4  |  Page : 964-968
Identification of a new homozygous CEP290 gene mutation in a Saudi Family causing joubert syndrome using next-generation sequencing


1 Department of Internal Medicine, King Abdulaziz Hospital, Ministry of National Guard Health Affairs, Al-Ahsa, Saudi Arabia
2 Department of Internal Medicine, College of Medicine, King Faisal University, Al-Ahsa, Saudi Arabia

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Date of Submission10-Aug-2018
Date of Acceptance14-Sep-2018
Date of Web Publication27-Aug-2019
 

   Abstract 


A 19-year-old female with a learning difficulty, ataxia, and nystagmus was referred to our clinic with advanced chronic kidney disease. Her renal biopsy revealed features of nephronophthisis (NPHP). Magnetic resonance imaging of the brain showed “molar tooth sign.” The clinical picture was consistent with Joubert syndrome (JS). Two of her siblings were subsequently found to have a similar condition. Genomic material from the patient, her twin sister, and later on from parents was analyzed for deletion/duplication mutations in the NPHP1 gene using multiplex ligation-dependent probe amplification. No genetic defect was discerned. However, applying the emerging “Next-Generation Sequencing (NGS)” method, we identified a novel c.5704G>T mutation in exon 41 of the CEP290 gene on chromosome 12q21. The identification of this novel mutation, that is, highly likely to be pathogenic was compatible with the diagnosis of JS. This mutation may be included in screening and diagnostic panel. NGS provides an excellent screening method for genetic testing.

How to cite this article:
Abdelgadir E, Al Sahlawi M, Al Turki L, Khamees K, Ahmed W. Identification of a new homozygous CEP290 gene mutation in a Saudi Family causing joubert syndrome using next-generation sequencing. Saudi J Kidney Dis Transpl 2019;30:964-8

How to cite this URL:
Abdelgadir E, Al Sahlawi M, Al Turki L, Khamees K, Ahmed W. Identification of a new homozygous CEP290 gene mutation in a Saudi Family causing joubert syndrome using next-generation sequencing. Saudi J Kidney Dis Transpl [serial online] 2019 [cited 2019 Sep 20];30:964-8. Available from: http://www.sjkdt.org/text.asp?2019/30/4/964/265475



   Introduction Top


Joubert syndrome (JS) is an autosomal reces-sively inherited disorder. It has an estimated prevalence of 1/5000 live births in the United Arab Emirates, however, the prevalence in most Arab countries, where consanguineous unions account for up to 60% of marriages, is unknown.[1] The syndrome was first described in four children with hyperpnea, abnormal eye movements, ataxia and cognitive deficits, related to agenesis of the cerebellar vermis.[2] A number of mutations have been identified in individuals with JS. Therefore, genomic material from the patient, her twin sister, and later on from parents was analyzed for deletion/ duplication mutations in the nephronophthisis 1 (NPHP1) gene using multiplex ligation-depen-dent probe amplification. No genetic defect was discerned. However, applying the emerging “Next-Generation Sequencing (NGS)” method, we identified a novel c.5704G>T mutation in exon 41 of the CEP290 gene on chromosome 12q21. The identification of this novel mutation that is highly likely to pathogenic was compatible with the diagnosis of JS.

We are reporting this rare case where regular genomic sequencing failed to detect the genetic defect, but NGS method identified a novel mutation that can be attributed to JS.


   Case Report Top


The patient has marked cognitive impairment and mental sub-normality, the consent was obtained from both of her parents.

A 19-year old female, Saudi national with cognitive impairment, dysarthria, ataxia, and nystagmus was referred to our department with polyuria and advanced chronic kidney disease (CKD) Stage 5. She is the twin sister of another patient with similar neurologic features and CKD Stage 4. The twins are the product of a second-degree consanguineous marriage. The twins had a younger brother with a similar central nervous system (CNS) phenotype, who died at the age of nine years of apparently advanced renal disease, and four other siblings who were healthy. The father, a 49-year-old Saudi, and the mother, 48-year-old, were both healthy with normal kidney function. The patient and her twin sister lived in a long-term care facility with parents visiting regularly. The patient did not attend school. On examination, cognitive impairment was evident along with dysarthria, generalized hypotonia, and broad gait ataxia. Fundus examination revealed slightly pale optic disc with evidence of retinitis pigmentosa. She was normotensive. Examination of the chest, heart, and abdomen was unremarkable, and in particular, the kidneys were not palpable. There was no peripheral edema. The Mini-Mental State Examination is 8/30.

Investigations

The laboratory investigations at the time of presentation showed the following: urea - 31.6 μmol/L, creatinine - 645 μmol/L, serum bicarbonate - 16 mmol/L, serum sodium – 135 mmol/L, potassium - 4.2 mmol/L, albumin -44 g/L, calcium: 2.4 mmol/L, phosphate: 1.74 mmol/L and PTH - 114 ng/L. Hemoglobin was 10.2 g/dL; the liver profile, lipids, and complement levels were all within normal ranges.

There was no serologic evidence of hepatitis B, hepatitis C, systemic lupus erythematosus, antineutrophil cytoplasmic antibody vasculitis, or glomerular basement membrane disease. The urine analysis revealed specific gravity of 1010 in the absence of any active sediment. The 24-h total urine protein was 0.18 g.

An ultrasound scan of the abdomen showed kidneys of normal size with bilaterally increased echogenicity and with no cysts or calculi noted. The magnetic resonance imaging of the brain showed localized cerebellar vermis atrophy with bilateral atrophied superior cere-bellar peduncles causing the “molar tooth appearance” [Figure 1].
Figure 1: Magnetic resonance imaging of the brain showed localized cerebellar vermis atrophy with bilateral atrophied superior cerebellar peduncles causing the “molar tooth appearance.”

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Her kidney biopsy showed the evidence of NPHP which represents cystic changes in the corticomedullary area, tubular atrophy and thickened membrane, and tubule-interstitial inflammation and fibrosis [Figure 2] and [Figure 3].
Figure 2: Kidney biopsy showing cystic changes in the corticomedullary area (Magnifier, x100).

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Figure 3: Kidney biopsy showing tubule- interstitial inflammation, fibrosis, and atrophy (Magnifier, x100).

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Genetic study results

The initial analysis of patient’s DNA sample, using multiplex ligation-dependent probe amplification (MPLA) technique, uncovered no deletion/duplication in the NPHP1 gene (chromosome 2q13). However, applying the powerful NGS method, a novel c.5704G>T mutation in exon 41 of the CEP290 gene on chromosome 12q21 was identified. The reported exchange of G to T leads to a premature stop codon at position 1902 of the protein (p.Glu1902*). This mutation may result in degradation of the mRNA (nonsense-mediated decay) or truncation of the CEP290 protein.

This is, therefore, highly likely to be a pathogenic mutation.

Blood samples from the patient’s affected sister, analyzed by polymerase chain reaction and direct sequencing (Sanger) of the CEP290 target, confirmed the presence of the same mutation. Blood samples from the parents were similarly analyzed for the CEP290 target. Results revealed that both parents were carriers of this gene mutation (heterozygous). Testing of the parent’s status served as a validation of this newly detected mutation.

Differential diagnosis and treatment

The pathogenesis of JS involves defectives organogenesis in utero and causes life-long dysfunctional homeostasis. The only effective management is prevention by adopting appropriate premarital screening. The treatment of JS is mainly supportive, usually focusing on monitoring and addressing the many clinical complications, including renal support through dialysis and transplantation.

Outcome and follow-up

The patient remains on hemodialysis and is enrolled in the transplantation waiting list.


   Discussion Top


JS is an autosomal recessively inherited disorder with an estimated prevalence of 1/5000 live births in the United Arab Emirates. However, the prevalence in most Arab countries, where consanguineous unions account for up to 60% of marriages, is unknown.[1] The syndrome was first described in four children with hyperpnea, abnormal eye movements, ataxia and cognitive deficits, related to agenesis of the cerebellar vermis.[2] Since then, the range of the JS clinical syndrome has expanded with the recognition of overlapping retinal, kidney, skeletal, and hepatic involvement. These disorders share the complex brainstem malformation known as the molar tooth sign. The sign is characterized by cere-bellar vermis hypoplasia or aplasia; elongated, thickened and mal-oriented superior cerebellar peduncles, and a deep interpeduncular fossa.

JS syndromes are associated with substantial genetic heterogeneity.[3] At least 29 causative genes have been identified to date. Mutations residing within these genes universally encode proteins localizing to the primary cilia, the cell organelles that function as environmental sensors and signaling pathways during development and homeostasis. JS is thus considered to be a “ciliopathy.”

Neurological deficits are a constant feature in JS. These include developmental delay, in particular, language and motor skills, hypo-tonia, ataxia, nystagmus, abnormal respiratory control, and oculomotor apraxia. The latter represents a frequent and distinctive feature of JS. It causes an inability to follow objects visually and thereby leads to compensatory head movements, and impairment of the vestibular-ocular reflex.[1] On the other hand, ataxia becomes apparent in the 1st year of life, when children start to walk.

In addition to the CNS features above, the presentations of JS may vary considerably and overlap according to the underlying genetic abnormality. These include renal abnormalities (cystic dysplastic kidneys or juvenile NPHP) that affect approximately 25% of patients with JS. Juvenile NPHP medullary cystic disease complex is characterized by the bilateral formation of cysts at the corticomedullary junctions. Histologically, chronic sclerosing tubule-interstitial nephropathy with tubular atrophy and dilatation is seen, leading ultimately to end-stage renal disease (ESRD), as described above in our patient. Kidney involvement may be asymptomatic until adolescence when CKD supersede.[1],[4] The treatment of patients with NPHP is supportive, and kidney transplantation is the treatment of choice when ESRD is established. Renal disease in JS is not known to recur after kidney transplantation.[5]

Ocular abnormalities, mainly retinal dystrophy, are probably the most common extra- CNS features. These are characterized by a gradual course and variably impaired vision. Another retinal manifestation is congenital retinal blindness, also known as Leber congenital amaurosis. Colobomas can be unilateral or bilateral involving the retinal pigmented epithelium.[1] In a recent report of 440 JS affected individuals, renal disease was the most commonly associated with retinal dystrophy [Odds ratio = 3, 0; 95% confidence interval (CI) 1.7–5.2] and liver fibrosis (Odds ratio = 3.0; 95% CI 1.6–5.5).[6] Our JS patients were among the subset of a patient who suffered simultaneously from retinal dystrophy (retinitis pigmentosa) and renal disease.

More than 29 genes associated with JS have thus far been identified, including NPHP1 at 2q13, CEP290 at 12q21.3 and the Meckel–Gruber syndrome-associated gene TMEM67 at 8q22.1. Mutations in these three genes are most frequently associated with JS cases with renal involvement. However, all of the reported genes in JS are known to encode for proteins localizing to the basal body, a micro- tubular system that protrudes from the surface of differentiated cells. These proteins act as environmental sensors, for mechanical and chemical inputs during organogenesis and later on in homeostasis. JS and many other cilio- pathy disorders, share many genetic causes and pathophysiologic features as well as overlapping clinical manifestations.[7]

Mutations of NPHP1, which are usually homozygous deletions, are found in a majority of patients with isolated NPHP (45%–60%).[5] CEP290 protein, on the other hand, is localized to the base (centrosome) and the stalk of primary cilia. This explains the clinical overlap between JS and other ciliopathies that include infantile and juvenile NPH. Around 17 CEP290 truncating mutations in CEP290 gene were previously identified.[8] The CEP290 mutation identified in this case report is also thought to be a truncating mutation. The renal disease phenotype in patients with CEP290 mutations is characterized mostly by juvenile NPHP, with the development of renal failure toward the end of the first decade or early in the second decade of life as seen in the case of these twins. However, the age of onset of renal impairment is extremely variable, with reported patients as young as four years, as observed in the brother who apparently died of advanced kidney disease. In another recent study of 30 Japanese families with JS, all CEP290 mutant families exhibited retina and/or kidney features.[9] Recent studies from Saudi Arabia reported various mutations in around 27 different genes in individuals with JS with CEP290-truncating mutations seen in 28 patients.[10] However, c.5704G>T mutation of the CEP290 gene, reported here, is identified for the first time in this Al Ahsa family with JS.

Overall, phenotyping classification of JS and related disorders appears to be of limited value in guiding laboratory diagnosis. We have identified this novel mutation using NGS in a diagnostic laboratory setting. The extreme heterogeneity of JS with the absence of a single or limited number of genes that predominate as the cause of the disease makes NGS the most efficient way for clinical diagnostic investigation as it does not require prioritizing single-gene testing.[6] The utility of this emerging powerful diagnostic technique is brilliantly illustrated in this case report. Genetic testing is imperative for providing individuals and families with JS with the information required to make family planning decisions and clinicians with data necessary for organ-specific surveillance and prognostication.

Furthermore, specific types of mutations, such as the one reported here, may be amenable to emerging read-through therapies.[11]


   Conclusion Top


JS is a devastating disease with significant morbidity and possibly mortality. It is a clinically diverse syndrome, with multiple affected organs. The genetic basis of JS is very diverse and not fully described at least in Middle- Eastern populations. Next-generation sequencing is a helpful tool that can now help in prompt diagnosis of genetic diseases of hitherto unknown responsible mutations. There is a need for regular updating of premarital screening protocols in communities with the common practice of consanguinity.

Conflict of interest: None declared.



 
   References Top

1.
Al-Gazali L, Hamamy H. Consanguinity and dysmorphology in Arabs. Hum Hered 2014; 77:93-107.  Back to cited text no. 1
    
2.
Joubert M, Eisenring JJ, Robb JP, Andermann F. Familial agenesis of the cerebellar vermis. A syndrome of episodic hyperpnea, abnormal eye movements, ataxia, and retardation. Neurology 1969;19:813-25.  Back to cited text no. 2
    
3.
Tory K, Lacoste T, Burglen L, et al. High NPHP1 and NPHP6 mutation rate in patients with Joubert syndrome and nephronophthisis: Potential epistatic effect of NPHP6 and AHI1 mutations in patients with NPHP1 mutations. J Am Soc Nephrol 2007;18:1566-75.  Back to cited text no. 3
    
4.
Apostolou T, Nikolopoulou N, Theodoridis M, et al. Late onset of renal disease in nephro-nophthisis with features of Joubert syndrome type B. Nephrol Dial Transplant 2001;16: 2412-5.  Back to cited text no. 4
    
5.
Hamiwka LA, Midgley JP, Wade AW, Martz KL, Grisaru S. Outcomes of kidney transplantation in children with nephronophthisis: An analysis of the North American pediatric renal trials and collaborative studies (NAPRTCS) registry. Pediatr Transplant 2008;12:878-82.  Back to cited text no. 5
    
6.
Bachmann-Gagescu R, Dempsey JC, Phelps IG, et al. Joubert syndrome: A model for untangling recessive disorders with extreme genetic heterogeneity. J Med Genet 2015;52: 514-22.  Back to cited text no. 6
    
7.
Hildebrandt F, Benzing T, Katsanis N. Ciliopathies. N Engl J Med 2011;364:1533-43.  Back to cited text no. 7
    
8.
Brancati F, Barrano G, Silhavy JL, et al. CEP290 mutations are frequently identified in the oculo-renal form of Joubert syndrome-related disorders. Am J Hum Genet 2007;81: 104-13.  Back to cited text no. 8
    
9.
Suzuki T, Miyake N, Tsurusaki Y, et al. Molecular genetic analysis of 30 families with Joubert syndrome. Clin Genet 2016;90:526-35.  Back to cited text no. 9
    
10.
Alazami AM, Alshammari MJ, Salih MA, et al. Molecular characterization of Joubert syndrome in Saudi Arabia. Hum Mutat 2012;33:1423-8.  Back to cited text no. 10
    
11.
Keeling KM, Xue X, Gunn G, Bedwell DM. Therapeutics based on stop codon readthrough. Annu Rev Genomics Hum Genet 2014;15:371- 94.  Back to cited text no. 11
    

Top
Correspondence Address:
Elbadri Abdelgadir
Department of Internal Medicine, King Abdulaziz Hospital, Ministry of National Guard Health Affairs, Al-Ahsaa
Saudi Arabia
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DOI: 10.4103/1319-2442.265475

PMID: 31464256

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    Figures

  [Figure 1], [Figure 2], [Figure 3]



 

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