Novel contiguous gene deletion in peruvian girl with Trichothiodystrophy type 4 and glutaric aciduria type 3

Accepted Manuscript Novel contiguous gene deletion in peruvian girl with Trichothiodystrophy type 4 and glutaric aciduria type 3 Jorge La Serna-Infantes, Miguel Chávez Pastor, Milana Trubnykova, Félix Chavesta Velásquez, Flor Vásquez Sotomayor, Hugo Abarca Barriga PII:

S1769-7212(17)30667-5

DOI:

10.1016/j.ejmg.2018.02.004

Reference:

EJMG 3421

To appear in:

European Journal of Medical Genetics

Received Date: 3 October 2017 Revised Date:

19 January 2018

Accepted Date: 3 February 2018

Please cite this article as: J. La Serna-Infantes, Miguel.Chá. Pastor, M. Trubnykova, Fé.Chavesta. Velásquez, Flor.Vá. Sotomayor, H.A. Barriga, Novel contiguous gene deletion in peruvian girl with Trichothiodystrophy type 4 and glutaric aciduria type 3, European Journal of Medical Genetics (2018), doi: 10.1016/j.ejmg.2018.02.004. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

ACCEPTED MANUSCRIPT CLINICAL REPORT Novel Contiguous Gene Deletion in Peruvian girl with Trichothiodystrophy type 4 and Glutaric Aciduria type 3.

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Jorge La Serna-Infantes1, Miguel Chávez Pastor2, Milana Trubnykova2, Félix Chavesta Velásquez2, Flor Vásquez Sotomayor2, Hugo Abarca Barriga2*.

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Department of Cytogenetics y Cytopathology, Hospital Nacional Guillermo Almenara, La Victoria Lima, Perú. 2

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Department of Genetic & Inborn Errors of Metabolism, Instituto Nacional de Salud del Niño, Breña, Lima, Perú.

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* Correspondence: Hugo Hernán Abarca Barriga, Genetic & Inborn Errors of Metabolism, Instituto Nacional de Salud del Niño, Av. Brasil 600, CP Lima 05, Lima, Perú, Phone +51 979301132, [email protected]

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ABSTRACT Trichothiodystrophy type 4 is a rare autosomal recessive and ectodermal disorder, characterized by dry, brittle, sparse and sulfur-deficient hair and other features like

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intellectual disability, ichthyotic skin and short stature, caused by a homozygous mutation in MPLKIP gene. Glutaric aciduria type 3 is caused by a homozygous mutation in SUGCT gene with no distinctive phenotype. Both genes are localized on chromosome 7 (7p14).

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We report an 8-year-old female with short stature, microcephaly, development delay, intellectual disability and hair characterized for dark, short, coarse, sparse and brittle

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associated to classical trichorrhexis microscopy pattern. Chromosome microarray analysis showed a 125 kb homozygous pathogenic deletion, which includes genes MPLKIP and SUGCT, not described before. This is the first case described in Peru of a novel contiguous gene deletion of Trichothiodystrophy type 4 and Glutaric aciduria type 3 performed by

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chromosome microarray analysis, highlighting the contribution and importance of molecular technologies on diagnosis of rare genetic conditions. Keywords: Trichothiodystrophy, Nonphotosensitive, Glutaric Aciduria 3, Glutaryl-CoA

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Oxidase Deficiency, Chromosome Microarray Analysis, MLKIP, SUGCT.

Novel Contiguous Gen Deletion TTD4 & GA3

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INTRODUCTION Trichothiodystrophy (TTD; MIM PS601675; ORPHA 33364; GARD 12109) is a rare autosomal recessive and ectodermal disorder described by Pollitt (1968), characterized by dry, brittle, sparse, sulfur-deficient hair and other features like intellectual disability,

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ichthyotic skin and short stature [Hashimoto & Egly 2009; Pode-Shakked et al. 2015].

Under polarizing microscopy, the hair displays a classical alternating light and dark banding pattern, called “tiger tail banding”, trichorrhexis or trichoschisis, due to thickening or

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weak points (nodes) causing easily hair broken [Gummer & Dawber 1985; Hashimoto & Egly 2009].

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Several acronyms are used to describe patient features: PIBIDS, IBIDS and BIDS for Photosensitivity, Ichthyosis, Brittle hair, Intellectual impairment, Decreased fertility, and Short stature [Bergmann E. & Egly JM 2017; Faghri, Tamura, Kraemer, & DiGiovanna 2008; Hashimoto & Egly 2009].

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TTD is clinically classified in photosensitive and non-photosensitive classical forms; however, a genetic classification into three groups has also been proposed by Morice-Picard et al. : i) the photosensitive group (A-I), genetically heterogeneous, where a complex of 10 essential

for

nucleotide

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proteins

excision-repair

(NER)

and

transcription

called

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Transcription/DNA repair Factor IIH (TFIIH) is affected by mutations of its subunits, causing decreased cellular concentrations of the affected protein; ii) non-photosensitive group, which includes patients with MPLKIP mutations (Group B-II); iii) and unknown molecular basis (group B-III) [Morice-Picard et al. 2009; Stefanini M. 2013]. TTD4 belongs to B-II group. Glutaric aciduria type 3 (GA3, MIM 231690; GARD 12469; ORPHA 35706) is generally considered a likely "non-disease", caused by mutations in the SUGCT gene, that produces deficiency of succinate-hydroxymethylglutarate coA-transferase, provoking decreased conversion of free glutaric acid to glutaryl-coA with no symptoms. It remains less

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well known, characterized and understood than other types of glutaric aciduria [Waters et al., 2017]. Here, we present the first patient reported in Peru with co-occurrence of

microarray analysis. CLINICAL REPORT

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Trichothiodystrophy type 4 and Glutaric Aciduria type 3 diagnosed by chromosome

An 8-year-old Peruvian female was born at term by natural birth from young parents

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(Father: 24y / Mother: 19y). There were no complications during gestation. Birth weight was 3500 g. Her parents were apparently unrelated, though the grandparents were originally from

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the same small town, located in Cajamarca Region, north of Peru. Family history included a paternal uncle with schizophrenia. (Figure 1a). Our patient presented global development delay: head control at 8 months, sat with support at 2 years 6 months, walked at 3 years 10 months and spoke at 4 years. She is currently on first grade at primary school.

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Upon examination (8-year-old), her weight was 20 kg (-2.3 SD), height 112 cm (-3.4 SD), cephalic perimeter 48.6 cm (-3.0 SD) and body mass index 15.9 (-0.17 SD). Her phenotype showed: microcephaly, short stature; prematurely aged and asymmetric face with

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hypoplasic superciliary / zygomatic arches; scalp, eyebrows and eyelashes hair showed short,

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coarse, sparse and brittle; alopecic parietal area; anteverted nares and thick nasal root, downslanding mouth corners; some small ´café au lait´ patches; dental caries and multiple teeth decay; follicular keratosis on the back; short, thin and irregular nails of the fingers; scoliosis, brachydactyly, bilateral clinodactyly of the 5th fingers, flat and valgus feet; normal muscle tone and deep tendon - plantar reflexes (Figure 1 b – f). Her mental development was moderately delayed with unsteady walking and high pitched voice. The

following

tests

were

normal:

blood

count,

thyroid

hormones,

electroencephalogram, auditory evoked potential response and fundoscopy. CT scan showed

Novel Contiguous Gen Deletion TTD4 & GA3

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mild lateral ventricles enlargement. The hair displayed classical diagnostic pattern called trichoschisis and/or trichorrhexis under light microscopy (Figure 1g). Chromosome Microarray Analysis (CMA) showed a 125 kb homozygous deletion {arr[hg19]7p14.1(40,140,770-40,265,451)x0} within the short arm of chromosome 7

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(7p14.1). This deletion contains genes MPLKIP and SUGCT, known to be related to Trichothiodystrophy type 4 and Glutaric Aciduria type 3, respectively.

The mother was heterozygous for the same 7p14.1 deletion detected in the proband

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child. Since the mother was a single woman, the father could not be contacted for further genetic investigation. The LOH region that contained the described CNV in the proband is

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smaller than 10Mbp, which did not suggest a possible UDP.

In order to confirm Glutaric Aciduria type 3 found by CMA, urinary organic acids test was performed at Children's Hospital Colorado Laboratory. The results showed increased glutaric acid without 3-hydroxyglutaric acid compatible to the diagnosis.

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METHODS

We follow the Ethical Statement regulations of the “Instituto Nacional de Salud del Niño” (Lima, Peru) and parental informed written consent was obtained for publication. The

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Chromosome Microarray Analysis (CMA) was performed from total DNA (250ng), it was

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amplified, labeled, and hybridized using GeneChip CytoScan 750K Array protocols (Affymetrix, USA) according to the manufacturer’s instructions. The array specifications include 550 000 non-polymorphic markers and 200 436 SNP markers. CEL files obtained by scanning the arrays were analyzed using the Chromosome Analysis Suite (ChAS) software (Affymetrix, USA). Gains and losses that affected a minimum of 25 markers and LOH regions that expand over 5Mbp were initially considered (See Thermo Fisher Sc Inc, 2017). The patient CNVs (Copy Number Variation) were compared with genomic variants in public databases, including Database of Chromosomal Imbalance and Phenotype in Humans

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using Ensemble Resources (DECIPHER), and UCSC (University of California, Santa Cruz – UCSC) Genome Browser. CNVs were classified as pathogenic, likely pathogenic, and of unknown clinical significance [Miller et al. 2010; Verma R. & Babu A. 1996]. DISCUSSION

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Trichothiodystrophy type 4 (TTD4; MIM 234050; ORPHA 1245), also called Nonphotosensitive Trichothiodystrophy 1 (TTDN1), Amish Brittle Hair Brain Syndrome (ABHS), Hair-Brain Syndrome, BIDS Syndrome, Pollitt Syndrome or Neurocutaneous-TTD

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Syndrome, is a genetically heterogeneous disorder caused by mutations at MPLKIP gene (Mphase-specific PLK1-interacting protein) in fewer than 20 percent of all cases. These

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mutations do not increase the risk of skin cancer, but they have been found to be associated with early mortality, until 20-fold increased risk for death before 10 years [Bergmann E. & Egly J.M. 2017; Faghri et al. 2008; Morice-Picard et al. 2009; Stefanini M. 2013]. MPLKIP gene encodes a nuclear protein which function is not completely known, but

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it is thought to interact with polo-like kinase 1 (PLK1), regulating cell cycle and mitosis. It is expressed in epidermis, fibroblasts and hair follicles (UniProt: Q8TAP9; NCBI – GTR: C1961117). Interactions between cell cycle regulation and transcription efficiency could

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explain the TTD phenotype observed in patients with MPLKIP mutations; however, no

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genotype–phenotype correlations have been found. Overexpression of MPLKIP in HeLa cells causes nuclear fragmentation, whereas knock-down results in multiple nuclei or multiplepolar mitotic spindles [Cheng & Bayliss 2008; Heller et al. 2015; Morice-Picard et al. 2009; Stefanini M. 2013; Stefanini, Botta, Lanzafame, & Orioli 2010]. Previous reports of MPLKIP have identified several heterogeneous deletions in the gene, ranging from one base pair to 11–31 kb in size. It has been identified in two types of non-photosensitive TTD4: Amish brittle-hair syndrome and non-photosensitive TTD with mental retardation and/or decreased fertility [Heller et al. 2015; Morice-Picard et al. 2009].

Novel Contiguous Gen Deletion TTD4 & GA3

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Phenotypically, non-cutaneous common aspects in TTD4 consist in: microcephaly, intellectual disability, growth failure, axial osteosclerosis, osteopenia and decreased fertility. The cutaneous features affect mainly nails and hair, the latter consists in short, woolly, sparse, brittle hair, trichorrhexis, reduced cystine or sulfur content of hair [Cheng & Bayliss

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2008; Stefanini M. 2013].

In Table I we summarize the clinical and molecular findings in our patient compared to other reported patients with TTD4 and mutations in MPLKIP gene, some of them had

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consanguineous parents. Despite the wide clinical variability; all cases described had dysmorphic facies, psychomotor delay; brittle and sparse eyebrows, eyelashes, and hair

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trichorrhexis nodosa with abnormal light microscopy appearance. The molecular findings showed different kinds of mutations in one or both alleles of MPLKIP, from point mutations to CNVs, causing dysfunctional or absent protein.

Glutaric Aciduria type 3 (GA3, MIM 231690; GARD 12469; ORPHA 35706) is a

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rare autosomic recessive metabolic disease caused by a peroxisomal dysfunction causing a glutaryl – CoA oxidase deficiency, and characterized by accumulation/excretion of glutaric acid without specific phenotype, although some individuals remain asymptomatic [Bennett,

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Pollitt, Goodman, Hale, & Vamecq, 1991].

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Bennett et al. described the first case reported of a patient with glutaric aciduria, a 1year-old girl with failure to thrive, hematologic evidence of beta-thalassemia, abnormal urinary amounts of glutaric acid and lack of detectable activity of peroxisomal glutaryl-CoA oxidase [Bennett et al. 1991]. Knerr et al. reported 3 cases with no distinctive phenotype [Knerr et al., 2002], Sherman et al. also reported 3 healthy children who excreted large quantities of glutarate but low 3-hydroxyglutarate, consistent with the phenotype of glutaric aciduria III after the screening of 1,223 Amish infants. They did not receive treatment and remained healthy for more than 15 years [Sherman et al. 2008].

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In conclusion, this is the first case described in Peru of a novel contiguous gene deletion of Trichothiodystrophy type 4 and Glutaric aciduria type 3 performed by chromosome microarray analysis, highlighting the contribution and importance of molecular

ACKNOWLEDGMENTS

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technologies on diagnosis of rare genetic conditions.

The authors wish to thank the family for their participation in this study. We would

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also like to thank Genetic and Inborn Errors of Metabolism Team of ´Instituto Nacional de

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conflicts of interest to declare.

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Salud del Niño´ for their contribution, assistance and suggestions. The authors have no

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REFERENCES Bennett, M. J., Pollitt, R. J., Goodman, S. I., Hale, D. E., & Vamecq, J. (1991). Atypical riboflavin-responsive glutaric aciduria, and deficient peroxisomal glutaryl-CoA oxidase activity: a new peroxisomal disorder. Journal of Inherited Metabolic Disease,

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14(2), 165–173.

Bergmann, E., & Egly, J.M. (2017). Trichothiodystrophy, a transcription syndrome: Trends in Genetics. TRENDS in Genetics, 17 (5), 279-286.

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Cheng, A. S., & Bayliss, S. J. (2008). The genetics of hair shaft disorders. Journal of the American Academy of Dermatology, 59(1), 1-22; 23-26.

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Faghri, S., Tamura, D., Kraemer, K. H., & DiGiovanna, J. J. (2008). Trichothiodystrophy: a systematic review of 112 published cases characterises a wide spectrum of clinical manifestations. Journal of medical genetics, 45(10), 609-621. Gummer, C. l., & Dawber, R. (1985). Trichothiodystrophy: an ultrastructural study of the hair

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follicle. British Journal of Dermatology, 113(3), 273-280.

Hashimoto, S., & Egly, J. M. (2009). Trichothiodystrophy view from the molecular basis of

230.

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DNA repair/transcription factor TFIIH. Human Molecular Genetics, 18(R2), R224-

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Heller, E. R., Khan, S. G., Kuschal, C., Tamura, D., DiGiovanna, J. J., & Kraemer, K. H. (2015).

Mutations

in

the

TTDN1

gene

are

associated

with

a

distinct

trichothiodystrophy phenotype. The Journal of investigative dermatology, 135(3), 734-741.

Knerr, I., Zschocke, J., Trautmann, U., Dorland, L., de Koning, T. J., Müller, P., … Hoffmann, G. F. (2002). Glutaric aciduria type III: a distinctive non-disease? Journal of Inherited Metabolic Disease, 25(6), 483–490.

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Miller, D. T., Adam, M. P., Aradhya, S., Biesecker, L. G., Brothman, A. R., Carter, N. P., … Ledbetter, D. H. (2010). Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. American Journal of Human Genetics, 86(5), 749-764.

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Morice-Picard, F., Cario-André, M., Rezvani, H., Lacombe, D., Sarasin, A., & Taïeb, A. (2009). New clinico-genetic classification of trichothiodystrophy. American Journal of Medical Genetics Part A, 149A(9), 2020-2030.

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Pode-Shakked, B., Marek-Yagel, D., Greenberger, S., Pode-Shakked, N., Pras, E., Barzilai, A., … Anikster, Y. (2015). A novel mutation in the C7orf11 gene causes

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nonphotosensitive trichothiodystrophy in a multiplex highly consanguineous kindred. European Journal of Medical Genetics, 58(12), 685–688.

Sherman, E. A., Strauss, K. A., Tortorelli, S., Bennett, M. J., Knerr, I., Morton, D. H., & Puffenberger, E. G. (2008). Genetic mapping of glutaric aciduria, type 3, to

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chromosome 7 and identification of mutations in c7orf10. American Journal of Human Genetics, 83(5), 604–609.

Stefanini M. (2013). Trichothiodystrophy: A Disorder Highlighting the Crosstalk between

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DNA Repair and Transcription. Landes Bioscience.

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Stefanini, M., Botta, E., Lanzafame, M., & Orioli, D. (2010). Trichothiodystrophy: from basic mechanisms to clinical implications. DNA Repair, 9(1), 2–10.

Verma, R., Babu, A. (1995). Human Chromosomes: Principles & Techniques, 2nd edition, McGraw-Hill Inc., New York.

Waters, P. J., Kitzler, T. M., Feigenbaum, A., Geraghty, M. T., Al-Dirbashi, O., Bherer, P., … Al-Hertani, W. (2017). Glutaric Aciduria Type 3: Three Unrelated Canadian Cases, with Different Routes of Ascertainment. In SpringerLink (pp. 1–8). Springer, Berlin, Heidelberg.

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Table I:

Comparative clinical/molecular features described in patients with TTD4.

Figure 1:

Clinical features of the patient.

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(a) Patient pedigree. It showed a paternal uncle with schizophrenia and no other familial medical condition described.

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(b), (c) Frontal and (d) lateral view clinical features. Microcephaly; prematurely aged face, asymmetric face with hypoplasic superciliary and zygomatic arches; dark, short, sparse, coarse and brittle scalp hair, eyebrows

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and eyelashes; widespread alopecic parietal area; mild anteverted ears with prominent antihelix and hypoplasic lobes; thick nasal root and anteverted nares

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with skin excoriation, downslanting mouth corners. Some small ´café au lait´ patches.

(e) Follicular keratosis on the back, ´café au lait´ patch. (f) Short, thin and irregular nails of the fingers; brachydactyly, bilateral

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clinodactyly of the 5th fingers.

(g) Trichoschisis or trichorrhexis, a classical diagnostic hair pattern observed

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under light and/or polarizing microscopy.

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n n + + + + + + + + + n + +

This paper

Nakabayashi et al., 2005 Rizzo et al. 1992

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Przedborski et al. , 1990

India Iraq Neth Morocco / Canad Italy F M F F F n M F 3 n 3 3 16 4 13 6 n n n n + + + n n n n + + + n n n n + + + + n n n n + - + + n n n n + + + + n n n n + + + + n n n n n n n n n n n n + + + + + n n n + + + + + n n n + + n n n + + + + n n n n + + + n + n n n + + + n + n n n + + + n + n + n n + + + n n n n + + + + n n n n + + + + n n n n n n n n + n n n + + n n

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F 3 N N N N N N N n n n n n n n n n n n n n

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Italy F 4 n n n n n n n n n n n n n n n n n n n n

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Italy F 8 + + n +

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Country / City / Ethnicity Sex Age (years) Consanguineous Parents Short stature Microcephaly Cortical atrophy (rare) Dysmorphic features Hypotonia Nystagmus Ataxia Psychomotor delay Dysmorphic/dyschromic nails Brittle, sparse eyebrows/eyelashes/hair Trichorrhexis nodosa Alopecia Areata Reduced cystine/sulfur hair content Abnormal light microscopy Abnormal electron microscopy Abnormal polarization microscopy Skin abnormalities Teeth abnormalities Other malformations

Botta et al. , 2007

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CLINICAL AND MOLECULAR CHARACTERISTICS

Fois et al. , 1988

Table I: Comparative clinical/molecular features described in patients with TTD-4.

Heller et al ., 2015

M 14 + + + + + + n + + + + + n +

Caucasian F F 4 2 + + + + + + + + + + + n n + + + n n n + n + + n n + +

M 1 + + + + + + n + n n n + n +

M 14 + + + + + + n n n + n n + +

Peru F 8 + + + + + + + + + n + n n + + +

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p.His50AlafsX8

c.148_152delCACAC

p.Arg77GlyfsX76

c.229delC

No protein

Deletion >150 kb

p.Ser93ProfsX60

c.277delT

57 residue truncated protein

c.187_188delCG

p.Met144Val

c.480A>G

No protein (probable)

Partial deletion of exon 1 and entire exon 2

n n n n n n n n p m p m

No protein

c.2T>C (initiation codon)

p

No protein

c.2T>G (initiation codon)

m

p.Gly76Alafs*77

c.227delG

p

No protein

Deletion of ~120kb

m

No protein

Deletion of ~92 kb

+ + + p

p.Ser93Profs*60

c. 277delT

+ + + m

No protein

4 bp insertion & deletion of ~5kb starting at c.279

No protein

Deletion 125kb

+ n + n + n + n p m p m

+ n n n

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p.Ser93ProfsX60

+ n n n m

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c.148_152delCACAC

+ n n n p + + + -

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Deletion of11-31kb

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p.His50AlafsX8

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No protein

n n n n n n + n n n n n n n n n n n n n n n n n p m p m p m p m p m p m

(+): Present at the study (-): Absent at study (n): Not described. (p): Paternal allele. (m): Maternal allele

Osteopenia Recurrent infections Autism Seizures Alleles (p : paternal / m : maternal)

Mutation in MPLKIP

Protein change

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+ + + -

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