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.

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 ACCEPTED MANUSCRIPT
CLINICAL REPORT

Novel Contiguous Gene Deletion in Peruvian girl with Trichothiodystrophy type 4 and

Glutaric Aciduria type 3.

Jorge La Serna-Infantes1, Miguel Chávez Pastor2, Milana Trubnykova2, Félix Chavesta

Velásquez2, Flor Vásquez Sotomayor2, Hugo Abarca Barriga2*.

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1
Department of Cytogenetics y Cytopathology, Hospital Nacional Guillermo Almenara, La

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Victoria Lima, Perú.
2
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,
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Instituto Nacional de Salud del Niño, Av. Brasil 600, CP Lima 05, Lima, Perú, Phone +51
979301132, habarca@insn.gob.pe
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 La Serna-Infantes et al. 2
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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

intellectual disability, ichthyotic skin and short stature, caused by a homozygous mutation in

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MPLKIP gene. Glutaric aciduria type 3 is caused by a homozygous mutation in SUGCT gene

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with no distinctive phenotype. Both genes are localized on chromosome 7 (7p14).

We report an 8-year-old female with short stature, microcephaly, development delay,

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intellectual disability and hair characterized for dark, short, coarse, sparse and brittle

associated to classical trichorrhexis microscopy pattern. Chromosome microarray analysis

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

chromosome microarray analysis, highlighting the contribution and importance of molecular

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technologies on diagnosis of rare genetic conditions.

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Keywords: Trichothiodystrophy, Nonphotosensitive, Glutaric Aciduria 3, Glutaryl-CoA

Oxidase Deficiency, Chromosome Microarray Analysis, MLKIP, SUGCT.

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 Novel Contiguous Gen Deletion TTD4 & GA3 3
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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,

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

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Under polarizing microscopy, the hair displays a classical alternating light and dark

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banding pattern, called “tiger tail banding”, trichorrhexis or trichoschisis, due to thickening or

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

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Egly 2009].

Several acronyms are used to describe patient features: PIBIDS, IBIDS and BIDS for

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Photosensitivity, Ichthyosis, Brittle hair, Intellectual impairment, Decreased fertility, and
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Short stature [Bergmann E. & Egly JM 2017; Faghri, Tamura, Kraemer, & DiGiovanna 2008;
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Hashimoto & Egly 2009].

TTD is clinically classified in photosensitive and non-photosensitive classical forms;

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however, a genetic classification into three groups has also been proposed by Morice-Picard
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et al. : i) the photosensitive group (A-I), genetically heterogeneous, where a complex of 10

proteins essential for nucleotide excision-repair (NER) and transcription called

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Transcription/DNA repair Factor IIH (TFIIH) is affected by mutations of its subunits, causing
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decreased cellular concentrations of the affected protein; ii) non-photosensitive group, which
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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
 La Serna-Infantes et al. 4
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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

Trichothiodystrophy type 4 and Glutaric Aciduria type 3 diagnosed by chromosome

microarray analysis.

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CLINICAL REPORT

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

(Father: 24y / Mother: 19y). There were no complications during gestation. Birth weight was

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3500 g. Her parents were apparently unrelated, though the grandparents were originally from

the same small town, located in Cajamarca Region, north of Peru. Family history included a

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paternal uncle with schizophrenia. (Figure 1a). Our patient presented global development
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delay: head control at 8 months, sat with support at 2 years 6 months, walked at 3 years 10
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months and spoke at 4 years. She is currently on first grade at primary school.

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

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,
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downslanding mouth corners; some small ´café au lait´ patches; dental caries and multiple
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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 5
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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

(7p14.1). This deletion contains genes MPLKIP and SUGCT, known to be related to

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Trichothiodystrophy type 4 and Glutaric Aciduria type 3, respectively.

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

child. Since the mother was a single woman, the father could not be contacted for further

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genetic investigation. The LOH region that contained the described CNV in the proband is

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

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

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

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
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(Affymetrix, USA) according to the manufacturer’s instructions. The array specifications

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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

 La Serna-Infantes et al. 6
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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

Trichothiodystrophy type 4 (TTD4; MIM 234050; ORPHA 1245), also called

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Nonphotosensitive Trichothiodystrophy 1 (TTDN1), Amish Brittle Hair Brain Syndrome

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(ABHS), Hair-Brain Syndrome, BIDS Syndrome, Pollitt Syndrome or Neurocutaneous-TTD

Syndrome, is a genetically heterogeneous disorder caused by mutations at MPLKIP gene (M-

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phase-specific PLK1-interacting protein) in fewer than 20 percent of all cases. These

mutations do not increase the risk of skin cancer, but they have been found to be associated

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with early mortality, until 20-fold increased risk for death before 10 years [Bergmann E. &
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Egly J.M. 2017; Faghri et al. 2008; Morice-Picard et al. 2009; Stefanini M. 2013].
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MPLKIP gene encodes a nuclear protein which function is not completely known, but

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

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

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causes nuclear fragmentation, whereas knock-down results in multiple nuclei or multiple-

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polar 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 7
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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

2008; Stefanini M. 2013].

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In Table I we summarize the clinical and molecular findings in our patient compared

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to other reported patients with TTD4 and mutations in MPLKIP gene, some of them had

consanguineous parents. Despite the wide clinical variability; all cases described had

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dysmorphic facies, psychomotor delay; brittle and sparse eyebrows, eyelashes, and hair

trichorrhexis nodosa with abnormal light microscopy appearance. The molecular findings

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showed different kinds of mutations in one or both alleles of MPLKIP, from point mutations
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to CNVs, causing dysfunctional or absent protein.
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Glutaric Aciduria type 3 (GA3, MIM 231690; GARD 12469; ORPHA 35706) is a

rare autosomic recessive metabolic disease caused by a peroxisomal dysfunction causing a

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glutaryl – CoA oxidase deficiency, and characterized by accumulation/excretion of glutaric

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acid without specific phenotype, although some individuals remain asymptomatic [Bennett,

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

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Bennett et al. described the first case reported of a patient with glutaric aciduria, a 1-
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year-old girl with failure to thrive, hematologic evidence of beta-thalassemia, abnormal

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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].

 La Serna-Infantes et al. 8
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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

technologies on diagnosis of rare genetic conditions.

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ACKNOWLEDGMENTS

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

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

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

conflicts of interest to declare.

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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,

14(2), 165–173.

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Bergmann, E., & Egly, J.M. (2017). Trichothiodystrophy, a transcription syndrome: Trends

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in Genetics. TRENDS in Genetics, 17 (5), 279-286.

Cheng, A. S., & Bayliss, S. J. (2008). The genetics of hair shaft disorders. Journal of the

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American Academy of Dermatology, 59(1), 1-22; 23-26.

Faghri, S., Tamura, D., Kraemer, K. H., & DiGiovanna, J. J. (2008). Trichothiodystrophy: a

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systematic review of 112 published cases characterises a wide spectrum of clinical
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manifestations. Journal of medical genetics, 45(10), 609-621.
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Gummer, C. l., & Dawber, R. (1985). Trichothiodystrophy: an ultrastructural study of the hair

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

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Hashimoto, S., & Egly, J. M. (2009). Trichothiodystrophy view from the molecular basis of
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DNA repair/transcription factor TFIIH. Human Molecular Genetics, 18(R2), R224-

230.
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Heller, E. R., Khan, S. G., Kuschal, C., Tamura, D., DiGiovanna, J. J., & Kraemer, K. H.
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(2015). Mutations in the TTDN1 gene are associated with a distinct

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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.

Morice-Picard, F., Cario-André, M., Rezvani, H., Lacombe, D., Sarasin, A., & Taïeb, A.

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(2009). New clinico-genetic classification of trichothiodystrophy. American Journal

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of Medical Genetics Part A, 149A(9), 2020-2030.

Pode-Shakked, B., Marek-Yagel, D., Greenberger, S., Pode-Shakked, N., Pras, E., Barzilai,

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A., … Anikster, Y. (2015). A novel mutation in the C7orf11 gene causes

nonphotosensitive trichothiodystrophy in a multiplex highly consanguineous kindred.

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European Journal of Medical Genetics, 58(12), 685–688.
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Sherman, E. A., Strauss, K. A., Tortorelli, S., Bennett, M. J., Knerr, I., Morton, D. H., &
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Puffenberger, E. G. (2008). Genetic mapping of glutaric aciduria, type 3, to

chromosome 7 and identification of mutations in c7orf10. American Journal of

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Human Genetics, 83(5), 604–609.

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

DNA Repair and Transcription. Landes Bioscience.

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

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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

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Berlin, Heidelberg.
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Table I: Comparative clinical/molecular features described in patients with TTD4.

Figure 1: Clinical features of the patient.

(a) Patient pedigree. It showed a paternal uncle with schizophrenia and no

other familial medical condition described.

(b), (c) Frontal and (d) lateral view clinical features. Microcephaly;

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prematurely aged face, asymmetric face with hypoplasic superciliary and

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zygomatic arches; dark, short, sparse, coarse and brittle scalp hair, eyebrows

and eyelashes; widespread alopecic parietal area; mild anteverted ears with

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prominent antihelix and hypoplasic lobes; thick nasal root and anteverted nares

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

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

clinodactyly of the 5th fingers.

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

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under light and/or polarizing microscopy.

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

Nakabayashi et
Przedborski et

This paper
Fois et al. ,

Rizzo et al.
al. , 1990

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1992
1988
CLINICAL AND MOLECULAR CHARACTERISTICS Botta et al. , 2007 Heller et al ., 2015

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Country / City / Ethnicity Italy Italy India Iraq Neth Morocco / Canad Italy Caucasian Peru

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Sex F F F F M F M F F n F M F F M M F
Age (years) 8 4 3 6 3 3 16 4 13 n 3 14 4 2 1 14 8

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Consanguineous Parents - n N n n n + + + n - - - - - - -
Short stature + n N n n n + + - n - - - - - + +

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Microcephaly + n N n n n + + + n + - - - - - +
Cortical atrophy (rare) n n N n n n + - + n + - - - - - -

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Dysmorphic features + n N n n n + + + n + + + + + + +
Hypotonia n N n n n + + + n + + + + + + -

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Nystagmus n n N n n n n n n n + + - - - - +
Ataxia n n n n n n + + + n n - - - - - -

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Psychomotor delay + n n n n n + + + + + + + + + + +
Dysmorphic/dyschromic nails + n n n n n - - - + + - - + + + +
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Brittle, sparse eyebrows/eyelashes/hair + n n n n n + + + + + + + + + + +
Trichorrhexis nodosa + n n n n n + + + n + + + + + n +
Alopecia Areata + n n n n n + + + n + n n n n n +
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Reduced cystine/sulfur hair content + n n n n n + + + n + + + + + n n

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Abnormal light microscopy + n n n n n + + + n + + + n n + +

Abnormal electron microscopy + n n n n n + + + n + + n n n n n
Abnormal polarization microscopy + n n n n n + + + n + + + n n n n
Skin abnormalities n n n n n n - - - n + + + + + + +
Teeth abnormalities + n n n n n - - - n + n n n n - +
Other malformations + n n n n n + + n n + + + + + +
 Protein change

Mutation in MPLKIP

Alleles (p : paternal / m : maternal)

Seizures
Autism
Recurrent infections
Osteopenia
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(+): Present at the study (-): Absent at study (n): Not described. (p): Paternal allele. (m): Maternal allele

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p m p m p m p m p m p m
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No protein Deletion of11-31kb

n
n

n
+
p.His50AlafsX8 c.148_152delCACAC

n
n
n
n
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p.Ser93ProfsX60 c.277delT

n
n
n
n
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p.His50AlafsX8 c.148_152delCACAC

p.Arg77GlyfsX76 c.229delC

n
n
n
n
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No protein Deletion >150 kb

n
n
n
n
p.Ser93ProfsX60 c.277delT

n
n
n
n
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n
n
n
+
p
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57 residue
c.187_188delCG
n
n
n
+
truncated protein
m
n
n
n
+
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p m p m

p.Met144Val c.480A>G
n
n
n
n

No protein Partial deletion of exon

n
n
n
n
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(probable) 1 and entire exon 2

No protein c.2T>C (initiation codon)
p
AC

+
+
+
-
m

No protein c.2T>G (initiation codon)

p.Gly76Alafs*77 c.227delG
p

+
+
+
-
m

No protein Deletion of ~120kb

No protein Deletion of ~92 kb

p
+

+
+
-
m

p.Ser93Profs*60 c. 277delT
+

+
+
-
p m p m

4 bp insertion & deletion

No protein
+
+
+
+

of ~5kb starting at c.279

No protein Deletion 125kb

n
n
n
n
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