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A patient with polymerase E1 deficiency (POLE1): clinical features and overlap with DNA breakage/instability syndromes

  • Isabelle Thiffault2, 3Email author,
  • Carol Saunders2, 3, 8,
  • Janda Jenkins1, 7, 8,
  • Nikita Raje4,
  • Kristi Canty5,
  • Mukta Sharma6,
  • Lauren Grote1, 7, 8,
  • Holly I Welsh1, 7, 8,
  • Emily Farrow2,
  • Greyson Twist2,
  • Neil Miller2,
  • David Zwick3,
  • Lee Zellmer2,
  • Stephen F Kingsmore2, 3, 7, 8 and
  • Nicole P Safina1, 7, 8
BMC Medical Genetics201516:31

https://doi.org/10.1186/s12881-015-0177-y

Received: 10 February 2015

Accepted: 24 April 2015

Published: 7 May 2015

Abstract

Background

Chromosome instability syndromes are a group of inherited conditions associated with chromosomal instability and breakage, often leading to immunodeficiency, growth retardation and increased risk of malignancy.

Case presentation

We performed exome sequencing on a girl with a suspected chromosome instability syndrome that manifested as growth retardation, microcephaly, developmental delay, dysmorphic features, poikiloderma, immune deficiency with pancytopenia, and myelodysplasia. She was homozygous for a previously reported splice variant, c.4444 + 3A > G in the POLE1 gene, which encodes the catalytic subunit of DNA polymerase E.

Conclusion

This is the second family with POLE1-deficency, with the affected individual demonstrating a more severe phenotype than previously described.

Keywords

POLE1 FILS syndrome Immunodeficiency Dysmorphism Primordial dwarfism

Background

Chromosome instability syndromes are a group of inherited conditions associated with chromosomal instability and breakage which includes LIG4 [1,2], Seckel type 1 [3,4], Bloom syndrome [5], Nijmegen breakage syndrome [6-8], and Fanconi anemia. These genetic conditions are characterized by pre and postnatal growth retardation, microcephaly, dysmorphic features and bone marrow failure [9-11]. There are other conditions with overlapping phenotypes including microcephaly, such as Rad50 deficiency [12,13], Cernunnos-XLF syndrome [14] and Warsaw breakage syndrome [15-18] which can complicate molecular diagnosis. FILS syndrome (facial dysmorphism, immunodeficiency, livedo, and short stature) is a recently described condition caused by variants in POLE1, encoding the catalytic subunit of polymerase E. We describe the second family with a homozygous variant in POLE1, and a more severely affected individual, suggesting a broader phenotypic spectrum for this condition.

Case presentation

Patient CMH812 is a female infant born to healthy non consanguineous Palestinian parents, weighing 1745 g and measuring 38.1 cm at birth. The pregnancy was complicated by subchorionic bleeding in the first trimester, fetal abnormalities on ultrasound including intrauterine growth restriction, short long bones, suspected skull abnormalities and oligohydramnios. TORCH titers were negative. Amniocentesis revealed normal 46,XX karyotype. She was delivered at 37 weeks gestation by elective C-section secondary to breech presentation. Dysmorphic features noted included malar and mandibular hypoplasia (Figure 1A, B). Initial clinical suspicion was for primordial dwarfism such as Seckel type 1 syndrome, however her microcephaly was not as severe. Over several months, lacy reticular pigmentation was noted of the face and extremities. She had recurrent pruritic papular eruptions and skin findings progressed to include appearance of poikiloderma (Figure 1C, D). Erupted teeth were found to be small and dysplastic. She developed a feeding aversion necessitating a gastrostomy tube. Growth remained poor postnatally (Figure 2). Her motor milestones were delayed but social development was normal.
Figure 1

Clinical characteristics of CMH812. Several congenital abnormalities were found, including (A) microcephaly, facial dysmorphism (small and bird-like face, malar and mandibular hypoplasia, prominent nasal bridge and columella, downslanting palpebral fissures, small mouth and low set, posteriorly rotated ears) (B) short stature with shortened long bones but no evidence of dysplasia or craniosynostosis. No major anomalies were found on imaging of her abdomen, brain, brain vasculature or heart. Genitalia and pubertal development were normal. No malabsorption or pituitary or thyroid insufficiency was found. (C-D) Skin findings in CMH812, showing one hypo- and three hyperpigmented patches on the skin. Biopsy of the skin was performed but not diagnostic. Microscopic examination displayed focal parakeratosis and mild spongiosis.

Figure 2

Growth charts of CMH812. The patient is a female with severe intrauterine and postnatal growth retardation head circumference (A) [<3rd centile]; weight (B) [<2nd centile], length (C) [<2nd centile], based on CDC growth chart for girls, age 0–20 months. Growth remained poor postnatally and she was briefly started on growth hormone, which was discontinued due to suspicion for a disorder of DNA repair/instability. At age 15 months she was ~5 SD below the mean for weight and length and ~3-4 SD below the mean for head circumference.

She suffered chronic rhinosinusitis and pulmonary infections with purulent otitis media. At age 20 months she was admitted to the hospital with pancytopenia, splenomegaly, hepatitis and acute CMV infection. Laboratory data showed mild bone marrow myelodysplasia, normal total B, T, and NK cells, low class switched and non switched memory B cells, and high memory T cells. She had high IgA, normal total IgG and low IgM, IgG2 and IgG4. There was no serologic response to pneumococcal vaccine (Table 1). Lymphocyte response to mitogens was normal but absent to pertussis and candida antigens [11]. Hepatitis and pancytopenia resolved following the CMV infection. Extensive molecular and cytogenetic testing was negative, including array-CGH, telomere length studies, chromosome breakage, and gene sequencing with deletion/duplication analysis for the following genes: ATM, ATR, BLM, CENPJ, CEP152, CEP63, ERCC6, ERCC8, LIG4, LMNA, MRE11A, NBN, PCNT, RBBP8, RECQL4, SHOX, WRN, and ZMPSTE24.
Table 1

Comparison of clinical features of POLE1 patients and other chromosome instability syndromes

Clinical features

TAR syndrome

Ataxia telangiectasia

RAD50 deficiency

Fanconi anemia

Seckel syndrome

NBS

RS/SC syndrome

Warsaw syndrome

Cernnos-XLF syndrome

Bloom syndrome

LIG4 syndrome2

FILS syndrome*

CMH812

MIM #

274000

208900

613078

227650

210600

251260

268300 /269000

613398

611291

210900

606593

615139

615139

Microcephaly

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

Malar hypoplasia

n.a

ν

n.a

n.a

ν

ν

ν

n.a

ν

ν

Sloping head

ν

n.a

ν

ν

ν

ν

ν

ν

ν

ν

Palpebral fissures, upslanting

n.a

ν

ν

ν

ν

Palpebral fissures, down-slanting

ν

ν

ν

ν

ν

ν

ν

Epicanthic folds

ν

ν

ν

ν

ν

ν

ν

ν

Micrognathia

ν

n.a

ν

ν

ν

ν

ν

ν

External ear abnormalities

n.a

ν

ν

ν

ν

ν

ν

ν

ν

ν

Long/Large nose

ν

ν

ν

ν

ν

ν

ν

ν

ν

Long philtrum

n.a

ν

ν

ν

ν

ν

ν

Cleft palate/high arched palate

n.a

ν

ν

ν

ν

Polydactily

n.a

ν

ν

ν

Clinodactily

n.a

ν

ν

ν

ν

ν

ν

ν

Syndactily

             

Growth retardation

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

Short stature

ν

ν

n.a

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

Bone disease or anomalies

ν

n.a

ν

ν

ν

n.a

ν

ν

ν

Thumb apasia/radial ray anormalities

ν

n.a

ν

ν

−/ν

n.a

ν

 

Skin abnormalities

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

Mental retardation

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

Developemental delay

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

Malignancy

ν

ν

ν

ν

ν

ν

n.a

ν

ν

ν

Recurrent infections

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

Genital abnormalities

ν

ν

ν

ν

n.a

ν

Ataxia

ν

ν

ν

n.a

n.a

n.a

n.a

Brain anomalie/degeneration

CA, CH, aCC, S

CA, CH,T, S

ND

ν

CA, CH, PG, S

ND

S

n.a

PG

n.a

n.a

n.a

Endocrine

AZ, D, DP, HH

HH

D, DP

POF

n.a

n.a

AZ, D RF

Immunologic Features

             

Pancytopenia

n.a

n.a

ν

ν

n.a

n.a

ν

ν

ν

Thrombocytopenia

ν

n.a

ν

n.a

n.a

ν

CID

ν

n.a

n.a

n.a

ν

n.a

ν

2/14

ν

SCID

ν

ν

n.a

n.a

ν

n.a

ν

n.a

-

Neutropenia

n.a

n.a

ν

n.a

ν

n.a

n.a

ν

N

ν

n.a

-*

B cell lymphocytopenia

ν

N

ν

n.a

n.a

ν

2/17

ν

ν

T cell lymphocytopenia

ν

N

ν

ν

ν

n.a

n.a

ν

ν

N

ν

ν

IgA

n.a

N

N

n.a

n.a

n.a

N

IgE

n.a

N

n.a

n.a

n.a

n.a

n.a

N

n.a

N

N

IgG

n.a

N

n.a

n.a

n.a

n.a

↓**

IgM

n.a

N

n.a

n.a

n.a

Anti-pseudomonae

n.a

n.a

N

n.a

n.a

n.a

n.a

ν

n.a

n.a

ν

ν

polysaccaride IgG

             

Auto-immunity

n.a

ν

n.a

ν

n.a

n.a

1/17

n.a

0/17

-

Sister chromatide

n.a

n.a

n.a

↑ or N

ν

ν

ν

n.a

ν

n.a

N

N

DNA breakage studies

n.a

ν

ν

ν

ν

ν

ν

ν

ν

ν

n.a

N

Radiosensitivity

n.a

ν

ν

ν

ν

ν

ν

ν

ν

ν

ν

n.a.

Gene

RBM8A

ATM

RAD50

FANC

ATR

NBS1

ESCO2

DDX11

NHEJ1

BLM

LIG4

POLE1

POLE1

Mode of Inheritance

AR

AR

AR

AR

AR

AR

AR

AR

AR

AR

AR

AR

AR

Legend

n.a; not reported/applicable.

−; negative.

ν; positive.

N; normal range.

↓; decreased.

↑; increased.

NBS: Nijmegen breakage syndrome.

TAR: Thrombocytopenia-absent radius syndrome.

RS: Roberts syndrome.

SC: SC phocomelia syndrome.

aCC; absence of corpus collosum.

AR; autosomal recessive.

AZ; azoospermia.

CA; cerebellar ataxia.

CH; cerebellar hypoplasia.

CID; combined immunodeficiency.

D; diabetes.

DP; delayed puberty.

HH; hypergonadotropic hypogonadism.

NBS; Nijmegen breakage syndrome.

ND; neurodegenerative.

OA; oculomotor apraxia.

PG; polygyria.

POF; primary ovarian failure.

RF; reduced fertility.

S; seizures.

SCID; severe combined immunodeficiency.

T; Tremor.

*consanguineous family reported.

£ Ataxia-telangiectasia-like disorder.

- * Transient pancytopenia associated with CMV infection.

↓** IgG2 and IgG 4 ↓. Total IgG N.

Trio-exome sequencing was performed on CMH812 and her healthy parents (CMH813 & CMH814) following informed consent, and with methods as previously published [19-22]. Variants were filtered to 1% minor allele frequency, then prioritized by the American College of Medical Genetics (ACMG) categorization [23,24], OMIM identity and phenotypic assessment. This individual was homozygous for a splice-site variant, c.4444 + 3A > G, in intron 34 of the POLE1 [11]. The parents were both heterozygous carriers (Additional file 1: Table S1). Homozygosity mapper was used to identify intervals of homozygosity and identity by descent segments (Additional file 2: Figure S1) [25].

The c.4444 + 3A > G variant was previously reported in consanguineous French family with three generations of affected members [11]. FILS phenotype was variable but included macrocephaly, recurrent respiratory infections, livedo and telangiectasia, bone dysplasia, short stature, and decreased IgM and IgG. The phenotype was considered similar to that of Bloom syndrome but with normal sister chromatid exchange. Table 1 compares the clinical and cellular features of CMH812 to those of individuals with inherited chromosomal instability and breakage syndromes, as well as the first reported FILS family. Features closely matched those reported in FILS with exceptions of microcephaly and intrauterine growth restriction. Although the POLE1 variant identified in the present case is the same as previously reported, CMH812 seems to have had more significantly impaired growth and immunity, raising the hypothesis that rare variant(s) in other POLƐ subunits or MMR genes may act as phenotypic modifiers. However, no rare variant were detected in MMR genes, POLE1 interacting proteins or other DNA breakage/instability syndrome genes.

The c.4444 + 3A > G POLE1 variant confers abnormal splicing whereby exon 34 is deleted [11] leading to significant decrease in the POLE1 subunit [11]. T- lymphocytes from affected individuals showed a proliferation defect as well as impaired cell cycle progression. The primary function of polymerase Ɛ1 is to synthesize DNA at the leading strand during replication [26,27], however, it is also involved in other cellular processes, including cell cycle progression and DNA repair/recombination [26,27]. Exonucleolytic proofreading and the MMR pathway act to maintain high-fidelity DNA replication and to protect against mutagenesis [28]. Somatic and germline heterozygous missense variants in POLƐ1 have been associated with an increased cancer risk [28-32]. Functional studies in yeast showed that heterozygosity for a pathogenic allele can cause complete MMR deficiency, and that subsequent loss of heterozygosity is not required for the development of POLE-related tumors [28]. Taken together, these findings suggest that POLE1 carriers are likely to be at increased risk for malignancy due to MMR deficiency.

Conclusions

In summary, we report a second family with POLE1-related disease. The clinical and immunologic features of our patient are reminiscent of LIG4 syndrome, possibly representing the more severe end of an ill-defined clinical spectrum. For this reason, POLE1 deficiency may be a more apt description of this disorder. This report illustrates the cost-effectiveness of trio-exome sequencing as a powerful diagnostic method considering that this family underwent an extensive diagnostic odyssey, with no molecular basis identified prior exome.

Consent statement

The project was approved by the research ethics committee of the Children’s Mercy Hospitals. Written informed consent was obtained from the patient’s legal guardians for publication of this case report. A copy of the written consent is available for review by the Editor-in-Chief of this journal.

Abbreviations

ACMG: 

American College of Medical Genetics

aCGH: 

Array of comparative genomic hybridization

DNA: 

Deoxyribonucleic acid

FILS: 

Facial dysmorphism immunodeficiency livedo and short stature

IUGR: 

Intrauterine growth restriction

LIG4: 

DNA ligase IV

Mb: 

Megabase pair

MMR: 

DNA mismatch repair

NK: 

Natural Killer

OMIM: 

Online Mendelian Inheritance in Man

NICU: 

Neonatal intensive-care unit

PCR: 

Polymerase chain reaction

POLE1: 

DNA polymerase E1

TAR: 

Thrombocytopenia absent radii syndrome

TORCH: 

Toxoplasmosis, other infections, rubella, cytomegalovirus (CMV), and herpes simplex virus (HSV). The “other infections” usually include syphilis, hepatitis B, coxsackie virus, Epstein-Barr virus, varicella-zoster virus, and human parvovirus

SD: 

Standard deviation

SNP: 

Single nucleotide polymorphism

XLF: 

XRCC4-like factor

Declarations

Acknowledgments

We are grateful to the patient and her family. We thank the other staff of the Center for Pediatric Genomic Medicine, Children’s Mercy Kansas City, and Dr. Geneviève de Saint Basile and her team for discussions. This work was supported by the Marion Merrell Dow Foundation, Children’s Mercy - Kansas City, Patton Trust, W.T. Kemper Foundation, Pat & Gil Clements Foundation, Claire Giannini Foundation, and Black & Veatch.

Bioinformatics

The accession numbers for the reference sequences are listed as follows: POLE1 NM_006231.2:,HGMD 290829429, ClinVarRCV000034317.25

1000 Genomes Project, http://www.1000genomes.org/

NHBLI Exome Sequencing Project (ESP) Exome Variant Server,

http://evs.gs.washington.edu/EVS/

Online Mendelian Inheritance in Man (OMIM), http://www.omim.org

SNPdb, http://www.ncbi.nlm.nih.gov/projects/SNP

UCSC Genome Browser, http://genome.ucsc.edu/

PolyPhen-2, http://www.genetics.bwh.harvard.edu/pph2/

ClinSeq, http://genome.gov/20519355

RefSeq, http://www-ncbi-nlm-nih-gov.proxy2.library.mcgill.ca/RefSeq

SIFT, sift.jcvi.org/

Authors’ Affiliations

(1)
Division of Clinical Genetics, Childrens Mercy Hospital
(2)
Center for Pediatric Genomic Medicine, Children’s Mercy Hospital
(3)
Department of Pathology and Laboratory Medicine, Childrens Mercy Hospitals
(4)
Pediatric Allergy, Asthma and Immunology Clinic, Children’s Mercy Hospitals
(5)
Dermatology Clinic, Children’s Mercy Hospitals
(6)
Department of Hematology and Oncology, Children’s Mercy Hospitals
(7)
Department of Pediatrics, Children’s Mercy Hospitals
(8)
University of Missouri, Kansas City School of Medicine

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© Thiffault et al.; licensee BioMed Central. 2015

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