de Novo TINF2 C.845G>A: Pathogenic Variant in Patient with Dyskeratosis Congenita.

Dyskeratosis congenita (DC) is a clinically and genetically heterogeneous, multisystem inherited syndrome with a very high risk for bone marrow failure (BMF) and cancer predisposition. The classical clinical form of DC is characterized by abnormal skin pigmentation, nail dystrophy, and oral leukoplakia. Bone marrow failure is considered to be an important and major complication of DC and the leading cause of death which develops in around 85% of cases. A number of genes involved in telomere maintenance are associated with DC, such as genes that encode the components of the telomerase complex (TERT, DKC1, TERC, NOP10, and NHP2), T-loop assembly protein (RTEL1), telomere capping (CTC1), telomere shelterin complex (TINF2), and telomerase trafficking protein (TCAB1). Mutations in TINF2 have been reported in 11-20% of all patients with DC and have been associated with bone marrow failure. Here we report on a 19-month old boy with very early presentation of bone marrow failure as a first clinical manifestation of DC. Upon first admission, the patient presented with thrombocytopenia and macrocytic anemia. Soon after, his blood counts deteriorated with the development of pancytopenia and aplastic anemia. Four months later, he developed nail dystrophy and skin hyperpigmentation. A de novo heterozygous pathogenic variant c.845G>A, p.(Arg282His) was located in exon 6 of TINF2 gene and was identified via clinical exome sequencing. The findings confirmed the diagnosis of DC. This is the first case with DC due to TINF2 pathogenic variant reported in North Macedonia.

INTRODUCTION

Dyskeratosis congenita (DC) is a clinically and genetically heterogeneous multisystem inherited syndrome caused by mutations in genes that encode the protein components of the telomerase complex and shelterin complex. DC is a rare disease with an estimated annual incidence of 1 in 1,000,000 [1]. Genotype–phenotype correlations are complex due to a variety of gene mutations, disease anticipation, and genetic and environmental modifier effects. The classical clinical form of the disease is characterized by the mucocutaneous triad of abnormal skin pigmentation, nail dystrophy, and leukoplakia [2, 3]. The abnormal skin pigmentation and nail changes usually appear first, often under 10 years of age. Additional features of the clinical presentation include BMF, myelodysplastic syndrome (MDS), epiphora, blepharitis, premature graining, alopecia, growth retardation, cerebellar hypoplasia and microcephaly, esophageal stenosis, urethral stenosis, liver disease, pulmonary fibrosis, and avascular necrosis of the hips or shoulders. DC patients have an increased risk of developing malignant disease [4, 5]. Bone marrow failure is considered to be an important and major complication of DC, and is a leading cause of death that develops in around 85% of cases. DC is caused by mutations in genes that encode protein components of the telomerase complex and shelterin complex. Since 1998 at least 14 DC genes involved in the telomere's shortening have been identified, accounting for approximately 70–80% of DC cases [6,7,8]. These genes encode proteins for the maintenance of telomeres, which are located at the ends of chromosomes. DC can be inherited in an X-linked, autosomal dominant (AD), or autosomal recessive (AR) pattern. Mutations in TINF2 have been reported in 11–20% of all patients with DC and have been associated with bone marrow failure [9]. In addition, mutations of TINF2 were also identified in patients with other diseases associated with bone marrow failure (e.g. ataxia-pancytopenia and aplastic anemia) [10, 11]. In this paper we report on a 19-month old boy with de novo heterozygous mutation in the TINF2 gene and a very early presentation of bone marrow failure as a first clinical manifestation of DC.

CASE PRESENTATION

A 19-month-old boy was referred to the hematology department at the University clinic for children's diseases in order to evaluate the possibility of thrombocytopenia. He is of Albanian ancestry, born after a normal pregnancy from healthy parents. There is no consanguinity in the family. Clinical examination at admission revealed pallor, cutaneous and mucosal hemorrhagic syndrome. He had growth retardation below the third percentile on the growth curve. Laboratory tests have shown thrombocytopenia (with PLT 27 × 109/l), with macrocytic anemia (Hb: 102 g/L, RBC 3.3 × 109/l, MCV: 98.2 fL) and WBC: 6.03 × 109/l, neutrophil count of 1.25 109/l. BM analysis showed megaloblastic maturation in BM with megakaryocyte hypoplasia. Chromosome analysis indicated no numerical or structural chromosomal abnormalities. The following month, the PLT number decreased to 7 × 109/l with the development of severe macrocytic anemia (Hb 72g/L; RBC 2.3 ×109/l). Blood counts deteriorated with the development of pancytopenia and aplastic anemia. Four months later, a physical examination revealed nail dystrophy and skin pigmentation involving the neck. Differential diagnosis suggested Fancony anemia or DC. The diagnosis of DC was established with the identification of a known pathogenic de novo TINF2 gene mutation. The clinical characteristic and hematology findings during the follow up are summarized in Table 1.

Table 1

Hematology results and clinical characteristic during the follow up

Analysis	I st admission	2 months	4 months
Hb (g/l)	102	86	72
RBC (109/l)	3.3	2.6	2.3
MCV (fl)	98.2	102	105
WBC (109/l)	6.03	4.8	4.9
Granulocyte (109/l)	1.25	1.0	0.8
PLT (109/l)	27	12	7
BM aspiration and BM biopsy	Megaloblastic maturation, Megakaryocytic hypoplasia		Hypo plastic, fatty bone marrow
Nail dystrophy	No	No	Present
Skin hyperpigmentation	No	No	Present
Mucosal Leucoplakia	No	No	No
Genetic analyses			c.845G>A, p. (Arg282His)

GENETIC ANALYSIS AND RESULTS

We performed clinical exome sequencing on a MiSeq desktop sequencer, using TruSight One kit (Illumina) for the proband. The analysis revealed the presence of the known pathogenic variant c.845G>A, p.(Arg282His), in a heterozygous state, in the TINF2 gene (Figure 1). Amplification and Sanger sequencing of TINF2 exon 6 showed the absence of the variant in the proband's parents. DNA analysis using the AmpFLSTR Identifiler PCR Amplification Kit confirmed the biological relationship between the child and his parents. Thus, the TINF2 c.845G>A variant has arisen as a de novo event in the proband. Schematic representation of the pathogenic TINF2 gene variants is presented in Figure 2.

Figure 1

TINF2 gene exon 6 direct sequencing results in the proband.

Figure 2

Schematic representation of the pathogenic TINF2 gene variants.

TREATMENT

The medical management of each DC patient is very complex and should take into consideration the patient's specific needs. Patients with DC and BMF do not respond to immunosuppressive therapy, and allogeneic hematopoietic stem cell transplantation (HSCT) is the only curative treatment for BMF. Our patient received corticosteroids for one month without any response to the therapy. After the confirmation of DC, HSCT was performed by an unrelated full matched donor. The patient experienced engraftment failure and underwent a second unrelated HSCT. One year after the second HSCT he was in a good clinical condition. Once the bone marrow failure issue was resolved, thrombocytes were around 30–40 × 109/l and the boy had a relatively good quality of life.

DISCUSSION

We report the clinical, laboratory and genetic findings of a 19-month-old Albanian boy from North Macedonia with aplastic anemia as a first clinical presentation of DC. A known pathogenic missense variant, c.845G>A, p.(Arg282His), located in exon 6 of the TINF2 gene, was identified as responsible for DC in our patient.

Autosomal dominant DC is a clinically and genetically heterogeneous group of the disease. To date, heterozygous variants in 4 genes (TERC, TERT, RTEL1 and TINF2) have been characterized. Patients harboring TINF2 variants are reported to have extremely short telomeres, and a frequent early age of presentation (less than 10 years old), and they often present severe manifestation of the disease [8, 14]. Nearly all patients have de novo TINF2 variants that give rise to a different mechanism that causes the disease. List of the known TINF2 pathogenic variants reported to date is given in Table 2. TINF2 mutations can be associated with a broad spectrum of phenotypes (Table 2, on the next page). The classical clinical form of the disease is characterized by dysplastic nails, lacy reticular pigmentation of the upper chest and/or neck and oral leukoplakia. BMF, myelodysplastic syndrome (MDS), epiphora, blepharitis, premature graining, alopecia, growth retardation, cerebellar hypoplasia and microcephaly, esophageal stenosis, urethral stenosis, liver disease, pulmonary fibrosis, and avascular necrosis of the hips or shoulders can be included in the clinical presentation. Progressive bone marrow failure may appear at any age and may be the only sign until the age of 10. Macrocytosis and elevated hemoglobin F levels may be seen in these patients. Patients have an increased risk of the development of malignant disease. Solid tumors may be the first manifestation of DC in persons who do not have BMF and are younger than 50 years of age [15]. Most DC patients have normal intelligence and development of motor skills. In severe forms of the disease, developmental delay may occur. In Hoyeraal Hreidaarsson syndrome, a severe form of the disease, affected individuals have an unusually small and underdeveloped cerebellum and intrauterine growth retardation. In addition to the other symptoms of dyskeratosis congenita, bilateral exudative retinopathy and intracranial calcifications are characteristic for the other severe variant of DC, called Revesz syndrome [16]. Pulmonary fibrosis was found in DC patients with the c.844C>T p.(Arg282Cys), c.851C>G p.(Thr284Arg) and c.872_875del p.(Arg291IlefsTer25) TINF2 pathogenic variants [14, 17, 18].

Table 2

List of known pathogenic TINF2 gene variants

Chr Position (GRCh37)	Nucleotide change (NM_001099274)	Amino acid change (NP_001092744)	rs ID	Phenotype	Publication (Reference)
chr14:24711458	c.81C>A	p.Cys27Ter	rs1060499576	DC, RS	/
chr14:24709890	c.796C>T	p.Arg266Ter	rs1064795632	N/A	/
chr14:24709881	c.805C>T	p.Gln269Ter	rs387907153	DC, mucocutaneous features, BMF	19, 18
chr14:24709875	c.811C>T	p.Gln271Ter	rs387907154	AA	19
chr14:24709860	c.826delA	p.Arg276GlyfsTer41	rs863223324	ND, BMF, lichenoid tongue, dry skin, intrauterine growth retardation	18
chr14:24709848	c.838A>T	p.Lys280Ter	rs121918543	DC, HHS, and RS	12, 15
chr14:24709848	c.838A>G	p.Lys280Glu	rs121918543	DC	12, 21, 8
chr14:24709847	c.839delA	p.Lys280ArgfsTer37	rs1594551449	DC, RS	19
chr14:24709842	c.844C>A	p.Arg282Ser	rs121918545	DC, RS	12, 17, 23
chr14:24709842	c.844C>T	p.Arg282Cys	rs121918545	DC, AA, PD and mucosal changes	20, 12, 17
chr14:24709841	c.845G>A	p.Arg282His	rs121918544	DC, HHS, RS	12, 22, 17, 24, 25, 26, 27, 28
chr14:24709839	c.847C>T	p.Pro283Ser	rs199422311	DC, HHS	12, 15
chr14:24709839	c.847C>G	p.Pro283Ala	rs199422311	DC	12, 15
chr14:24709838	c.848C>A	p.Pro283His	rs199422313	DC	12, 15
chr14:24709837	c.849delC	p.Thr284GlnfsTer33	/	ND, BMF	18
chr14:24709837	c.849_850insC	p.Thr284HisfsTer8	rs199422315	DC, AA	12, 15
chr14:24709836	c.850A>G	p.Thr284Ala	rs199422314	DC	12, 15
chr14:24709835	c.851C>A	p.Thr284Lys	/	DC	18
chr14:24709835	c.851C>G	p.Thr284Arg	/	BMF, hair loss, dental loss, PD, short stature, osteoporosis	18
chr14:24709829	c.857delTinsGC	p.Met286SerfsTer5	/	ND, BMF, microcephaly, low immunoglobulins	18
chr14:24709826	c.860T>C	p.Leu287Pro	rs199422316	DC	12, 15
chr14-24709824	c.862T>C	p.Phe288Leu	rs199422317	DC	12, 15
chr14:24709821	c.865C>T	p.Pro289Ser	rs1555304055	N/A	29
chr14:24709820	c.865_866delinsAG	p.Pro289Ser	rs199422318	DC	12, 15
chr14:24709819	c.867_868insC	p.Phe290LeufsTer2	/	DC	12
chr14:24709815	c.871A>G	p.Arg291Gly	rs199422319	DC	12, 15
chr14:24709812	c.872_875del	p.Arg291IlefsTer25	/	DC, PD	14
chr14:24709794	c.892delC	p.Gln298ArgfsTer19	rs199422320	DC	12, 15
chr14:24709508	c.1090dup	p.Leu364ProfsTer9	rs1566366182	DC	/

DC - Dyskeratosis congenita, HHS - Hoyeraal Hreidarsson syndrome, RS - Revesz syndrome, BMF - Bone marrow failure, AA - Aplastic anemia, PD - Pulmonary disease, ND - Nail dystrophy

The TINF2 pathogenic variant c.845G>A, p.Arg282His that was identified in our patient has been previously reported in patients with severe clinical presentations, such as Hoyeraal Hreidarsson syndrome and Revesz syndrome (8, 11).

CONCLUSION

DC is a rare genetic disorder with genetic and clinical heterogeneity. Patients with aplastic anemia should be screened for this rare condition, even when they do not have a classical clinical form. Reporting different cases increases our knowledge of the disease and its heterogeneity. Early diagnosis allows for prevention of severe invasive infections and non-infectious complications, thus improving the success of transplantation and overall prognosis of DC.