Genes and Immunity (2017), 1–3 © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved 1466-4879/17 www.nature.com/gene

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Autosomal recessive agammaglobulinemia due to defect in μ heavy chain caused by a novel mutation in the IGHM gene P Silva1, A Justicia2, A Regueiro2, S Fariña2, JM Couselo2 and L Loidi1 Agammaglobulinemia is a primary immunodeficiency disorder characterized by profoundly low or absent serum antibodies and low or absent circulating B cells. The most common form is X-linked agammaglobulinemia (XLA) caused by mutations in BTK gene. The remaining cases, clinically similar to XLA, are autosomal recessive agammaglobulinemia (ARA). Nearly 30% of ARA cases present mutations in the μ heavy constant region gene IGHM. Here, we present a 7-month-old patient, born from non-consanguineous parents, who is affected by ARA due to defect in the μ heavy chain. The genetic study showed that the patient is compound heterozygous for an IGHM gene deletion and the novel nonsense mutation X57331.1:g.275C4A (p.Tyr43*) (ClinVar Accession Number: SCV000537868.1). This finding allows for an adequate genetic counseling to the family and also broadens the spectrum of already described point mutations at this locus. The IGHM gene is very complex and it is likely that yet unidentified mutations appear in other patients. Genes and Immunity advance online publication, 3 August 2017; doi:10.1038/gene.2017.14

INTRODUCTION Agammaglobulinemia is a primary immunodeficiency disorder characterized by profoundly low or absent serum antibodies and low or absent circulating B cells due to an early blockage of B-cell development. The most frequent variety, which affects 85% of male patients, is X-linked agammaglobulinemia (XLA) or Bruton disease, which is caused by mutations in the BTK (Bruton Tyrosin Kinase) gene. The remaining 15% of the cases represent a genotypically heterogeneous group of autosomal recessive agammaglobulinemia (ARA) and their incidence is very low, about 1/2 000 000 births (Orphanet, ORPHA33110). ARA is associated with mutations in several genes as IGHM (Immunoglobulin Heavy Constant Mu), CD79A (B-Cell Antigen Receptor ComplexAssociated Protein Alpha Chain), CD79B (B-Cell Antigen Receptor Complex-Associated Protein Beta Chain), IGLL1 (Immunoglobulin Lambda Like Polypeptide), BLNK (B-Cell Linker), LRRC8A (Leucine Rich repeat Containing 8 Family member A) or PIK3R1 (Phosphoinositide-3-Kinase Regulatory Subunit).1 ARA accounts for up to 15% of patients with agammaglobulinemia. Both XLA and ARA share 3 diagnostic criteria; profoundly decreased levels of serum globulins, recurrent bacterial infections in the first 5 years of life and absence of circulating B cells. However, clinical course may vary and genetic analysis is needed to identify etiology and to enable more informed genetic counseling.1 In 1996, Yel et al.2 showed for the first time that mutations in the IGHM gene encoding for the μ heavy chain caused an agammaglobulinemia similar to XLA. Since them, several families have been reported with mutations in IGHM.3–7 Patients with defects in IGHM present earlier onset and more severe complications of the disease than patients with mutations in BTK. This can be partially explained because mutations in BTK result in a partial blockage of B-cell development, while the

μ heavy chain defect results in a complete blockage.4 This disorder accounts for ~ 5% of patients with agammaglobulinemia. Many patient, 30–60%, present large deletions encompassing the IGHM gene and a relatively small number of point mutations have been reported.1,8

RESULTS AND DISCUSSION The genetic study of the patient affected by ARA allowed the identification of a novel nonsense mutation in the IGHM gene: X57331:g.275C4A (p.Tyr43*) (chr14:106322192) (SCV000537868.1). This mutation consisted of a C to A nucleotide substitution that results in a premature stop signal at codon 43 and therefore in a predicted truncated protein. No normal sequence was detected at this position by NGS (next generation sequencing) suggesting a homozygous or hemizygous mutation because of nonconsanguinity. The later could not be confirmed by NGS because this analysis is not reliable to detect gross deletions. No other variants were detected in any of the sequenced genes but for benign or probably benign variants. Further Sanger sequencing of IGHM exon 1 after specific PCR amplification confirmed the presence of the mutation. The patient’s mother was heterozygous for the same mutation while the father showed normal sequence (Figure 1). These results suggested a heterozygous deletion in the paternal allele. A semiquantitative PCR showed a heterozygous deletion, which encompassed at least the exon 1 of IGHM, in the patient and in her father. Therefore, the patient was a compound heterozygous for the novel g.275C4A (p.Tyr43*) mutation and an IGHM deletion. The genetic result confirmed a diagnosis of ARA due to IGHM defect (OMIM #601495). The patient presented severe agammaglobulinemia with early onset as was previously described in other published cases since the expression of a surface μ heavy

1 Fundación Pública Galega de Medicina Xenómica. Rua Choupana SN, Santiago de Compostela, Spain and 2Pedriatics Service. Complejo Hospitalario Universitario de Santiago de Compostela. Rua Choupana SN, Santiago de Compostela, Spain. Correspondence: Dr L Loidi, Fundación Pública Galega de Medicina Xenómica, Rua Choupana SN, 15706 Santiago de Compostela, Spain. E-mail: [email protected] Received 18 January 2017; revised 2 June 2017; accepted 22 June 2017

IGHM defect by a novel nonsense mutation P Silva et al

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Figure 1. Trio pedigree (upper panel). DNA electropherograms showing the sequence of a fragment of IGHM exon 1 (middle panel). Wild-type sequence vs. sequence with the point mutation (bottom panel).

chain is essential for the progression of B-cell differentiation beyond the pre-B cell stage.3,5,9 Many patients suffering from IGHM defects showed gross deletions ranging in size from 40 to 732 Kb which encompassed the IGHM gene. The high incidence of these large deletions may be explained by the complexity of the IGH locus. On the other hand, the spectrum of point mutations in the μ constant region described so far is scarce and there is just one nonsense mutation reported by López Granados et al.,4 which is located in exon 3, upstream of the nonsense mutation presented here. Here, we report a new case of a 7-month-old girl with a severe agammaglobulinemia due to defect in μ heavy chain that is a compound heterozygous for a novel point mutation and a deletion in the IGHM gene. The diagnosis of an ARA due to the presence of a point mutation and a deletion in a compound heterozygous state could lead to a genetic misdiagnosis in patients born from non-consanguineous parents. The correct identification of both mutations is important to give adequate genetic counseling to the families and to perform a reliable prenatal diagnosis. In the present family, it would be possible to do a prenatal diagnosis discriminating between an affected and a non-affected fetus, although it would be difficult to assess the carrier status of a deletion in the later. The IGHM gene is very complex and it is likely that yet unidentified mutations appear in some patients. In this case report, we show a compound heterozygous patient for a deletion and the novel nonsense mutation X57331.1:g.275C4A (p.Tyr43*) in IGHM, which broadens the small spectrum of described mutations at this gene. The identification of new genetic alterations in the IGHM gene provides a basis for more accurate diagnosis and allows more informed genetic counseling Genes and Immunity (2017), 1 – 3

comprising the identification of carrier status, it also enables prenatal testing. PATIENTS AND METHODS The patient, a 7-month-old girl, was the first of healthy and nonconsanguineous parents. She was born after a normal pregnancy and delivery at 38 weeks of gestation. She was well vaccinated, including 3 doses of Rotavirus vaccine. No medical history of interest. She had two healthy half-brothers on her father’s side and one healthy half-sister in her mother’s side. The patient was admitted to the hospital with a history of 4 days fever. Physical examination revealed affected general condition, tachycardia, tachypnea and increased capillary refill time. Blood examination showed leukocyte and neutrophil counts, 4980/μl and 250/μl, respectively. Hemoglobin and platelets levels were normal. Blood, urine and cerebrospinal fluid (CSF) cultures were performed. Empirical antibiotic treatment was initiated with clinical suspicion of sepsis, thus the patient showed an initial clinical improvement. Nevertheless, in the third day of admission she showed deterioration, and she had clinical image compatible with peritonitis, obtained by ultrasonography and computed tomography. The blood test showed persistent neutropenia and persistent hypoglammaglobulinemia (undetectable IgA and IgM levels and 50 mg dl–1 IgG levels). Blood culture was positive for Pseudomonas aerugiosa and urine culture was positive for Escherichia coli. CSF culture was sterile. The patient was treated with broad spectrum antibiotics and two doses of intravenous immunoglobulin therapy. Clinical improvement was achieved after 3 weeks of hospitalization. Considering the severity of the clinical condition and the analytical results, extended immunological work-up was performed confirming undetectable IgA and IgM (IgG level was non assessable because of the previous doses of the intravenous © 2017 Macmillan Publishers Limited, part of Springer Nature.

IGHM defect by a novel nonsense mutation P Silva et al

immunoglobulin therapy). Laboratory test showed absence of circulating CD19+ cells in the peripheral blood, normal number of CD4 and CD8 T lymphocytes and NK cells. A bone marrow (BM) aspirate was performed and analyzed by flow cytometry. BM immunophenotyping revealed as follows: 10.35% of T lymphocytes (6.3% CD4+; 4.04% CD8+), 1.27% of NK cells and 4.56% B lymphocytes (2.4% CD34+; 1.16% CD34 − ), which CD10+, CD38+, CD20 − , CD45+d, cytoplasmatic and surface membrane IgM negative and CD22+d, consistent with a developmental arrest at the pro- to pre-B-cell checkpoint. These data indicate that the patient’s B-cell development suffered a premature arrest in the BM between pro-B and pre-B cell stages. Since the diagnosis, the patient has been treated with intravenous replacement immunoglobulin therapy (500 mg Kg–1 every 3–4 weeks, with ore-administration levels of 552–743 mg dl–1). During the 14 months follow-up, a central catheter venous colonization by Candida parapsilosis (resolved) and a viral rhinitis infection were diagnosed, which did not cause severe complications. Furthermore, she had two febrile typical simple seizures. CSF analysis was normal in both episodes. She neither had episodes of diarrhea or failure to thrive until the present time. The analysis of classical markers of the B-cell lineage in the patient’s BM indicated that the deficiency was the consequence of an impaired differentiation at an early stage of B-cell development, in accordance with the absence of IgM and IgD expression and the total absence of immature and mature B cells. The patient, with the clinical diagnosis of agammaglobulinemia was referred for genetic analysis to precisely diagnose her disease. Informed consent was obtained from the parent to perform the genetic analysis. For the genetic analysis, a targeted next generation sequencing (NGS) of a panel of agammaglobulinemia related genes was performed (Ion AmpliSeq Custom Panel). The panel included the genes associated with ARA: BLNK, CD79A, CD79B, IGHM, IGLL1, LRRC8A and PIK3R1, and BTK which is associated with XLA. In order to validate the mutation detected by NGS, the exon 1 of IGHM was amplified by PCR and directly sequence by the Sanger method. A semiquantitative PCR was performed for the assessment of IGHM gene deletion.

© 2017 Macmillan Publishers Limited, part of Springer Nature.

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CONFLICT OF INTEREST The authors declare no conflict of interest.

ACKNOWLEDGEMENTS We would like to thank the patient's parents for their cooperation in this study.

REFERENCES 1 Conley ME, Dobbs AK, Farmer DM, Kilic S, Paris K, Grigoriadou S et al. Primary B cell immunodeficiencies: comparisons and contrasts. Annu Rev Immunol 2009; 27: 199–227. 2 Yel L, Minegishi Y, Coustan-Smith E, Buckley RH, Trübel H, Pachman LM et al. Mutations in the mu heavy chain gene in patients with agammaglobulinemia. N Engl J Med 1996; 335: 1486–1493. 3 Schiff C, Lemmers B, Deville A, Fougereau M, Meffre E. Autosomal primary immunodeficiencies affecting human BM B-cell differentiation. Immunol Rev 2000; 178: 91–98. 4 López Granados E, Porpiglia AS, Hogan MB, Matamoros N, Krasovec S, Pignata C et al. Clinical and molecular analysis of patients with defects in mu heavy chain gene. J Clin Invest 2002; 110: 1029–1035. 5 Milili M, Antunes H, Blanco-Betancourt C, Nogueiras A, Santos E, Vasconcelos J et al. A new case of autosomal recessive agammaglobulinemia with impaired pre-B cell differentiation due to a large deletion of the IGH locus. Eur J Pediatr 2002; 161: 479–484. 6 Ferrari S, Zuntini R, Lougaris V, Soresina A, Sourková V, Fiorini M et al. Molecular analysis of the pre-B complex in a large cohort of patients affected by autosomalrecessive agammaglobulinemia. Genes Imun 2007; 8: 325–333. 7 Mohammadzadeh I, Yeganeh M, Aghamohammadi A, Parvaneh N, Behniafard N, Abolhassani H et al. Severe primary antibody deficiency due to a novel mutation of μ heavy chain. J Investig Allergol Clin Immunol 2012; 22: 63–79. 8 van Zelm M, Geertsema C, Nieuwenhuis N, de Ridder D, Conley ME, Schiff C et al. Gross deletions involving IGHM, BTK, or Artemis: a Model for genomic lesions mediated by transposable elements. Am J Hum Genet 2008; 82: 320–322. 9 Meffre E, Milili M, Blanco-Betancourt C, Antunes H, Nussenzweig MC, Schiff C. Inmunoglobulin heavy chain expression shapes the B cell receptor repertoire in human B cell development. J Clin Invest 2001; 108: 879–886.

Genes and Immunity (2017), 1 – 3

Autosomal recessive agammaglobulinemia due to defect in μ heavy chain caused by a novel mutation in the IGHM gene.

Agammaglobulinemia is a primary immunodeficiency disorder characterized by profoundly low or absent serum antibodies and low or absent circulating B c...
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