- Email: [email protected]
Chronic granulomatous disease caused by maternal uniparental isodisomy of chromosome 16
Clinical Communications Chronic granulomatous disease caused by maternal uniparental isodisomy of chromosome 16 María Bravo García-Morato, BSca,b, Julián Nevado, PhDc,d, Luis Ignacio González-Granado, MDe, Ana Sastre Urgelles, MDf, Rebeca Rodríguez Pena, MD, PhDa,b, and Antonio Ferreira Cerdán, MD, PhDa,b Clinical Implications
Uniparental isodisomies are usually de novo genetic defects that can lead to recessive conditions with a single parental carrier. We report the first patient diagnosed with chronic granulomatous disease due to a maternal isodisomy of chromosome 16.
TO THE EDITOR: Primary immunodeficiencies (PID) are a group of almost 300 genetic rare disorders characterized by the failure of one or more components of the immune system.1 Chronic granulomatous disease (CGD) is a PID caused by mutations in 5 of the genes that encode the subunits of the phagocytic nicotinamide adenine dinucleotide phosphate oxidase. Thus, mutations in the CYBA, NCF1, NCF2, and NCF4 genes lead to autosomal recessive CGD, whereas mutations in the CYBB gene cause an X-linked form of the disease.2 Patients with CGD suffer from bacterial and fungal infections that affect mainly lungs, gastrointestinal tract, and skin. In most cases, symptoms appear early in childhood and can be life threatening. Hematopoietic stem cell transplantation is, to date, the only curative therapy for the disease. For all these reasons, identifying mutation carriers in an affected kindred is necessary for an adequate genetic counseling. The majority of PID are monogenic diseases caused by point changes. Although deletions affecting several genes and partial gene deletions have also been described, they are very infrequent. Other chromosomal rearrangements such as uniparental disomy (UPD) have been anecdotally reported.3-5 UPD refers to a condition in which both copies of a chromosome or a chromosomal region are inherited from the same parent.6 Its incidence is estimated in 1:3500 live births. There are 2 types of UPD: uniparental heterodisomy (UPHD) and uniparental isodisomy (UPID).7 UPHD consists in the inheritance of 2 homologous chromosomes from the same parent. It is due to an error of disjunction in Meiosis I (Figure 1). After Meiosis II, the affected gamete has 2 chromatids that belong to both homologous chromosomes. When fecundation occurs, the resultant zygote has a trisomy of one chromosome. A mechanism known as trisomy rescue, by which the chromosome belonging to the other progenitor is eliminated, occurs, which transforms trisomy into UPHD. UPHD can be pathogenic if it involves an imprinted chromosome.8
UPID consists in the inheritance of 2 sister chromatids from the same parent. In most cases, it is due to an error of disjunction in Meiosis II (Figure 1). The affected gamete has 2 almost identical chromatids (excepting regions where recombination has happened). When fecundation occurs, the resultant zygote has a trisomy of one of its chromosomes, which can turn into UPID after trisomy rescue. Other mechanism that can lead to UPID is the one known as monosomy rescue. It occurs when a zygote with monosomy for a chromosome duplicates it to compensate the defect. UPID can be pathogenic, apart from imprinting errors, because of homozygosity for a recessive allele with a single carrier parent.8 In the majority of cases UPD should be considered as a de novo mutation, so the recurrence risk on siblings of the proband is minor. In cases in which a chromosomal translocation is found in one of the parents, recurrence risk assessment is more difficult but always much lower than those characteristic of Mendelian inheritance.7 To our knowledge, only 2 patients diagnosed with a PID due to a UPID have been reported, neither of them with CGD.4,5 Here we describe the third patient, who has a maternal isodisomy involving the CYBA gene (MIM: 608508), located on chromosome 16, as the genetic cause of the disease. Our patient is a 9-month-old boy born to healthy unrelated parents. At the age of 3 months, he had a bronchiolitis that required hospital admission. At 4 months of age, he developed laterocervical lymphadenopathy. At the age of 9 months, he was admitted to ICU with fever of 3 months of duration, hepatosplenomegaly, and spleen abscesses. Candida parapsilosis was isolated in urine. Attending to his symptoms a dihydrorhodamine flow cytometry test and a ferricytochrome c reduction
Recombination
Meiosis I
Meiosis II
Non-disjunction in Meiosis I
Meiosis II
Uniparental heterodisomy
Meiosis I
Non-disjunction in Meiosis II
Uniparental isodisomy
FIGURE 1. Schematic view of errors during meiosis that lead to uniparental hetero- and isodisomy. 1
2
CLINICAL COMMUNICATIONS
J ALLERGY CLIN IMMUNOL PRACT MONTH 2017
FIGURE 2. SNP array; image of the patient’s chromosome 16. The formula [arr[hg19] 3q26.31 (173,239,453-173,289,281)x3; 6q21 (173,239,453-173,289,281)x1; 8q24.12 (120,829,331-120,960,461)x3; 9p21.3 (25,035,251-25,336,447)x1; 16q23.2 (79,616,381-79,638,121)x1; 16p13.3 (139,367-11,617,658)x2 LOH; 16q21-q24.3 (63,770,084-90,274,695)x2 LOH] was found. SNP, Single nucleotide polymorphism.
assay were performed. In both, results showed that superoxide anion production was completely absent. Sanger sequencing of the disease-related genes (see above) was performed. A homozygous mutation c.354 C>A, p.Ser118Arg (NM_000101) in the CYBA gene was found. Parents’ analysis showed that his mother was a carrier of the mutation and his father was wild type. After confirming the paternity, a single nucleotide polymorphism (SNP) array was made to detect either a deletion or an UPID, which could explain the non-Mendelian inheritance pattern observed. Genomic DNA (200 ng) from peripheral blood was used to conduct a genome-wide scan of 850,000 tag SNP array (CytoSNP-850k Bead Chip) following the manufacturer’s specifications (Illumina, San Diego, Calif). Genomic positions were based on NCBI Build 37 (dbSNP version 130). Interestingly, the SNP array showed a few copy number variants and a significant loss of heterozygosity affecting the end of both arms of chromosome 16 (Figure 2) with a normal genic dosage, indicating that the homozygosity was due to maternal UPID. The CYBA gene at 16q24.3 band was located within the affected region of chromosome 16 (Figure 2). As the homozygosity does not affect the whole chromosome, this result is compatible with an error of disjunction in Meiosis II after recombination of both homologous chromosomes. In summary, we first described a patient with CGD whose disease is mediated by an UPID. Although karyotype of the patient’s peripheral blood cannot be made because of hematopoietic stem cell transplantation, the recurrence risk for siblings is much lower than it would be if the disease had been inherited in an autosomal recessive manner, as it usually happens for this pathology. Thus, genetic counseling for the patient’s parents implies a better prognosis after the putative mechanism of the disease is described. Detecting the UPD has also prompted us to refer the patient for medical assessment by clinical geneticists that can evaluate other possible anomalies mediated by his genomic
rearrangement and follow him up in the future. This work also focuses on technical principles of the SNP array technology and their utilization to detect submicroscopic genomic rearrangements and regions of homozigosity associated with disease. It is predictable that SNP arrays will also take up a position in routine diagnostic processes in the future.
Acknowledgment We thank the patient and his family. Grant from Fondo de Investigación Sanitaria (FIS-PI16/2053) to L. I. GonzálezGranado. a
Department of Immunology, La Paz University Hospital, Madrid, Spain Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, IdiPAZ, Madrid, Spain c Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, IdiPAZ, Madrid, Spain d CIBERER, Centre for Biomedical Investigation on Rare Diseases, Madrid, Spain e Immunodeficiencies Unit, Department of Pediatrics, 12 Octubre Institute of Biomedical Research (iþ12), Madrid, Spain f Department of Pediatric Hematology/Oncology, La Paz University Hospital, Madrid, Spain No funding was received for this work. Conflicts of interest: The authors declare that they have no relevant conflicts of interest. Received for publication December 9, 2016; revised January 10, 2017; accepted for publication January 20, 2017. Available online -Corresponding author: María Bravo García-Morato, BSc, Hospital Universitario La Paz, Immunology Department, Paseo de la Castellana, 261, 28046 Madrid, Spain. E-mail: [email protected]. 2213-2198 Ó 2017 American Academy of Allergy, Asthma & Immunology http://dx.doi.org/10.1016/j.jaip.2017.01.018 b
REFERENCES 1. Picard C, Al-Herz W, Bousfiha A, Casanova JL, Chatila T, Conley ME, et al. Primary immunodeficiency diseases: an update on the classification from the
J ALLERGY CLIN IMMUNOL PRACT VOLUME -, NUMBER -
International Union of Immunological Societies Expert Committee for Primary Immunodeficiency 2015. J Clin Immunol 2015;35:696-726. 2. Roos D. Chronic granulomatous disease. Br Med Bull 2016;118:50-63. 3. Sawada A, Takihara Y, Kim JY, Matsuda-Hashii Y, Tokimasa S, Fujisaki H, et al. A congenital mutation of the novel gene LRRC8 causes agammaglobulinemia in humans. J Clin Invest 2003;112:1707-13. 4. Prando C, Boisson-Dupuis S, Grant AV, Kong XF, Bustamante J, Feinberg J, et al. Paternal uniparental isodisomy of chromosome 6 causing a complex syndrome including complete IFN-g receptor 1 deficiency. Am J Med Genet A 2010;152A:622-9.
CLINICAL COMMUNICATIONS
3
5. Al-Jasmi F, Abdelhaleem M, Stockley T, Lee KS, Clarke JT. Novel mutation of the perforin gene and maternal uniparental disomy 10 in a patient with familial hemophagocytic lymphohistiocytosis. J Pediatr Hematol Oncol 2008;30:621-4. 6. Engel E. A new genetic concept: uniparental disomy and its potential effect, isodisomy. Am J Med Genet 1980;6:137-43. 7. Kearney HM, Kearney JB, Conlin LK. Diagnostic implications of excessive homozygosity detected by SNP-based microarrays: consanguinity, uniparental disomy, and recessive single-gene mutations. Clin Lab Med 2011;31:595-613. 8. Yamazawa K, Ogata T, Ferguson-Smith AC. Uniparental disomy and human disease: an overview. Am J Med Genet C Semin Med Genet 2010;154C:329-34.
Uniparental isodisomies are usually de novo genetic defects that can lead to recessive conditions with a single parental carrier. We report the first patient diagnosed with chronic granulomatous disease due to a maternal isodisomy of chromosome 16.
TO THE EDITOR: Primary immunodeficiencies (PID) are a group of almost 300 genetic rare disorders characterized by the failure of one or more components of the immune system.1 Chronic granulomatous disease (CGD) is a PID caused by mutations in 5 of the genes that encode the subunits of the phagocytic nicotinamide adenine dinucleotide phosphate oxidase. Thus, mutations in the CYBA, NCF1, NCF2, and NCF4 genes lead to autosomal recessive CGD, whereas mutations in the CYBB gene cause an X-linked form of the disease.2 Patients with CGD suffer from bacterial and fungal infections that affect mainly lungs, gastrointestinal tract, and skin. In most cases, symptoms appear early in childhood and can be life threatening. Hematopoietic stem cell transplantation is, to date, the only curative therapy for the disease. For all these reasons, identifying mutation carriers in an affected kindred is necessary for an adequate genetic counseling. The majority of PID are monogenic diseases caused by point changes. Although deletions affecting several genes and partial gene deletions have also been described, they are very infrequent. Other chromosomal rearrangements such as uniparental disomy (UPD) have been anecdotally reported.3-5 UPD refers to a condition in which both copies of a chromosome or a chromosomal region are inherited from the same parent.6 Its incidence is estimated in 1:3500 live births. There are 2 types of UPD: uniparental heterodisomy (UPHD) and uniparental isodisomy (UPID).7 UPHD consists in the inheritance of 2 homologous chromosomes from the same parent. It is due to an error of disjunction in Meiosis I (Figure 1). After Meiosis II, the affected gamete has 2 chromatids that belong to both homologous chromosomes. When fecundation occurs, the resultant zygote has a trisomy of one chromosome. A mechanism known as trisomy rescue, by which the chromosome belonging to the other progenitor is eliminated, occurs, which transforms trisomy into UPHD. UPHD can be pathogenic if it involves an imprinted chromosome.8
UPID consists in the inheritance of 2 sister chromatids from the same parent. In most cases, it is due to an error of disjunction in Meiosis II (Figure 1). The affected gamete has 2 almost identical chromatids (excepting regions where recombination has happened). When fecundation occurs, the resultant zygote has a trisomy of one of its chromosomes, which can turn into UPID after trisomy rescue. Other mechanism that can lead to UPID is the one known as monosomy rescue. It occurs when a zygote with monosomy for a chromosome duplicates it to compensate the defect. UPID can be pathogenic, apart from imprinting errors, because of homozygosity for a recessive allele with a single carrier parent.8 In the majority of cases UPD should be considered as a de novo mutation, so the recurrence risk on siblings of the proband is minor. In cases in which a chromosomal translocation is found in one of the parents, recurrence risk assessment is more difficult but always much lower than those characteristic of Mendelian inheritance.7 To our knowledge, only 2 patients diagnosed with a PID due to a UPID have been reported, neither of them with CGD.4,5 Here we describe the third patient, who has a maternal isodisomy involving the CYBA gene (MIM: 608508), located on chromosome 16, as the genetic cause of the disease. Our patient is a 9-month-old boy born to healthy unrelated parents. At the age of 3 months, he had a bronchiolitis that required hospital admission. At 4 months of age, he developed laterocervical lymphadenopathy. At the age of 9 months, he was admitted to ICU with fever of 3 months of duration, hepatosplenomegaly, and spleen abscesses. Candida parapsilosis was isolated in urine. Attending to his symptoms a dihydrorhodamine flow cytometry test and a ferricytochrome c reduction
Recombination
Meiosis I
Meiosis II
Non-disjunction in Meiosis I
Meiosis II
Uniparental heterodisomy
Meiosis I
Non-disjunction in Meiosis II
Uniparental isodisomy
FIGURE 1. Schematic view of errors during meiosis that lead to uniparental hetero- and isodisomy. 1
2
CLINICAL COMMUNICATIONS
J ALLERGY CLIN IMMUNOL PRACT MONTH 2017
FIGURE 2. SNP array; image of the patient’s chromosome 16. The formula [arr[hg19] 3q26.31 (173,239,453-173,289,281)x3; 6q21 (173,239,453-173,289,281)x1; 8q24.12 (120,829,331-120,960,461)x3; 9p21.3 (25,035,251-25,336,447)x1; 16q23.2 (79,616,381-79,638,121)x1; 16p13.3 (139,367-11,617,658)x2 LOH; 16q21-q24.3 (63,770,084-90,274,695)x2 LOH] was found. SNP, Single nucleotide polymorphism.
assay were performed. In both, results showed that superoxide anion production was completely absent. Sanger sequencing of the disease-related genes (see above) was performed. A homozygous mutation c.354 C>A, p.Ser118Arg (NM_000101) in the CYBA gene was found. Parents’ analysis showed that his mother was a carrier of the mutation and his father was wild type. After confirming the paternity, a single nucleotide polymorphism (SNP) array was made to detect either a deletion or an UPID, which could explain the non-Mendelian inheritance pattern observed. Genomic DNA (200 ng) from peripheral blood was used to conduct a genome-wide scan of 850,000 tag SNP array (CytoSNP-850k Bead Chip) following the manufacturer’s specifications (Illumina, San Diego, Calif). Genomic positions were based on NCBI Build 37 (dbSNP version 130). Interestingly, the SNP array showed a few copy number variants and a significant loss of heterozygosity affecting the end of both arms of chromosome 16 (Figure 2) with a normal genic dosage, indicating that the homozygosity was due to maternal UPID. The CYBA gene at 16q24.3 band was located within the affected region of chromosome 16 (Figure 2). As the homozygosity does not affect the whole chromosome, this result is compatible with an error of disjunction in Meiosis II after recombination of both homologous chromosomes. In summary, we first described a patient with CGD whose disease is mediated by an UPID. Although karyotype of the patient’s peripheral blood cannot be made because of hematopoietic stem cell transplantation, the recurrence risk for siblings is much lower than it would be if the disease had been inherited in an autosomal recessive manner, as it usually happens for this pathology. Thus, genetic counseling for the patient’s parents implies a better prognosis after the putative mechanism of the disease is described. Detecting the UPD has also prompted us to refer the patient for medical assessment by clinical geneticists that can evaluate other possible anomalies mediated by his genomic
rearrangement and follow him up in the future. This work also focuses on technical principles of the SNP array technology and their utilization to detect submicroscopic genomic rearrangements and regions of homozigosity associated with disease. It is predictable that SNP arrays will also take up a position in routine diagnostic processes in the future.
Acknowledgment We thank the patient and his family. Grant from Fondo de Investigación Sanitaria (FIS-PI16/2053) to L. I. GonzálezGranado. a
Department of Immunology, La Paz University Hospital, Madrid, Spain Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, IdiPAZ, Madrid, Spain c Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, IdiPAZ, Madrid, Spain d CIBERER, Centre for Biomedical Investigation on Rare Diseases, Madrid, Spain e Immunodeficiencies Unit, Department of Pediatrics, 12 Octubre Institute of Biomedical Research (iþ12), Madrid, Spain f Department of Pediatric Hematology/Oncology, La Paz University Hospital, Madrid, Spain No funding was received for this work. Conflicts of interest: The authors declare that they have no relevant conflicts of interest. Received for publication December 9, 2016; revised January 10, 2017; accepted for publication January 20, 2017. Available online -Corresponding author: María Bravo García-Morato, BSc, Hospital Universitario La Paz, Immunology Department, Paseo de la Castellana, 261, 28046 Madrid, Spain. E-mail: [email protected]. 2213-2198 Ó 2017 American Academy of Allergy, Asthma & Immunology http://dx.doi.org/10.1016/j.jaip.2017.01.018 b
REFERENCES 1. Picard C, Al-Herz W, Bousfiha A, Casanova JL, Chatila T, Conley ME, et al. Primary immunodeficiency diseases: an update on the classification from the
J ALLERGY CLIN IMMUNOL PRACT VOLUME -, NUMBER -
International Union of Immunological Societies Expert Committee for Primary Immunodeficiency 2015. J Clin Immunol 2015;35:696-726. 2. Roos D. Chronic granulomatous disease. Br Med Bull 2016;118:50-63. 3. Sawada A, Takihara Y, Kim JY, Matsuda-Hashii Y, Tokimasa S, Fujisaki H, et al. A congenital mutation of the novel gene LRRC8 causes agammaglobulinemia in humans. J Clin Invest 2003;112:1707-13. 4. Prando C, Boisson-Dupuis S, Grant AV, Kong XF, Bustamante J, Feinberg J, et al. Paternal uniparental isodisomy of chromosome 6 causing a complex syndrome including complete IFN-g receptor 1 deficiency. Am J Med Genet A 2010;152A:622-9.
CLINICAL COMMUNICATIONS
3
5. Al-Jasmi F, Abdelhaleem M, Stockley T, Lee KS, Clarke JT. Novel mutation of the perforin gene and maternal uniparental disomy 10 in a patient with familial hemophagocytic lymphohistiocytosis. J Pediatr Hematol Oncol 2008;30:621-4. 6. Engel E. A new genetic concept: uniparental disomy and its potential effect, isodisomy. Am J Med Genet 1980;6:137-43. 7. Kearney HM, Kearney JB, Conlin LK. Diagnostic implications of excessive homozygosity detected by SNP-based microarrays: consanguinity, uniparental disomy, and recessive single-gene mutations. Clin Lab Med 2011;31:595-613. 8. Yamazawa K, Ogata T, Ferguson-Smith AC. Uniparental disomy and human disease: an overview. Am J Med Genet C Semin Med Genet 2010;154C:329-34.