Abstract
Background
Chronic granulomatous disease (CGD) is characterized by mutation in any one of the five genes coding NADPH oxidase components that leads to functional abnormality preventing the killing of phagocytosed microbes by affecting the progression of a respiratory burst. CGD patients have an increased susceptibility to infections by opportunistic and pathogenic organisms. Though initial diagnosis of CGD using a nitroblue tetrazolium (NBT) test or dihydrorhodamine (DHR) test is relatively easy, molecular diagnosis is challenging due to involvement of multiple genes, presence of pseudogenes, large deletions, and GC-rich regions, among other factors. The strategies for molecular diagnosis vary depending on the affected gene and the mutation pattern prevalent in the target population. There is a paucity of molecular data related to CGD for Indian population.
Method
This report includes data for a large cohort of CGD patients (n = 90) from India, describing the diagnostic approach, mutation spectrum, and novel mutations identified. We have used mosaicism in mothers and the expression pattern of different NADPH components by flow cytometry as a screening tool to identify the underlying affected gene. The techniques like Sanger sequencing, next-generation sequencing (NGS), and Genescan analysis were used for further molecular analysis.
Result
Of the total molecularly characterized patients (n = 90), 56% of the patients had a mutation in the NCF1 gene, 30% had mutation in the CYBB gene, and 7% each had mutation in the CYBA and NCF2 genes. Among the patients with NCF1 gene mutation, 82% of the patients had 2-bp deletion (DelGT) mutations in the NCF1 gene. In our cohort, 41 different mutations including 9 novel mutations in the CYBB gene and 2 novel mutations each in the NCF2, CYBA, and NCF1 genes were identified.
Conclusion
Substantial number of the patients lack NCF1 gene on both the alleles. This is often missed by advanced molecular techniques like Sanger sequencing and NGS due to the presence of pseudogenes and requires a simple Genescan method for confirmation. Thus, the diagnostic approach may depend on the prevalence of affected genes in respective population. This study identifies potential gene targets with the help of flow cytometric analysis of NADPH oxidase components to design an algorithm for diagnosis of CGD in India. In Indian population, the Genescan method should be preferred as the primary molecular test to rule out NCF1 gene mutations prior to Sanger sequencing and NGS.
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References
Wolach B, Gavrieli R, de Boer M, van Leeuwen K, Berger-Achituv S, Stauber T, et al. Chronic granulomatous disease: clinical, functional, molecular, and genetic studies. The Israeli experience with 84 patients: research article. Am J Hematol. 2017;92(1):28–36.
Diebold BA, Bokoch GM. Molecular basis for Rac2 regulation of phagocyte NADPH oxidase. Nat Immunol. 2001;2(3):211–5.
Ambruso DR, Knall C, Abell AN, Panepinto J, Kurkchubasche A, Thurman G, et al. Human neutrophil immunodeficiency syndrome is associated with an inhibitory Rac2 mutation. Proc Natl Acad Sci. 2000;97(9):4654–9.
Zhou Q, Hui X, Ying W, Hou J, Wang W, Liu D, et al. A cohort of 169 chronic granulomatous disease patients exposed to BCG vaccination: a retrospective study from a single center in Shanghai, China (2004–2017). J Clin Immunol. 2018;38(3):260–72.
Ishibashi F, Nunoi H, Endo F, Matsuda I, Kanegasaki S. Statistical and mutational analysis of chronic granulomatous disease in Japan with special reference to gp91-phox and p22-phox deficiency. Hum Genet. 2000;106(5):473–81.
Winkelstein JA, Marino MC, Johnston RB, Boyle J, Curnutte J, Gallin JI, et al. Chronic granulomatous disease. Report on a national registry of 368 patients. Medicine (Baltimore). 2000;79(3):155–69.
Jones LBKR, McGrogan P, Flood TJ, Gennery AR, Morton L, Thrasher A, et al. Special article: chronic granulomatous disease in the United Kingdom and Ireland: a comprehensive national patient-based registry: CGD registry in the UK and Ireland. Clin Exp Immunol. 2008;152(2):211–8.
Köker MY, Camcıoğlu Y, van Leeuwen K, Kılıç SŞ, Barlan I, Yılmaz M, et al. Clinical, functional, and genetic characterization of chronic granulomatous disease in 89 Turkish patients. J Allergy Clin Immunol. 2013;132(5):1156–1163.e5.
Meshaal S, El Hawary R, Abd Elaziz D, Alkady R, Galal N, Boutros J, et al. Chronic granulomatous disease: review of a cohort of Egyptian patients. Allergol Immunopathol (Madr). 2015;43(3):279–85.
Al-Zadjali S, Al-Tamemi S, Elnour I, AlKindi S, Lapoumeroulie C, Al-Maamari S, et al. Clinical and molecular findings of chronic granulomatous disease in Oman: family studies. Clin Genet. 2015;87(2):185–9.
Fattahi F, Badalzadeh M, Sedighipour L, Movahedi M, Fazlollahi MR, Mansouri SD, et al. Inheritance pattern and clinical aspects of 93 Iranian patients with chronic granulomatous disease. J Clin Immunol. 2011;31(5):792–801.
Rawat A, Singh S, Suri D, Gupta A, Saikia B, Minz RW, et al. Chronic granulomatous disease: two decades of experience from a tertiary care centre in North West India. J Clin Immunol. 2014;34(1):58–67.
Jirapongsananuruk O, Malech HL, Kuhns DB, Niemela JE, Brown MR, Anderson-Cohen M, et al. Diagnostic paradigm for evaluation of male patients with chronic granulomatous disease, based on the dihydrorhodamine 123 assay. J Allergy Clin Immunol. 2003;111(2):374–9.
Freudenberg F, Wintergerst U, Roesen-Wolff A, Albert MH, Prell C, Strahm B, et al. Therapeutic strategy in p47-phox deficient chronic granulomatous disease presenting as inflammatory bowel disease. J Allergy Clin Immunol. 2010;125(4):943–946.e1.
Wada T, Muraoka M, Toma T, Imai T, Shigemura T, Agematsu K, et al. Rapid detection of intracellular p47phox and p67phox by flow cytometry; useful screening tests for chronic granulomatous disease. J Clin Immunol. 2013;33(4):857–64.
Kulkarni M, Desai M, Gupta M, Dalvi A, Taur P, Terrance A, et al. Clinical, immunological, and molecular findings of patients with p47phox defect chronic granulomatous disease (CGD) in Indian families. J Clin Immunol. 2016;36(8):774–84.
Matute JD, Arias AA, Wright NAM, Wrobel I, Waterhouse CCM, Li XJ, et al. A new genetic subgroup of chronic granulomatous disease with autosomal recessive mutations in p40phox and selective defects in neutrophil NADPH oxidase activity. Blood. 2009;114(15):3309–15.
Roos D, de Boer M, Köker MY, Dekker J, Singh-Gupta V, Ahlin A, et al. Chronic granulomatous disease caused by mutations other than the common GT deletion in NCF1, the gene encoding the p47phox component of the phagocyte NADPH oxidase. Hum Mutat. 2006;27(12):1218–29.
Dekker J, de Boer M, Roos D. Gene-scan method for the recognition of carriers and patients with p47(phox)-deficient autosomal recessive chronic granulomatous disease. Exp Hematol. 2001;29(11):1319–25.
Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31(13):3812–4.
Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013;Chapter 7:Unit7.20.
Schwarz JM, Rödelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7(8):575–6.
Desmet F-O, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human splicing finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009;37(9):e67.
Rawat A, Vignesh P, Sharma A, Shandilya JK, Sharma M, Suri D, et al. Infection profile in chronic granulomatous disease: a 23-year experience from a tertiary care center in North India. J Clin Immunol. 2017;37(3):319–28.
Teimourian S, de Boer M, Roos D. Molecular basis of autosomal recessive chronic granulomatous disease in Iran. J Clin Immunol. 2010;30(4):587–92.
Vowells SJ, Fleisher TA, Sekhsaria S, Alling DW, Maguire TE, Malech HL. Genotype-dependent variability in flow cytometric evaluation of reduced nicotinamide adenine dinucleotide phosphate oxidase function in patients with chronic granulomatous disease. J Pediatr. 1996;128(1):104–7.
Kuhns DB, Alvord WG, Heller T, Feld JJ, Pike KM, Marciano BE, et al. Residual NADPH oxidase and survival in chronic granulomatous disease. N Engl J Med. 2010;363(27):2600–10.
van den Berg JM, van Koppen E, Åhlin A, Belohradsky BH, Bernatowska E, Corbeel L, et al. Chronic granulomatous disease: the European experience. PLoS One. 2009;4(4):e5234.
Roesler J. Remarks on the article genetics and immunopathology of chronic granulomatous disease by Marie José Stasia and Xing Jun Li. Semin Immunopathol. 2008;30(3):365 author reply 368.
Köker MY, Leeuwen KV, Boer MD, Çelmeli F, Metin A, Özgür TT, et al. Six different CYBA mutations including three novel mutations in ten families from Turkey, resulting in autosomal recessive chronic granulomatous disease. Eur J Clin Investig. 2009;39(4):311–9.
Kawai C, Yamauchi A, Kuribayashi F. Monoclonal antibody 7D5 recognizes the R147 epitope on the gp91 phox , phagocyte flavocytochrome b 558 large subunit: macrophages, dendritic cells, and leukocytes. Microbiol Immunol. 2018;62(4):269–80.
Roos D, de Boer M. Molecular diagnosis of chronic granulomatous disease: molecular diagnosis of CGD. Clin Exp Immunol. 2014;175(2):139–49.
Mousallem T, Urban TJ, McSweeney KM, Kleinstein SE, Zhu M, Adeli M, et al. Clinical application of whole-genome sequencing in patients with primary immunodeficiency. J Allergy Clin Immunol. 2015;136(2):476–479.e6.
Roos D. Chronic granulomatous disease. Br Med Bull. 2016;118(1):50–63.
Richardson AM, Moyer AM, Hasadsri L, Abraham RS. Diagnostic tools for inborn errors of human immunity (primary Immunodeficiencies and immune dysregulatory diseases). Curr Allergy Asthma Rep. 2018 [cited 2018 Jun 4];18(3):19. https://doi.org/10.1007/s11882-018-0770-1.
Heyworth PG, Noack D, Cross AR. Identification of a novel NCF-1 (p47-phox) pseudogene not containing the signature GT deletion: significance for A47 degrees chronic granulomatous disease carrier detection. Blood. 2002;100(5):1845–51.
Roos D, Kuhns DB, Maddalena A, Bustamante J, Kannengiesser C, de Boer M, et al. Hematologically important mutations: the autosomal recessive forms of chronic granulomatous disease (second update). Blood Cells Mol Dis. 2010;44(4):291–9.
Roos D, Kuhns DB, Maddalena A, Roesler J, Lopez JA, Ariga T, et al. Hematologically important mutations: X-linked chronic granulomatous disease (third update). Blood Cells Mol Dis. 2010;45(3):246–65.
Funding
This work was funded by the Indian Council of Medical Research (ICMR). It is also supported by the Foundation of Primary Immunodeficiency (FPID). Manasi Kulkarni is the recipient of Senior Research Fellowship from ICMR (ICMR SRF F. no. 45/8/2014-HAE-BMS).
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MK performed the experiments, analyzed the data, and wrote the manuscript. GH, JA, MG, AD, and SM were involved in performing laboratory investigations of the different cases. MD supervised the clinical details of the patients. PT helped in the collecting of samples and the details of the patients. MB and KL provided the NGS data of the patients. MK and PK are involved in molecular analysis of patients. MM supervised the study and reviewed the manuscript.
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Pateint’s sample and additional samples (parents and siblings) were collected in the case of a strong family history after obtaining a proper informed consent. A clinical protocol has been followed per the guidelines of the Institutional Ethics Committee and Declaration of Helsinki.
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The authors declare that they have no conflict of interest.
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Kulkarni, M., Hule, G., de Boer, M. et al. Approach to Molecular Diagnosis of Chronic Granulomatous Disease (CGD): an Experience from a Large Cohort of 90 Indian Patients. J Clin Immunol 38, 898–916 (2018). https://doi.org/10.1007/s10875-018-0567-y
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DOI: https://doi.org/10.1007/s10875-018-0567-y