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De Novo Somatic Mosaicism of CYBB Caused by Intronic LINE-1 Element Insertion Resulting in Chronic Granulomatous Disease

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Abstract

Chronic granulomatosis disease (CGD) is a rare inborn error of immunity, characterized by phagocytic respiratory outbreak dysfunction. Mutations causing CGD occur in CYBB on the X chromosome and in the autosomal genes CYBA, NCF1, NCF2, NCF4, RAC2, and CYBC1. Nevertheless, some patients are clinically diagnosed with CGD, due to abnormal respiratory outbursts, while the pathogenic gene mutation is unidentified. Here, we report a patient with CGD who first presented with Bacillus Calmette-Guérin disease and had recurrent pneumonia. He was diagnosed with CGD by nitro blue tetrazolium and respiratory burst tests. Detailed assessment of neutrophil activity revealed that patient neutrophils were almost entirely nonfunctional. Sanger sequencing detected a 6-kb insertion of a LINE-1 transposable element in the third intron of CYBB, leading to abnormal splicing and pseudoexon insertion, as well as introduction of a premature termination codon, resulting in predicted protein truncation. Clonal analysis demonstrated that the patient had somatic mosaicism, and the phagocytes were almost all variant CYBB, while the mosaicism rate of PBMC was about 65%. Finally, deep RNA sequencing and gp91phox expression analysis confirmed the pathogenicity of the mutation. In conclusion, we demonstrate that insertion of a LINE-1 transposon in a CYBB intron was responsible for CGD in our patient. Intron LINE-1 transposon element insertion should be examined in CGD patients without any known disease-causing gene mutation, in addition to identification of new genes.

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Data Availability

The dataset described in this study is available from the corresponding authors upon reasonable request.

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Acknowledgements

We thank the patient and his family for participating in this study.

Funding

This work was supported by the Graduate Mentor Team of Chongqing Municipal Education Commission (Grant number 2019–09-66), the National Natural Science Foundation of China (Grant number 82070135), and the CQMU Program for Youth Innovation in Future Medicine (W0100).

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Authors and Affiliations

  1. National Clinical Research Center for Child Health and Disorders (Chongqing), Children’s Hospital of Chongqing Medical University, Chongqing, China

    Lang Yu, Wenhui Li, Ge Lv, Gan Sun, Lu Yang, Junjie Chen, Lina Zhou, Yuan Ding, Zhiyong Zhang, Xuemei Tang, Yunfei An & Xiaodong Zhao

  2. Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, Chongqing, China

    Lang Yu, Wenhui Li, Ge Lv, Gan Sun, Lu Yang, Junjie Chen, Lina Zhou, Yuan Ding, Zhiyong Zhang, Xuemei Tang, Yunfei An & Xiaodong Zhao

  3. Chongqing Key Laboratory of Child Infection and Immunity, Children’s Hospital of Chongqing Medical University, Chongqing, China

    Lang Yu, Wenhui Li, Ge Lv, Gan Sun, Lu Yang, Junjie Chen, Lina Zhou, Yuan Ding, Zhiyong Zhang, Xuemei Tang, Yunfei An & Xiaodong Zhao

  4. Department of Rheumatology & Immunology, Children’s Hospital of Chongqing Medical University, Chongqing, China

    Zhiyong Zhang, Xuemei Tang & Yunfei An

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  1. Lang Yu
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  3. Ge Lv
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Contributions

XD.Z and YF.A designed this study, and reviewed and revised the manuscript. L.Yu collected clinical data, followed the patient, performed experiments, and drafted the manuscript. WH.L., G.L., G.S., L.Yang, JJ.C., and LN.Z. performed some experiments. Y.D., ZY.Z., and XM.T. provided essential help for clinical management and follow-up of the patient. All authors contributed to the final version of the manuscript and approved submission of the final version.

Corresponding authors

Correspondence to Yunfei An or Xiaodong Zhao.

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Ethics Approval

The study was performed following the Declaration of Helsinki and approved by the ethics committee of Children’s Hospital of Chongqing Medical University (Chongqing, China). Written informed consent for participation in this study was obtained from patient’s parents.

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Written informed consent was obtained from patient’s parents.

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Written informed consent for publication of the study was obtained from patient’s parents. All the authors approved the final version of the manuscript.

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The authors declare no competing interests.

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Yu, L., Li, W., Lv, G. et al. De Novo Somatic Mosaicism of CYBB Caused by Intronic LINE-1 Element Insertion Resulting in Chronic Granulomatous Disease. J Clin Immunol 43, 88–100 (2023). https://doi.org/10.1007/s10875-022-01347-w

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