Orientation Regulation of Class-switch Recombination in Human B Cells

• Published in: The Journal of immunology (1950) Vol. 213; no. 8; pp. 1093 - 1104
• Main Authors: Du, Likun, Oksenych, Valentyn, Wan, Hui, Ye, Xiaofei, Dong, Junchao, Ye, Adam Yongxin, Abolhassani, Hassan, Vlachiotis, Stelios, Zhang, Xuefei, de la Rosa, Kathrin, Hammarström, Lennart, van der Burg, Mirjam, Alt, Frederick W, Pan-Hammarström, Qiang
• Format: Journal Article
• Language: English
• Published: United States AAI 15.10.2024
• Subjects: B-Lymphocytes - immunology; Clinical and Human Immunology; DNA End-Joining Repair - genetics; DNA End-Joining Repair - immunology; High-Throughput Nucleotide Sequencing; Humans; Immunoglobulin Class Switching - genetics; Immunoglobulin Class Switching - immunology; Medicin och hälsovetenskap; Recombination, Genetic - immunology
• ISSN: 0022-1767; 1550-6606; 1550-6606
• DOI: 10.4049/jimmunol.2300842

We developed a linear amplification-mediated high-throughput genome-wide translocation sequencing method to profile Ig class-switch recombination (CSR) in human B cells in an unbiased and quantitative manner. This enables us to characterize CSR junctions resulting from either deletional recombination or inversion for each Ig class/subclass. Our data showed that more than 90% of CSR junctions detected in peripheral blood in healthy control subjects were due to deletional recombination. We further identified two major CSR junction signatures/patterns in human B cells. Signature 1 consists of recombination junctions resulting from both IgG and IgA switching, with a dominance of Sµ-Sγ junctions (72%) and deletional recombination (87%). Signature 2 is contributed mainly by Sµ-Sα junctions (96%), and these junctions were almost all due to deletional recombination (99%) and were characterized by longer microhomologies. CSR junctions identified in healthy individuals can be assigned to both signatures but with a dominance of signature 1, whereas almost all CSR junctions found in patients with defects in DNA-PKcs or Artemis, two classical nonhomologous end joining (c-NHEJ) factors, align with signature 2. Thus, signature 1 may represent c-NHEJ activity during CSR, whereas signature 2 is associated with microhomology-mediated alternative end joining in the absence of the studied c-NHEJ factors. Our findings suggest that in human B cells, the efficiency of the c-NHEJ machinery and the features of switch regions are crucial for the regulation of CSR orientation. Finally, our high-throughput method can also be applied to study the mechanism of rare types of recombination, such as switching to IgD and locus suicide switching.