Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia
Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia
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DOI：
10.1073/pnas.1503587112
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发表时间：
2015-04-07
影响因子：
11.1
通讯作者：
Byrd, John C.
中科院分区：
文献类型：
--
作者：
Blachly, James S.;Ruppert, Amy S.;Byrd, John C.
免疫球蛋白（Ig）是由B淋巴细胞作为分泌抗体或作为B细胞受体的一部分产生的。由于数以百计的种系基因片段、基因片段连接成完整转录物过程中的随机核苷酸整合以及单个核苷酸的体细胞超突变过程，潜在的Ig转录物具有巨大的多样性（bbb1x10(12)）。这种重组和突变过程发生在成熟的B细胞中，并负责潜在表位识别的多样性。成熟B细胞产生的癌症以克隆产生Ig重链（ight @）和轻链转录本为特征，尽管该序列是否经历了体细胞超突变取决于肿瘤克隆产生的成熟阶段。慢性淋巴细胞白血病（CLL）是成人中最常见的白血病，起源于成熟B细胞，具有突变或未突变的ight @转录物，后者预后较差，临床常规进行评估。目前，通过Sanger测序并将转录本与已知种系基因进行比较来评估IGHV突变状态。在本文中，我们证明了完整的ight @ V-D-J序列可以从未选择的RNA-seq读取中计算出来，结果等于或优于临床程序：在唯一不一致的情况下，临床转录本是框外的。因此，单个RNA-seq分析可以同时获得基因表达谱、SNP和突变信息，以及IGHV突变状态，有朝一日可能作为一种常规测试来获取CLL的多维临床相关数据。
Immunoglobulins (Ig) are produced by B lymphocytes as secreted antibodies or as part of the B-cell receptor. There is tremendous diversity of potential Ig transcripts (>1 x 10(12)) as a result of hundreds of germ-line gene segments, random nucleotide incorporation during joining of gene segments into a complete transcript, and the process of somatic hypermutation at individual nucleotides. This recombination and mutation process takes place in the maturing B cell and is responsible for the diversity of potential epitope recognition. Cancers arising from mature B cells are characterized by clonal production of Ig heavy (IGH@) and light chain transcripts, although whether the sequence has undergone somatic hypermutation is dependent on the maturation stage at which the neoplastic clone arose. Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults and arises from a mature B cell with either mutated or unmutated IGH@ transcripts, the latter having worse prognosis and the assessment of which is routinely performed in the clinic. Currently, IGHV mutation status is assessed by Sanger sequencing and comparing the transcript to known germ-line genes. In this paper, we demonstrate that complete IGH@ V-D-J sequences can be computed from unselected RNA-seq reads with results equal or superior to the clinical procedure: in the only discordant case, the clinical transcript was out-of-frame. Therefore, a single RNA-seq assay can simultaneously yield gene expression profile, SNP and mutation information, as well as IGHV mutation status, and may one day be performed as a general test to capture multidimensional clinically relevant data in CLL.