Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer.
Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer.
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DOI：
10.1186/s13059-020-02240-8
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发表时间：
2021-01-04
期刊：
影响因子：
12.3
通讯作者：
Seki M
中科院分区：
文献类型：
--
作者：
Oka M;Xu L;Suzuki T;Yoshikawa T;Sakamoto H;Uemura H;Yoshizawa AC;Suzuki Y;Nakatsura T;Ishihama Y;Suzuki A;Seki M
全长cDNA的长读段测序使得能够检测癌细胞中异常剪接同种型的结构。这些同种型偶尔被翻译，由HLA分子呈递，并被识别为新抗原。本研究使用长读测序仪（MinION）构建了非小细胞肺癌异常剪接异构体的综合目录，通过该目录鉴定了新的异构体和潜在的新抗原。使用22个细胞系进行全长cDNA测序，共鉴定出2021种新型剪接异构体。然后通过蛋白质组分析验证这些同种型中的一些的蛋白质表达。无义介导的mRNA衰变（NMD）因子UPF 1和剪接因子SF 3B 1的消融被发现会增加异常转录本的比例。对每种类型HLA分子的结合亲和力的NetMHC评估揭示了一些同种型潜在地产生新抗原候选物。我们还确定了异常剪接异构体在7个非小细胞肺癌标本。酶联免疫吸附斑点试验表明，大约一半的候选肽具有通过与HLA分子相互作用激活T细胞应答的潜力。最后，我们通过参考构建的目录来估计癌症基因组图谱（TCGA）数据集中的异构体数量，并发现NMD因子的破坏与TCGA-肺腺癌数据收集中发现的剪接异构体数量显著相关。我们的研究结果表明，全长cDNA的长读段测序对于精确鉴定癌细胞中的异常转录结构是必不可少的。在线版本包含补充材料，可通过10.1186/s13059-020-02240-8获得。
Long-read sequencing of full-length cDNAs enables the detection of structures of aberrant splicing isoforms in cancer cells. These isoforms are occasionally translated, presented by HLA molecules, and recognized as neoantigens. This study used a long-read sequencer (MinION) to construct a comprehensive catalog of aberrant splicing isoforms in non-small-cell lung cancers, by which novel isoforms and potential neoantigens are identified. Full-length cDNA sequencing is performed using 22 cell lines, and a total of 2021 novel splicing isoforms are identified. The protein expression of some of these isoforms is then validated by proteome analysis. Ablations of a nonsense-mediated mRNA decay (NMD) factor, UPF1, and a splicing factor, SF3B1, are found to increase the proportion of aberrant transcripts. NetMHC evaluation of the binding affinities to each type of HLA molecule reveals that some of the isoforms potentially generate neoantigen candidates. We also identify aberrant splicing isoforms in seven non-small-cell lung cancer specimens. An enzyme-linked immune absorbent spot assay indicates that approximately half the peptide candidates have the potential to activate T cell responses through their interaction with HLA molecules. Finally, we estimate the number of isoforms in The Cancer Genome Atlas (TCGA) datasets by referring to the constructed catalog and found that disruption of NMD factors is significantly correlated with the number of splicing isoforms found in the TCGA-Lung Adenocarcinoma data collection. Our results indicate that long-read sequencing of full-length cDNAs is essential for the precise identification of aberrant transcript structures in cancer cells. The online version contains supplementary material available at 10.1186/s13059-020-02240-8.
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DOI：
10.4049/jimmunol.1700893
发表时间：
2017-11-01
期刊：
Journal of immunology (Baltimore, Md. : 1950)
影响因子：
--
作者：
Jurtz V;Paul S;Andreatta M;Marcatili P;Peters B;Nielsen M
通讯作者：
Nielsen M
实现癌症基因组数据的共同愿景。
DOI：
10.1056/nejmp1607591
发表时间：
2016-09-22
期刊：
The New England journal of medicine
影响因子：
--
作者：
Grossman RL;Heath AP;Ferretti V;Varmus HE;Lowy DR;Kibbe WA;Staudt LM
通讯作者：
Staudt LM
DOI：
10.1002/wnan.1321
发表时间：
2015-05
影响因子：
8.6
作者：
Cui, Yi;Irudayaraj, Joseph
通讯作者：
Irudayaraj, Joseph
影响因子：
7
作者：
Imamachi N;Salam KA;Suzuki Y;Akimitsu N
通讯作者：
Akimitsu N
影响因子：
14.9
作者：
Deutsch EW;Csordas A;Sun Z;Jarnuczak A;Perez-Riverol Y;Ternent T;Campbell DS;Bernal-Llinares M;Okuda S;Kawano S;Moritz RL;Carver JJ;Wang M;Ishihama Y;Bandeira N;Hermjakob H;Vizcaíno JA
通讯作者：
Vizcaíno JA