Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer.
Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer.
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DOI：
10.1371/journal.pgen.1011043
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发表时间：
2023-11
期刊：
影响因子：
4.5
通讯作者：
中科院分区：
文献类型：
--
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癌症突变的一个重要来源是细胞APOBEC3酶的单链DNA胞嘧啶脱氨作用，这导致TCA和TCT基序的标志性C-to-T和C-to-G突变。虽然涉及多种酶，但报告相互矛盾，并且不清楚哪种蛋白质负责。在这里，我们报告了一种可选择系统的发展，以量化基因组突变，并通过比较三种主要候选基因——apobec3a、APOBEC3B和APOBEC3H的致突变活性来证明其实用性。人类细胞系HAP1被设计表达HSV-1的胸苷激酶（TK）基因，该基因对更昔洛韦敏感。APOBEC3A和APOBEC3B的表达，而不是催化突变对照或APOBEC3H的表达，会引发TK突变的频率增加，并在可选择的TK报告基因中引发类似的tc偏倚胞嘧啶突变谱。来自独立克隆的全基因组序列可以分析数千个单碱基替换突变，并提取局部序列偏好，其中APOBEC3A倾向于70%的YTCW基序，APOBEC3B倾向于50%的YTCW基序（Y = C/T; W = A/T）。与乳腺肿瘤全基因组序列的特征比较表明，大多数恶性肿瘤在YTCW基序中表现出中等比例的APOBEC3特征突变，大多数在50%至70%之间，这表明这两种酶以组合方式参与了整体突变格局。尽管绝大多数APOBEC3A-和apobec3b诱导的单碱基替换突变发生在预测的染色体DNA发夹结构之外，但全基因组序列分析和支持的生化研究也表明，这两种酶都能够以较高的速率脱氨DNA发夹的单链环区域。这些研究结合起来有助于解决长期以来关于癌症中APOBEC3特征突变来源的病因学争论，并表明未来的诊断和治疗工作应集中在APOBEC3A和APOBEC3B上。癌症突变的一个主要来源是APOBEC3家族酶对单链DNA胞嘧啶到尿嘧啶（C-to-U）的脱胺作用。染色体DNA U直接模板腺嘌呤(A)的插入，导致C/ g到t /A突变。染色体U也会触发容易出错的DNA修复过程，这种修复过程不太直接导致C/ g到t /A突变，C/ g到g /C突变，以及更复杂的事件，如插入/删除突变。我们报告了一种用于癌症突变研究的人类细胞系，其中突变可以被选择性地识别或通过基因组DNA测序。只有APOBEC3A和APOBEC3B被证明能够造成上述类型的单碱基置换突变。有趣的是，70%和50%可归因于APOBEC3A和APOBEC3B的单碱基替换突变分别发生在TCA和TCT三核苷酸基序中，其前面有一个嘧啶（T或C）。这一点很重要，因为大多数apobec3阳性的乳腺肿瘤在这些更广泛的四核苷酸基序中表现出中等比例的特征突变，这支持了APOBEC3A和APOBEC3B以组合方式参与这些肿瘤整体突变景观的观点。
A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates—APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and similar TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from independent clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs 70% of the time and APOBEC3B 50% of the time (Y = C/T; W = A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes contribute in a combinatorial manner to the overall mutation landscape. Although the vast majority of APOBEC3A- and APOBEC3B-induced single base substitution mutations occur outside of predicted chromosomal DNA hairpin structures, whole genome sequence analyses and supporting biochemical studies also indicate that both enzymes are capable of deaminating the single-stranded loop regions of DNA hairpins at elevated rates. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B. A large source of mutation in cancer is attributable to single-stranded DNA cytosine to uracil (C-to-U) deamination by APOBEC3 family enzymes. Chromosomal DNA U’s directly template the insertion of adenine (A), which results in C/G-to-T/A mutations. Chromosomal U’s also trigger error-prone DNA repair processes, which less directly result in C/G-to-T/A mutations, C/G-to-G/C mutations, and more complex events such as insertion/deletion mutations. We report a human cell line for cancer mutation studies, where mutations can be identified selectively or by genomic DNA sequencing. Only APOBEC3A and APOBEC3B proved capable of inflicting the aforementioned types of single base substitution mutations. Interestingly, 70% and 50% of the single base substitution mutations attributable to APOBEC3A and APOBEC3B, respectively, occurred in TCA and TCT trinucleotide motifs preceded by a pyrimidine (T or C). This is significant because most APOBEC3-positive breast tumors exhibit an intermediate percentage of signature mutations in these broader tetranucleotide motifs, which supports the idea that both APOBEC3A and APOBEC3B contribute in a combinatorial manner to the overall mutation landscape in these tumors.
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影响因子：
30.8
作者：
Burns, Michael B.;Temiz, Nuri A.;Harris, Reuben S.
通讯作者：
Harris, Reuben S.
影响因子：
12.3
作者：
Blokzijl F;Janssen R;van Boxtel R;Cuppen E
通讯作者：
Cuppen E
影响因子：
3.7
作者：
Akre MK;Starrett GJ;Quist JS;Temiz NA;Carpenter MA;Tutt AN;Grigoriadis A;Harris RS
通讯作者：
Harris RS
影响因子：
4.6
作者：
Ito F;Yang H;Xiao X;Li SX;Wolfe A;Zirkle B;Arutiunian V;Chen XS
通讯作者：
Chen XS
DOI：
10.1126/science.1253462
发表时间：
2014-10-10
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
de Bruin EC;McGranahan N;Mitter R;Salm M;Wedge DC;Yates L;Jamal-Hanjani M;Shafi S;Murugaesu N;Rowan AJ;Grönroos E;Muhammad MA;Horswell S;Gerlinger M;Varela I;Jones D;Marshall J;Voet T;Van Loo P;Rassl DM;Rintoul RC;Janes SM;Lee SM;Forster M;Ahmad T;Lawrence D;Falzon M;Capitanio A;Harkins TT;Lee CC;Tom W;Teefe E;Chen SC;Begum S;Rabinowitz A;Phillimore B;Spencer-Dene B;Stamp G;Szallasi Z;Matthews N;Stewart A;Campbell P;Swanton C
通讯作者：
Swanton C