Qualitative de novo analysis of full length cDNA and quantitative analysis of gene expression for common marmoset (Callithrix jacchus) transcriptomes using parallel long-read technology and short-read sequencing.
Qualitative de novo analysis of full length cDNA and quantitative analysis of gene expression for common marmoset (Callithrix jacchus) transcriptomes using parallel long-read technology and short-read sequencing.
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DOI：
10.1371/journal.pone.0100936
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Yamazaki H
中科院分区：
文献类型：
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作者：
Shimizu M;Iwano S;Uno Y;Uehara S;Inoue T;Murayama N;Onodera J;Sasaki E;Yamazaki H
普通绒猴（Callithrix jacchus）是一种非人类灵长类动物，可用作人体药代动力学和生物医学研究模型。细胞色素P450（P450）是一个超家族的酶，具有关键作用的药物代谢和处置通过单氧化的广泛的外源性物质;然而，一些绒猴P450的信息目前是有限的。因此，在将绒猴用作药物开发的动物模型之前，需要对组织特异性mRNA转录本，包括P450和含黄素单加氧酶（FMO，另一个单加氧酶家族）的mRNA转录本进行详细的鉴定和定量分析。用来自三只雄性和三只雌性绒猴的合并肝、肠、肾和脑样品进行绒猴转录物的从头组装和表达分析。在47，883个转录本中，通过拼接软件自动比对后，重叠群的平均长度为718 bp（标准差为457 bp）。大约30%的转录本与已知的绒猴序列相匹配。18个绒猴P450基因和4个FMO样基因的表达具有一定的组织特异性。其中，在绒猴肝脏中表达最高的三个是P450 2D-、2 E-和3A-样基因。在肝外组织中，包括脑，这些单加氧酶的基因表达低于肝脏中的那些，尽管肠中的P450 3A 4（以前的P450 3A 21）和肾中的P450 4A 11-和FMO 1-like基因相对高表达。通过将大规模并行长读段测序和短读段技术应用于绒猴的肝脏、肠、肾脏和大脑，本文报道的组合下一代测序分析能够鉴定到目前为止很少报道的新型绒猴药物代谢P450转录物。这些结果为研究其作用机制奠定了基础，并为将来利用绒猴作为药物开发的模式动物奠定了基础。
The common marmoset (Callithrix jacchus) is a non-human primate that could prove useful as human pharmacokinetic and biomedical research models. The cytochromes P450 (P450s) are a superfamily of enzymes that have critical roles in drug metabolism and disposition via monooxygenation of a broad range of xenobiotics; however, information on some marmoset P450s is currently limited. Therefore, identification and quantitative analysis of tissue-specific mRNA transcripts, including those of P450s and flavin-containing monooxygenases (FMO, another monooxygenase family), need to be carried out in detail before the marmoset can be used as an animal model in drug development. De novo assembly and expression analysis of marmoset transcripts were conducted with pooled liver, intestine, kidney, and brain samples from three male and three female marmosets. After unique sequences were automatically aligned by assembling software, the mean contig length was 718 bp (with a standard deviation of 457 bp) among a total of 47,883 transcripts. Approximately 30% of the total transcripts were matched to known marmoset sequences. Gene expression in 18 marmoset P450- and 4 FMO-like genes displayed some tissue-specific patterns. Of these, the three most highly expressed in marmoset liver were P450 2D-, 2E-, and 3A-like genes. In extrahepatic tissues, including brain, gene expressions of these monooxygenases were lower than those in liver, although P450 3A4 (previously P450 3A21) in intestine and P450 4A11- and FMO1-like genes in kidney were relatively highly expressed. By means of massive parallel long-read sequencing and short-read technology applied to marmoset liver, intestine, kidney, and brain, the combined next-generation sequencing analyses reported here were able to identify novel marmoset drug-metabolizing P450 transcripts that have until now been little reported. These results provide a foundation for mechanistic studies and pave the way for the use of marmosets as model animals for drug development in the future.
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