Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.
Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.
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DOI：
10.1080/15476286.2022.2141938
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发表时间：
2022-01
期刊：
影响因子：
4.1
通讯作者：
Sheynkman, Gloria M.
中科院分区：
文献类型：
--
作者：
Mehlferber, Madison M.;Jeffery, Erin D.;Saquing, Jamie;Jordan, Ben T.;Sheynkman, Leon;Murali, Mayank;Genet, Gael;Acharya, Bipul R.;Hirschi, Karen K.;Sheynkman, Gloria M.
关键词：
血管内皮细胞(ECs)构成所有血管的管腔衬里，对心血管系统的功能至关重要。它们的表型可以通过RNA的选择性剪接来调节，以产生不同的蛋白质亚型。为了表征内皮细胞中的RNA和蛋白质异构体，我们应用长阅读蛋白质组学方法分析了人脐静脉内皮细胞(HUVECs)。PacBio测序显示的转录本是特定样本蛋白质数据库的基础，用于下游质谱仪(MS)分析，以推断蛋白质异构体的表达。我们从10,426个基因中检测到53,863个转录异构体，其中22,195个是新的转录本。此外，HUVECs中的主要异构体在25%的时间内与公认的“参考异构体”不一致，这一组中存在与血管通路相关的基因。我们发现2,597种蛋白质异构体由独特的多肽支持，另外2,280种异构体在纳入长时间阅读的转录证据后被提名。我们鉴定了一种新的内皮相关基因CDH5的替代受体，暗示了其相关信号通路的潜在变化。最后，我们确定了由独特定位的新肽支持的各种RNA剪接机制产生的新的蛋白质异构体。我们的结果代表了已知的和新的与内皮表型和功能相关的新亚型的高分辨率图谱。
Endothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system. Their phenotypes can be modulated by alternative splicing of RNA to produce distinct protein isoforms. To characterize the RNA and protein isoform landscape within ECs, we applied a long read proteogenomics approach to analyse human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream mass-spectrometry (MS) analysis to infer protein isoform expression. We detected 53,863 transcript isoforms from 10,426 genes, with 22,195 of those transcripts being novel. Furthermore, the predominant isoform in HUVECs does not correspond with the accepted “reference isoform” 25% of the time, with vascular pathway-related genes among this group. We found 2,597 protein isoforms supported through unique peptides, with an additional 2,280 isoforms nominated upon incorporation of long-read transcript evidence. We characterized a novel alternative acceptor for endothelial-related gene CDH5, suggesting potential changes in its associated signalling pathways. Finally, we identified novel protein isoforms arising from a diversity of RNA splicing mechanisms supported by uniquely mapped novel peptides. Our results represent a high-resolution atlas of known and novel isoforms of potential relevance to endothelial phenotypes and function.
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影响因子：
14.9
作者：
Edwards JM;Long J;de Moor CH;Emsley J;Searle MS
通讯作者：
Searle MS
影响因子：
3.4
作者：
Blakeley, Paul;Siepen, Jennifer A.;Lawless, Craig;Hubbard, Simon J.
通讯作者：
Hubbard, Simon J.
一种将样品多路复用与靶向蛋白质组学测定法相结合的策略，以进行高通量蛋白质特征。
影响因子：
16
作者：
Erickson BK;Rose CM;Braun CR;Erickson AR;Knott J;McAlister GC;Wühr M;Paulo JA;Everley RA;Gygi SP
通讯作者：
Gygi SP
影响因子：
14.9
作者：
Frankish A;Diekhans M;Ferreira AM;Johnson R;Jungreis I;Loveland J;Mudge JM;Sisu C;Wright J;Armstrong J;Barnes I;Berry A;Bignell A;Carbonell Sala S;Chrast J;Cunningham F;Di Domenico T;Donaldson S;Fiddes IT;García Girón C;Gonzalez JM;Grego T;Hardy M;Hourlier T;Hunt T;Izuogu OG;Lagarde J;Martin FJ;Martínez L;Mohanan S;Muir P;Navarro FCP;Parker A;Pei B;Pozo F;Ruffier M;Schmitt BM;Stapleton E;Suner MM;Sycheva I;Uszczynska-Ratajczak B;Xu J;Yates A;Zerbino D;Zhang Y;Aken B;Choudhary JS;Gerstein M;Guigó R;Hubbard TJP;Kellis M;Paten B;Reymond A;Tress ML;Flicek P
通讯作者：
Flicek P
影响因子：
5.5
作者：
Cao, GY;O'Brien, CD;DeLisser, HM
通讯作者：
DeLisser, HM