Unveiling novel targets of paclitaxel resistance by single molecule long-read RNA sequencing in breast cancer
RNA sequencing has become one of the most common technology to study transcriptomes in cancer, whereas its length limits its application on alternative splicing (AS) events and novel isoforms. Firstly, we applied single molecule long-read RNA sequencing (Iso-seq) and de novo assembly with short-read...
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| Veröffentlicht in: | Scientific reports 2019-04, Vol.9 (1), p.6032, Article 6032 |
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| description | RNA sequencing has become one of the most common technology to study transcriptomes in cancer, whereas its length limits its application on alternative splicing (AS) events and novel isoforms. Firstly, we applied single molecule long-read RNA sequencing (Iso-seq) and de novo assembly with short-read RNA sequencing (RNA-seq) in both wild type (231-WT) and paclitaxel resistant type (231-PTX) of human breast cancer cell MDA-MBA-231. The two sequencing technology provide both the accurate transcript sequences and the deep transcript coverage. Then we combined shor-read and long-read RNA-seq to analyze alternative events and novel isoforms. Last but not the least, we selected BAK1 as our candidate target to verify our analysis. Our results implied that improved characterization of cancer genomic function may require the application of the single molecule long-read RNA sequencing to get the deeper and more precise view to transcriptional level. Our results imply that improved characterization of cancer genomic function may require the application of the single molecule long-read RNA sequencing to get the deeper and more precise view to transcriptional level. |
| doi_str_mv | 10.1038/s41598-019-42184-z |
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Firstly, we applied single molecule long-read RNA sequencing (Iso-seq) and de novo assembly with short-read RNA sequencing (RNA-seq) in both wild type (231-WT) and paclitaxel resistant type (231-PTX) of human breast cancer cell MDA-MBA-231. The two sequencing technology provide both the accurate transcript sequences and the deep transcript coverage. Then we combined shor-read and long-read RNA-seq to analyze alternative events and novel isoforms. Last but not the least, we selected BAK1 as our candidate target to verify our analysis. Our results implied that improved characterization of cancer genomic function may require the application of the single molecule long-read RNA sequencing to get the deeper and more precise view to transcriptional level. Our results imply that improved characterization of cancer genomic function may require the application of the single molecule long-read RNA sequencing to get the deeper and more precise view to transcriptional level.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-019-42184-z</identifier><identifier>PMID: 30988345</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>45/77 ; 631/114/2164 ; 631/1647/514/1949 ; 631/67/1347 ; Alternative splicing ; Alternative Splicing - drug effects ; Antineoplastic Agents, Phytogenic - pharmacology ; Breast cancer ; Breast Neoplasms - drug therapy ; Breast Neoplasms - genetics ; Cell Line, Tumor ; Drug Resistance, Neoplasm ; Female ; Humanities and Social Sciences ; Humans ; Isoforms ; multidisciplinary ; Paclitaxel ; Paclitaxel - pharmacology ; Ribonucleic acid ; RNA ; RNA Isoforms - genetics ; Science ; Science (multidisciplinary) ; Sequence Analysis, RNA ; Transcription ; Transcriptome - drug effects</subject><ispartof>Scientific reports, 2019-04, Vol.9 (1), p.6032, Article 6032</ispartof><rights>The Author(s) 2019</rights><rights>The Author(s) 2019. 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Firstly, we applied single molecule long-read RNA sequencing (Iso-seq) and de novo assembly with short-read RNA sequencing (RNA-seq) in both wild type (231-WT) and paclitaxel resistant type (231-PTX) of human breast cancer cell MDA-MBA-231. The two sequencing technology provide both the accurate transcript sequences and the deep transcript coverage. Then we combined shor-read and long-read RNA-seq to analyze alternative events and novel isoforms. Last but not the least, we selected BAK1 as our candidate target to verify our analysis. Our results implied that improved characterization of cancer genomic function may require the application of the single molecule long-read RNA sequencing to get the deeper and more precise view to transcriptional level. 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Hu, Xin ; Shao, Zhi-ming</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c540t-a98128f4f4aac975488fa6dd97e5946d98cbdef4126378814c621ac6af9403b63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>45/77</topic><topic>631/114/2164</topic><topic>631/1647/514/1949</topic><topic>631/67/1347</topic><topic>Alternative splicing</topic><topic>Alternative Splicing - drug effects</topic><topic>Antineoplastic Agents, Phytogenic - pharmacology</topic><topic>Breast cancer</topic><topic>Breast Neoplasms - drug therapy</topic><topic>Breast Neoplasms - genetics</topic><topic>Cell Line, Tumor</topic><topic>Drug Resistance, Neoplasm</topic><topic>Female</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Isoforms</topic><topic>multidisciplinary</topic><topic>Paclitaxel</topic><topic>Paclitaxel - pharmacology</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA Isoforms - genetics</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>Sequence Analysis, RNA</topic><topic>Transcription</topic><topic>Transcriptome - drug effects</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lian, Bi</creatorcontrib><creatorcontrib>Hu, Xin</creatorcontrib><creatorcontrib>Shao, Zhi-ming</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lian, Bi</au><au>Hu, Xin</au><au>Shao, Zhi-ming</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Unveiling novel targets of paclitaxel resistance by single molecule long-read RNA sequencing in breast cancer</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2019-04-15</date><risdate>2019</risdate><volume>9</volume><issue>1</issue><spage>6032</spage><pages>6032-</pages><artnum>6032</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>RNA sequencing has become one of the most common technology to study transcriptomes in cancer, whereas its length limits its application on alternative splicing (AS) events and novel isoforms. Firstly, we applied single molecule long-read RNA sequencing (Iso-seq) and de novo assembly with short-read RNA sequencing (RNA-seq) in both wild type (231-WT) and paclitaxel resistant type (231-PTX) of human breast cancer cell MDA-MBA-231. The two sequencing technology provide both the accurate transcript sequences and the deep transcript coverage. Then we combined shor-read and long-read RNA-seq to analyze alternative events and novel isoforms. Last but not the least, we selected BAK1 as our candidate target to verify our analysis. Our results implied that improved characterization of cancer genomic function may require the application of the single molecule long-read RNA sequencing to get the deeper and more precise view to transcriptional level. Our results imply that improved characterization of cancer genomic function may require the application of the single molecule long-read RNA sequencing to get the deeper and more precise view to transcriptional level.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>30988345</pmid><doi>10.1038/s41598-019-42184-z</doi><oa>free_for_read</oa></addata></record> |
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| subjects | 45/77 631/114/2164 631/1647/514/1949 631/67/1347 Alternative splicing Alternative Splicing - drug effects Antineoplastic Agents, Phytogenic - pharmacology Breast cancer Breast Neoplasms - drug therapy Breast Neoplasms - genetics Cell Line, Tumor Drug Resistance, Neoplasm Female Humanities and Social Sciences Humans Isoforms multidisciplinary Paclitaxel Paclitaxel - pharmacology Ribonucleic acid RNA RNA Isoforms - genetics Science Science (multidisciplinary) Sequence Analysis, RNA Transcription Transcriptome - drug effects |
| title | Unveiling novel targets of paclitaxel resistance by single molecule long-read RNA sequencing in breast cancer |
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