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Evaluation of off‐target effects of gapmer antisense oligonucleotides using human cells
Antisense oligonucleotide (ASO) has the potential to induce off‐target effects due to complementary binding between the ASO and unintended RNA with a sequence similar to the target RNA. Conventional animal studies cannot be used to assess toxicity induced by off‐target effects because of differences...
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Published in: | Genes to cells : devoted to molecular & cellular mechanisms 2019-12, Vol.24 (12), p.827-835 |
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creator | Yoshida, Tokuyuki Naito, Yuki Yasuhara, Hidenori Sasaki, Kiyomi Kawaji, Hideya Kawai, Jun Naito, Mikihiko Okuda, Haruhiro Obika, Satoshi Inoue, Takao |
description | Antisense oligonucleotide (ASO) has the potential to induce off‐target effects due to complementary binding between the ASO and unintended RNA with a sequence similar to the target RNA. Conventional animal studies cannot be used to assess toxicity induced by off‐target effects because of differences in the genome sequence between humans and other animals. Consequently, the assessment of off‐target effects with in silico analysis using a human RNA database and/or in vitro expression analysis using human cells has been proposed.
Our previous study showed that the number of complementary regions of ASOs with mismatches in the human RNA sequences increases dramatically as the number of tolerated mismatches increases. However, to what extent the expression of genes with mismatches is affected by off‐target effects at the cellular level is not clear. In this study, we evaluated off‐target effects of gapmer ASOs, which cleave the target RNA in an RNase H‐dependent manner, by introducing the ASO into human cells and performing microarray analysis. Our data indicate that gapmer ASOs induce off‐target effects depending on the degree of complementarity between the ASO and off‐target candidate genes. Based on our results, we also propose a scheme for the assessment of off‐target effects of gapmer ASOs.
We showed that gapmer oligonucleotide (ASO) induce off‐target effects depending on the degree of complementarity between the ASO and off‐target candidate genes. Based on our results, we also proposed a scheme for the assessment of off‐target effects of gapmer ASOs. |
doi_str_mv | 10.1111/gtc.12730 |
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Our previous study showed that the number of complementary regions of ASOs with mismatches in the human RNA sequences increases dramatically as the number of tolerated mismatches increases. However, to what extent the expression of genes with mismatches is affected by off‐target effects at the cellular level is not clear. In this study, we evaluated off‐target effects of gapmer ASOs, which cleave the target RNA in an RNase H‐dependent manner, by introducing the ASO into human cells and performing microarray analysis. Our data indicate that gapmer ASOs induce off‐target effects depending on the degree of complementarity between the ASO and off‐target candidate genes. Based on our results, we also propose a scheme for the assessment of off‐target effects of gapmer ASOs.
We showed that gapmer oligonucleotide (ASO) induce off‐target effects depending on the degree of complementarity between the ASO and off‐target candidate genes. Based on our results, we also proposed a scheme for the assessment of off‐target effects of gapmer ASOs.</description><identifier>ISSN: 1356-9597</identifier><identifier>EISSN: 1365-2443</identifier><identifier>DOI: 10.1111/gtc.12730</identifier><identifier>PMID: 31637814</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>Algorithms ; antisense ; Antisense oligonucleotides ; Base Pair Mismatch ; Base Pairing ; Cell Line, Tumor ; Complementarity ; Gapmer ; Genomes ; Humans ; microarray analysis ; Nucleotide sequence ; off‐target effects ; Oligonucleotides, Antisense - chemistry ; Oligonucleotides, Antisense - genetics ; Oligonucleotides, Antisense - metabolism ; Original ; pre‐mRNA ; Ribonuclease H ; Ribonucleic acid ; RNA ; RNA - chemistry ; RNA - genetics ; RNA - metabolism ; Sequence Analysis, RNA - methods ; Toxicity</subject><ispartof>Genes to cells : devoted to molecular & cellular mechanisms, 2019-12, Vol.24 (12), p.827-835</ispartof><rights>2019 The Authors. published by Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd</rights><rights>2019 The Authors. Genes to Cells published by Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.</rights><rights>2019 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5090-539d524581cc1bc54193d4d6e17fcd9d337f7fb37a5bd34527fa3a91771d792f3</citedby><cites>FETCH-LOGICAL-c5090-539d524581cc1bc54193d4d6e17fcd9d337f7fb37a5bd34527fa3a91771d792f3</cites><orcidid>0000-0002-6507-9480</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31637814$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yoshida, Tokuyuki</creatorcontrib><creatorcontrib>Naito, Yuki</creatorcontrib><creatorcontrib>Yasuhara, Hidenori</creatorcontrib><creatorcontrib>Sasaki, Kiyomi</creatorcontrib><creatorcontrib>Kawaji, Hideya</creatorcontrib><creatorcontrib>Kawai, Jun</creatorcontrib><creatorcontrib>Naito, Mikihiko</creatorcontrib><creatorcontrib>Okuda, Haruhiro</creatorcontrib><creatorcontrib>Obika, Satoshi</creatorcontrib><creatorcontrib>Inoue, Takao</creatorcontrib><title>Evaluation of off‐target effects of gapmer antisense oligonucleotides using human cells</title><title>Genes to cells : devoted to molecular & cellular mechanisms</title><addtitle>Genes Cells</addtitle><description>Antisense oligonucleotide (ASO) has the potential to induce off‐target effects due to complementary binding between the ASO and unintended RNA with a sequence similar to the target RNA. Conventional animal studies cannot be used to assess toxicity induced by off‐target effects because of differences in the genome sequence between humans and other animals. Consequently, the assessment of off‐target effects with in silico analysis using a human RNA database and/or in vitro expression analysis using human cells has been proposed.
Our previous study showed that the number of complementary regions of ASOs with mismatches in the human RNA sequences increases dramatically as the number of tolerated mismatches increases. However, to what extent the expression of genes with mismatches is affected by off‐target effects at the cellular level is not clear. In this study, we evaluated off‐target effects of gapmer ASOs, which cleave the target RNA in an RNase H‐dependent manner, by introducing the ASO into human cells and performing microarray analysis. Our data indicate that gapmer ASOs induce off‐target effects depending on the degree of complementarity between the ASO and off‐target candidate genes. Based on our results, we also propose a scheme for the assessment of off‐target effects of gapmer ASOs.
We showed that gapmer oligonucleotide (ASO) induce off‐target effects depending on the degree of complementarity between the ASO and off‐target candidate genes. Based on our results, we also proposed a scheme for the assessment of off‐target effects of gapmer ASOs.</description><subject>Algorithms</subject><subject>antisense</subject><subject>Antisense oligonucleotides</subject><subject>Base Pair Mismatch</subject><subject>Base Pairing</subject><subject>Cell Line, Tumor</subject><subject>Complementarity</subject><subject>Gapmer</subject><subject>Genomes</subject><subject>Humans</subject><subject>microarray analysis</subject><subject>Nucleotide sequence</subject><subject>off‐target effects</subject><subject>Oligonucleotides, Antisense - chemistry</subject><subject>Oligonucleotides, Antisense - genetics</subject><subject>Oligonucleotides, Antisense - metabolism</subject><subject>Original</subject><subject>pre‐mRNA</subject><subject>Ribonuclease H</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA - chemistry</subject><subject>RNA - genetics</subject><subject>RNA - metabolism</subject><subject>Sequence Analysis, RNA - methods</subject><subject>Toxicity</subject><issn>1356-9597</issn><issn>1365-2443</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><recordid>eNp1kc1qFTEUx4Mo9kMXvoAMuLGLaXMmk0mzEcqlH0Khm7pwFXKTk2nKTHJNMpXufASf0SdxprcWFRoCOZz8-HEOf0LeAT2E-Rz1xRxCIxh9QXaBdbxu2pa9XGre1ZJLsUP2cr6lFFhD-Wuyw6Bj4hjaXfL19E4Pky4-hiq6-bpfP34WnXosFTqHpuSl3-vNiKnSofiMIWMVB9_HMJkBY_EWczVlH_rqZhp1qAwOQ35DXjk9ZHz7-O6TL2en16uL-vLq_PPq5LI2nEpacyYtb1p-DMbA2vAWJLOt7RCEM1ZaxoQTbs2E5mvLWt4Ip5mWIARYIRvH9smnrXczrUe0BkNJelCb5Eed7lXUXv37E_yN6uOd6iRwSeUs-PgoSPHbhLmo0edlBR0wTlk1jArBOikX9MN_6G2cUpjXm6kGWAvwQB1sKZNizgnd0zBA1RKYmgNTD4HN7Pu_p38i_yQ0A0db4Lsf8P55kzq_Xm2VvwE0ZaGm</recordid><startdate>201912</startdate><enddate>201912</enddate><creator>Yoshida, Tokuyuki</creator><creator>Naito, Yuki</creator><creator>Yasuhara, Hidenori</creator><creator>Sasaki, Kiyomi</creator><creator>Kawaji, Hideya</creator><creator>Kawai, Jun</creator><creator>Naito, Mikihiko</creator><creator>Okuda, Haruhiro</creator><creator>Obika, Satoshi</creator><creator>Inoue, Takao</creator><general>Wiley Subscription Services, Inc</general><general>John Wiley and Sons Inc</general><scope>24P</scope><scope>WIN</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-6507-9480</orcidid></search><sort><creationdate>201912</creationdate><title>Evaluation of off‐target effects of gapmer antisense oligonucleotides using human cells</title><author>Yoshida, Tokuyuki ; Naito, Yuki ; Yasuhara, Hidenori ; Sasaki, Kiyomi ; Kawaji, Hideya ; Kawai, Jun ; Naito, Mikihiko ; Okuda, Haruhiro ; Obika, Satoshi ; Inoue, Takao</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5090-539d524581cc1bc54193d4d6e17fcd9d337f7fb37a5bd34527fa3a91771d792f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Algorithms</topic><topic>antisense</topic><topic>Antisense oligonucleotides</topic><topic>Base Pair Mismatch</topic><topic>Base Pairing</topic><topic>Cell Line, Tumor</topic><topic>Complementarity</topic><topic>Gapmer</topic><topic>Genomes</topic><topic>Humans</topic><topic>microarray analysis</topic><topic>Nucleotide sequence</topic><topic>off‐target effects</topic><topic>Oligonucleotides, Antisense - chemistry</topic><topic>Oligonucleotides, Antisense - genetics</topic><topic>Oligonucleotides, Antisense - metabolism</topic><topic>Original</topic><topic>pre‐mRNA</topic><topic>Ribonuclease H</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA - chemistry</topic><topic>RNA - genetics</topic><topic>RNA - metabolism</topic><topic>Sequence Analysis, RNA - methods</topic><topic>Toxicity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yoshida, Tokuyuki</creatorcontrib><creatorcontrib>Naito, Yuki</creatorcontrib><creatorcontrib>Yasuhara, Hidenori</creatorcontrib><creatorcontrib>Sasaki, Kiyomi</creatorcontrib><creatorcontrib>Kawaji, Hideya</creatorcontrib><creatorcontrib>Kawai, Jun</creatorcontrib><creatorcontrib>Naito, Mikihiko</creatorcontrib><creatorcontrib>Okuda, Haruhiro</creatorcontrib><creatorcontrib>Obika, Satoshi</creatorcontrib><creatorcontrib>Inoue, Takao</creatorcontrib><collection>Wiley Open Access</collection><collection>Wiley Free Archive</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes to cells : devoted to molecular & cellular mechanisms</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yoshida, Tokuyuki</au><au>Naito, Yuki</au><au>Yasuhara, Hidenori</au><au>Sasaki, Kiyomi</au><au>Kawaji, Hideya</au><au>Kawai, Jun</au><au>Naito, Mikihiko</au><au>Okuda, Haruhiro</au><au>Obika, Satoshi</au><au>Inoue, Takao</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evaluation of off‐target effects of gapmer antisense oligonucleotides using human cells</atitle><jtitle>Genes to cells : devoted to molecular & cellular mechanisms</jtitle><addtitle>Genes Cells</addtitle><date>2019-12</date><risdate>2019</risdate><volume>24</volume><issue>12</issue><spage>827</spage><epage>835</epage><pages>827-835</pages><issn>1356-9597</issn><eissn>1365-2443</eissn><abstract>Antisense oligonucleotide (ASO) has the potential to induce off‐target effects due to complementary binding between the ASO and unintended RNA with a sequence similar to the target RNA. Conventional animal studies cannot be used to assess toxicity induced by off‐target effects because of differences in the genome sequence between humans and other animals. Consequently, the assessment of off‐target effects with in silico analysis using a human RNA database and/or in vitro expression analysis using human cells has been proposed.
Our previous study showed that the number of complementary regions of ASOs with mismatches in the human RNA sequences increases dramatically as the number of tolerated mismatches increases. However, to what extent the expression of genes with mismatches is affected by off‐target effects at the cellular level is not clear. In this study, we evaluated off‐target effects of gapmer ASOs, which cleave the target RNA in an RNase H‐dependent manner, by introducing the ASO into human cells and performing microarray analysis. Our data indicate that gapmer ASOs induce off‐target effects depending on the degree of complementarity between the ASO and off‐target candidate genes. Based on our results, we also propose a scheme for the assessment of off‐target effects of gapmer ASOs.
We showed that gapmer oligonucleotide (ASO) induce off‐target effects depending on the degree of complementarity between the ASO and off‐target candidate genes. Based on our results, we also proposed a scheme for the assessment of off‐target effects of gapmer ASOs.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>31637814</pmid><doi>10.1111/gtc.12730</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0002-6507-9480</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Algorithms antisense Antisense oligonucleotides Base Pair Mismatch Base Pairing Cell Line, Tumor Complementarity Gapmer Genomes Humans microarray analysis Nucleotide sequence off‐target effects Oligonucleotides, Antisense - chemistry Oligonucleotides, Antisense - genetics Oligonucleotides, Antisense - metabolism Original pre‐mRNA Ribonuclease H Ribonucleic acid RNA RNA - chemistry RNA - genetics RNA - metabolism Sequence Analysis, RNA - methods Toxicity |
title | Evaluation of off‐target effects of gapmer antisense oligonucleotides using human cells |
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