Identification of Specific Long Non-Coding RNA Expression: Profile and Analysis of Association with Clinicopathologic Characteristics and BRAF Mutation in Papillary Thyroid Cancer
Background: In recent years, long non-coding RNAs (lncRNAs) have been shown to play a critical regulatory role in cancer biology. However, the contribution of lncRNAs to papillary thyroid cancer (PTC) remains largely unknown. Methods: RNA sequencing and quantitative reverse transcription polymerase...
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| Veröffentlicht in: | Thyroid (New York, N.Y.) N.Y.), 2016-12, Vol.26 (12), p.1719-1732 |
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| creator | Wang, Qiangfeng Yang, Huanxia Wu, Lingjiao Yao, Jian Meng, Xiaohua Jiang, Han Xiao, Cheng Wu, Fusheng |
| description | Background:
In recent years, long non-coding RNAs (lncRNAs) have been shown to play a critical regulatory role in cancer biology. However, the contribution of lncRNAs to papillary thyroid cancer (PTC) remains largely unknown.
Methods:
RNA sequencing and quantitative reverse transcription polymerase chain reaction were used to detect and verify changes to the transcriptome profile in 12 PTC tissues compared to paired normal adjacent tissues. The statistical correlation between differentially expressed lncRNAs and clinicopathologic characteristics was analyzed, and potential lncRNA functions were predicted by examining annotations for the co-expressed mRNAs. Furthermore, the specific subgroup patterns of the PTC transcriptome remodeled by
BRAF
mutations were also analyzed.
Results:
A total of 188 lncRNAs and 505 mRNAs were differentially expressed in 50% or more of the PTC tissues (fold change >2;
p
|
| doi_str_mv | 10.1089/thy.2016.0024 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1834996463</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1834996463</sourcerecordid><originalsourceid>FETCH-LOGICAL-c337t-cc767885ea7ec6dd05abb091521c3e7be20575c34061fe944e9c59dda872ee1e3</originalsourceid><addsrcrecordid>eNqFkcFu1DAQQC1ERUvhyBX5yCWLHcdxwi1ELa20LVUp58ixJ41R1g62V2W_ix-s05ReOXk0en4a6SH0gZINJVX9OY6HTU5ouSEkL16hE8q5yGoixOs0E04ykfPyGL0N4RdJWCXYG3ScC8EryqoT9PdSg41mMEpG4yx2A_4xg1oWeOvsPb52NmudNmm8vW7w2Z_ZQwgJ_YJvvBvMBFhajRsrp0MwYRE0IThlVt-DiSNuJ2ONcrOMo5vcfVK3o_RSRfAmRKPCk-LrbXOOr_Zx_WgsvpGzmSbpD_huPHhnNG6lVeDfoaNBTgHeP7-n6Of52V17kW2_f7tsm22mGBMxU0qUoqo4SAGq1Jpw2fekpjynioHoISdccMUKUtIB6qKAWvFaa1mJHIACO0WfVu_s3e89hNjtTFCQTrLg9qGjFSvquixKltBsRZV3IXgYutmbXTq9o6RbOnWpU7d06pZOif_4rN73O9Av9L8wCWArsKyltZOBHnz8j_YRxpqjDA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1834996463</pqid></control><display><type>article</type><title>Identification of Specific Long Non-Coding RNA Expression: Profile and Analysis of Association with Clinicopathologic Characteristics and BRAF Mutation in Papillary Thyroid Cancer</title><source>MEDLINE</source><source>Alma/SFX Local Collection</source><creator>Wang, Qiangfeng ; Yang, Huanxia ; Wu, Lingjiao ; Yao, Jian ; Meng, Xiaohua ; Jiang, Han ; Xiao, Cheng ; Wu, Fusheng</creator><creatorcontrib>Wang, Qiangfeng ; Yang, Huanxia ; Wu, Lingjiao ; Yao, Jian ; Meng, Xiaohua ; Jiang, Han ; Xiao, Cheng ; Wu, Fusheng</creatorcontrib><description>Background:
In recent years, long non-coding RNAs (lncRNAs) have been shown to play a critical regulatory role in cancer biology. However, the contribution of lncRNAs to papillary thyroid cancer (PTC) remains largely unknown.
Methods:
RNA sequencing and quantitative reverse transcription polymerase chain reaction were used to detect and verify changes to the transcriptome profile in 12 PTC tissues compared to paired normal adjacent tissues. The statistical correlation between differentially expressed lncRNAs and clinicopathologic characteristics was analyzed, and potential lncRNA functions were predicted by examining annotations for the co-expressed mRNAs. Furthermore, the specific subgroup patterns of the PTC transcriptome remodeled by
BRAF
mutations were also analyzed.
Results:
A total of 188 lncRNAs and 505 mRNAs were differentially expressed in 50% or more of the PTC tissues (fold change >2;
p
< 0.05) as assessed by RNA-sequencing compared with paired normal adjacent tissues. Forty-seven lncRNAs and 39 mRNAs were verified in 31 pairs of PTC specimens using quantitative reverse transcription polymerase chain reaction, and the results were consistent with the RNA sequencing data. The lncRNAs NONHSAT076747 and NONHSAT122730 were associated with lymph node metastasis, and NONHSAG051968 expression was negatively correlated with tumor size. A co-expression network between differentially expressed lncRNAs and protein-coding RNAs was constructed and analyzed, and functional analysis suggested that the differentially expressed genes mainly participate in ECM–receptor interactions and the focal adhesion pathway. Furthermore, a specific PTC transcriptome subtype pattern stratified by
BRAF
mutation was also uncovered. The
p53
signaling pathway was the most highly enriched pathway among the
BRAF
mutation-related genes.
Conclusions:
This study reveals specific changes to the lncRNA profile associated with PTC, and provides new insight into its pathogenesis. The PTC-associated lncRNAs NONHSAG051968, NONHSAT076747, and NONHSAT122730 might be potential diagnostic and therapeutic targets for PTC patients, and lncRNAs with subtype-specific expression stratified by
BRAF
mutation might be significant in individual molecular subtypes.</description><identifier>ISSN: 1050-7256</identifier><identifier>EISSN: 1557-9077</identifier><identifier>DOI: 10.1089/thy.2016.0024</identifier><identifier>PMID: 27758138</identifier><language>eng</language><publisher>United States: Mary Ann Liebert, Inc</publisher><subject>Adult ; Carcinoma, Papillary - genetics ; Carcinoma, Papillary - pathology ; Cell Line, Tumor ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Middle Aged ; Mutation ; Proto-Oncogene Proteins B-raf - genetics ; RNA, Long Noncoding - genetics ; Sequence Analysis, RNA ; Thyroid Cancer and Nodules ; Thyroid Neoplasms - genetics ; Thyroid Neoplasms - pathology</subject><ispartof>Thyroid (New York, N.Y.), 2016-12, Vol.26 (12), p.1719-1732</ispartof><rights>2016, Mary Ann Liebert, Inc.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c337t-cc767885ea7ec6dd05abb091521c3e7be20575c34061fe944e9c59dda872ee1e3</citedby><cites>FETCH-LOGICAL-c337t-cc767885ea7ec6dd05abb091521c3e7be20575c34061fe944e9c59dda872ee1e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27758138$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Qiangfeng</creatorcontrib><creatorcontrib>Yang, Huanxia</creatorcontrib><creatorcontrib>Wu, Lingjiao</creatorcontrib><creatorcontrib>Yao, Jian</creatorcontrib><creatorcontrib>Meng, Xiaohua</creatorcontrib><creatorcontrib>Jiang, Han</creatorcontrib><creatorcontrib>Xiao, Cheng</creatorcontrib><creatorcontrib>Wu, Fusheng</creatorcontrib><title>Identification of Specific Long Non-Coding RNA Expression: Profile and Analysis of Association with Clinicopathologic Characteristics and BRAF Mutation in Papillary Thyroid Cancer</title><title>Thyroid (New York, N.Y.)</title><addtitle>Thyroid</addtitle><description>Background:
In recent years, long non-coding RNAs (lncRNAs) have been shown to play a critical regulatory role in cancer biology. However, the contribution of lncRNAs to papillary thyroid cancer (PTC) remains largely unknown.
Methods:
RNA sequencing and quantitative reverse transcription polymerase chain reaction were used to detect and verify changes to the transcriptome profile in 12 PTC tissues compared to paired normal adjacent tissues. The statistical correlation between differentially expressed lncRNAs and clinicopathologic characteristics was analyzed, and potential lncRNA functions were predicted by examining annotations for the co-expressed mRNAs. Furthermore, the specific subgroup patterns of the PTC transcriptome remodeled by
BRAF
mutations were also analyzed.
Results:
A total of 188 lncRNAs and 505 mRNAs were differentially expressed in 50% or more of the PTC tissues (fold change >2;
p
< 0.05) as assessed by RNA-sequencing compared with paired normal adjacent tissues. Forty-seven lncRNAs and 39 mRNAs were verified in 31 pairs of PTC specimens using quantitative reverse transcription polymerase chain reaction, and the results were consistent with the RNA sequencing data. The lncRNAs NONHSAT076747 and NONHSAT122730 were associated with lymph node metastasis, and NONHSAG051968 expression was negatively correlated with tumor size. A co-expression network between differentially expressed lncRNAs and protein-coding RNAs was constructed and analyzed, and functional analysis suggested that the differentially expressed genes mainly participate in ECM–receptor interactions and the focal adhesion pathway. Furthermore, a specific PTC transcriptome subtype pattern stratified by
BRAF
mutation was also uncovered. The
p53
signaling pathway was the most highly enriched pathway among the
BRAF
mutation-related genes.
Conclusions:
This study reveals specific changes to the lncRNA profile associated with PTC, and provides new insight into its pathogenesis. The PTC-associated lncRNAs NONHSAG051968, NONHSAT076747, and NONHSAT122730 might be potential diagnostic and therapeutic targets for PTC patients, and lncRNAs with subtype-specific expression stratified by
BRAF
mutation might be significant in individual molecular subtypes.</description><subject>Adult</subject><subject>Carcinoma, Papillary - genetics</subject><subject>Carcinoma, Papillary - pathology</subject><subject>Cell Line, Tumor</subject><subject>Female</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Humans</subject><subject>Male</subject><subject>Middle Aged</subject><subject>Mutation</subject><subject>Proto-Oncogene Proteins B-raf - genetics</subject><subject>RNA, Long Noncoding - genetics</subject><subject>Sequence Analysis, RNA</subject><subject>Thyroid Cancer and Nodules</subject><subject>Thyroid Neoplasms - genetics</subject><subject>Thyroid Neoplasms - pathology</subject><issn>1050-7256</issn><issn>1557-9077</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkcFu1DAQQC1ERUvhyBX5yCWLHcdxwi1ELa20LVUp58ixJ41R1g62V2W_ix-s05ReOXk0en4a6SH0gZINJVX9OY6HTU5ouSEkL16hE8q5yGoixOs0E04ykfPyGL0N4RdJWCXYG3ScC8EryqoT9PdSg41mMEpG4yx2A_4xg1oWeOvsPb52NmudNmm8vW7w2Z_ZQwgJ_YJvvBvMBFhajRsrp0MwYRE0IThlVt-DiSNuJ2ONcrOMo5vcfVK3o_RSRfAmRKPCk-LrbXOOr_Zx_WgsvpGzmSbpD_huPHhnNG6lVeDfoaNBTgHeP7-n6Of52V17kW2_f7tsm22mGBMxU0qUoqo4SAGq1Jpw2fekpjynioHoISdccMUKUtIB6qKAWvFaa1mJHIACO0WfVu_s3e89hNjtTFCQTrLg9qGjFSvquixKltBsRZV3IXgYutmbXTq9o6RbOnWpU7d06pZOif_4rN73O9Av9L8wCWArsKyltZOBHnz8j_YRxpqjDA</recordid><startdate>20161201</startdate><enddate>20161201</enddate><creator>Wang, Qiangfeng</creator><creator>Yang, Huanxia</creator><creator>Wu, Lingjiao</creator><creator>Yao, Jian</creator><creator>Meng, Xiaohua</creator><creator>Jiang, Han</creator><creator>Xiao, Cheng</creator><creator>Wu, Fusheng</creator><general>Mary Ann Liebert, Inc</general><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>7X8</scope></search><sort><creationdate>20161201</creationdate><title>Identification of Specific Long Non-Coding RNA Expression: Profile and Analysis of Association with Clinicopathologic Characteristics and BRAF Mutation in Papillary Thyroid Cancer</title><author>Wang, Qiangfeng ; Yang, Huanxia ; Wu, Lingjiao ; Yao, Jian ; Meng, Xiaohua ; Jiang, Han ; Xiao, Cheng ; Wu, Fusheng</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c337t-cc767885ea7ec6dd05abb091521c3e7be20575c34061fe944e9c59dda872ee1e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Adult</topic><topic>Carcinoma, Papillary - genetics</topic><topic>Carcinoma, Papillary - pathology</topic><topic>Cell Line, Tumor</topic><topic>Female</topic><topic>Gene Expression Regulation, Neoplastic</topic><topic>Humans</topic><topic>Male</topic><topic>Middle Aged</topic><topic>Mutation</topic><topic>Proto-Oncogene Proteins B-raf - genetics</topic><topic>RNA, Long Noncoding - genetics</topic><topic>Sequence Analysis, RNA</topic><topic>Thyroid Cancer and Nodules</topic><topic>Thyroid Neoplasms - genetics</topic><topic>Thyroid Neoplasms - pathology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Qiangfeng</creatorcontrib><creatorcontrib>Yang, Huanxia</creatorcontrib><creatorcontrib>Wu, Lingjiao</creatorcontrib><creatorcontrib>Yao, Jian</creatorcontrib><creatorcontrib>Meng, Xiaohua</creatorcontrib><creatorcontrib>Jiang, Han</creatorcontrib><creatorcontrib>Xiao, Cheng</creatorcontrib><creatorcontrib>Wu, Fusheng</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Thyroid (New York, N.Y.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Qiangfeng</au><au>Yang, Huanxia</au><au>Wu, Lingjiao</au><au>Yao, Jian</au><au>Meng, Xiaohua</au><au>Jiang, Han</au><au>Xiao, Cheng</au><au>Wu, Fusheng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of Specific Long Non-Coding RNA Expression: Profile and Analysis of Association with Clinicopathologic Characteristics and BRAF Mutation in Papillary Thyroid Cancer</atitle><jtitle>Thyroid (New York, N.Y.)</jtitle><addtitle>Thyroid</addtitle><date>2016-12-01</date><risdate>2016</risdate><volume>26</volume><issue>12</issue><spage>1719</spage><epage>1732</epage><pages>1719-1732</pages><issn>1050-7256</issn><eissn>1557-9077</eissn><abstract>Background:
In recent years, long non-coding RNAs (lncRNAs) have been shown to play a critical regulatory role in cancer biology. However, the contribution of lncRNAs to papillary thyroid cancer (PTC) remains largely unknown.
Methods:
RNA sequencing and quantitative reverse transcription polymerase chain reaction were used to detect and verify changes to the transcriptome profile in 12 PTC tissues compared to paired normal adjacent tissues. The statistical correlation between differentially expressed lncRNAs and clinicopathologic characteristics was analyzed, and potential lncRNA functions were predicted by examining annotations for the co-expressed mRNAs. Furthermore, the specific subgroup patterns of the PTC transcriptome remodeled by
BRAF
mutations were also analyzed.
Results:
A total of 188 lncRNAs and 505 mRNAs were differentially expressed in 50% or more of the PTC tissues (fold change >2;
p
< 0.05) as assessed by RNA-sequencing compared with paired normal adjacent tissues. Forty-seven lncRNAs and 39 mRNAs were verified in 31 pairs of PTC specimens using quantitative reverse transcription polymerase chain reaction, and the results were consistent with the RNA sequencing data. The lncRNAs NONHSAT076747 and NONHSAT122730 were associated with lymph node metastasis, and NONHSAG051968 expression was negatively correlated with tumor size. A co-expression network between differentially expressed lncRNAs and protein-coding RNAs was constructed and analyzed, and functional analysis suggested that the differentially expressed genes mainly participate in ECM–receptor interactions and the focal adhesion pathway. Furthermore, a specific PTC transcriptome subtype pattern stratified by
BRAF
mutation was also uncovered. The
p53
signaling pathway was the most highly enriched pathway among the
BRAF
mutation-related genes.
Conclusions:
This study reveals specific changes to the lncRNA profile associated with PTC, and provides new insight into its pathogenesis. The PTC-associated lncRNAs NONHSAG051968, NONHSAT076747, and NONHSAT122730 might be potential diagnostic and therapeutic targets for PTC patients, and lncRNAs with subtype-specific expression stratified by
BRAF
mutation might be significant in individual molecular subtypes.</abstract><cop>United States</cop><pub>Mary Ann Liebert, Inc</pub><pmid>27758138</pmid><doi>10.1089/thy.2016.0024</doi><tpages>14</tpages></addata></record> |
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| ispartof | Thyroid (New York, N.Y.), 2016-12, Vol.26 (12), p.1719-1732 |
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| source | MEDLINE; Alma/SFX Local Collection |
| subjects | Adult Carcinoma, Papillary - genetics Carcinoma, Papillary - pathology Cell Line, Tumor Female Gene Expression Regulation, Neoplastic Humans Male Middle Aged Mutation Proto-Oncogene Proteins B-raf - genetics RNA, Long Noncoding - genetics Sequence Analysis, RNA Thyroid Cancer and Nodules Thyroid Neoplasms - genetics Thyroid Neoplasms - pathology |
| title | Identification of Specific Long Non-Coding RNA Expression: Profile and Analysis of Association with Clinicopathologic Characteristics and BRAF Mutation in Papillary Thyroid Cancer |
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