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Comprehensive Analysis of Key mRNAs and lncRNAs in Osteosarcoma Response to Preoperative Chemotherapy with Prognostic Values
Objective Osteosarcoma is one of the most common types of bone sarcoma with a poor prognosis. However, identifying the predictive factors that contribute to the response to neoadjuvant chemotherapy remains a significant challenge. Methods A public data series (GSE87437) was downloaded to identify di...
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| Published in: | Current medical science 2021-10, Vol.41 (5), p.916-929 |
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| Main Authors: | , , , , , , , |
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| container_title | Current medical science |
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| creator | Li, Mi Cheng, Wei-ting Li, Hao Zhang, Zhi Lu, Xiao-li Deng, Si-si Li, Jian Yang, Cai-hong |
| description | Objective
Osteosarcoma is one of the most common types of bone sarcoma with a poor prognosis. However, identifying the predictive factors that contribute to the response to neoadjuvant chemotherapy remains a significant challenge.
Methods
A public data series (GSE87437) was downloaded to identify differentially expressed genes (DEGs) and differentially expressed lncRNAs (DElncRNAs) between osteosarcoma patients that do and do not respond to preoperative chemotherapy. Subsequently, functional analysis of the transcriptome expression profile, regulatory networks of DEGs and DElncRNAs, competing endogenous RNAs (ceRNA) and protein-protein interaction networks were performed. Furthermore, the function, pathway, and survival analysis of hub genes was performed and drug and disease relationship prediction of DElncRNA was carried out.
Results
A total of 626 DEGs, 26 DElncRNAs, and 18 hub genes were identified. However, only one gene and two lncRNAs were found to be suitable as candidate gene and lncRNAs respectively.
Conclusion
The DEGs, hub genes, candidate gene, and candidate lncRNAs screened out in this context were considered as potential biomarkers for the response to neoadjuvant chemotherapy of osteosarcoma. |
| doi_str_mv | 10.1007/s11596-021-2430-2 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2585462093</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2585462093</sourcerecordid><originalsourceid>FETCH-LOGICAL-c332t-102366bb668c3f3f0a8e55f316a2a2c9c6b362c67c6bbc0db66be7cabd4014383</originalsourceid><addsrcrecordid>eNp9kEtPwzAQhC0EgqrwA7ggH7kE_Ejc5FhVvASiqALEzXLcDQ1K7OBNQZX48bi0cOS0s5rZWekj5JizM87Y6Bw5zwqVMMETkUqWiB0yEJmQSV4UL7tRs-jGnR2QI8S6ZJILJXku9smBTNWIFywdkK-Jb7sAC3BYfwAdO9OssEbqK3oLK9rO7sdIjZvTxtkfXTs6xR48mmB9a-gMsPMOgfaePgTwHQTTr6smC2h9v4hrt6Kfdb-Itn91Hvva0mfTLAEPyV5lGoSj7RySp8uLx8l1cje9upmM7xIrpegTzoRUqiyVyq2sZMVMDllWSa6MMMIWVpVSCatGUZSWzWOwhJE15TxlPJW5HJLTTW8X_Hv82-u2RgtNYxz4JWqR5VmqIjAZo3wTtcEjBqh0F-rWhJXmTK-56w13HbnrNXct4s3Jtn5ZtjD_u_ilHANiE8BouVcI-s0vQ0SN_7R-A6X7j2I</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2585462093</pqid></control><display><type>article</type><title>Comprehensive Analysis of Key mRNAs and lncRNAs in Osteosarcoma Response to Preoperative Chemotherapy with Prognostic Values</title><source>Springer Nature</source><creator>Li, Mi ; Cheng, Wei-ting ; Li, Hao ; Zhang, Zhi ; Lu, Xiao-li ; Deng, Si-si ; Li, Jian ; Yang, Cai-hong</creator><creatorcontrib>Li, Mi ; Cheng, Wei-ting ; Li, Hao ; Zhang, Zhi ; Lu, Xiao-li ; Deng, Si-si ; Li, Jian ; Yang, Cai-hong</creatorcontrib><description>Objective
Osteosarcoma is one of the most common types of bone sarcoma with a poor prognosis. However, identifying the predictive factors that contribute to the response to neoadjuvant chemotherapy remains a significant challenge.
Methods
A public data series (GSE87437) was downloaded to identify differentially expressed genes (DEGs) and differentially expressed lncRNAs (DElncRNAs) between osteosarcoma patients that do and do not respond to preoperative chemotherapy. Subsequently, functional analysis of the transcriptome expression profile, regulatory networks of DEGs and DElncRNAs, competing endogenous RNAs (ceRNA) and protein-protein interaction networks were performed. Furthermore, the function, pathway, and survival analysis of hub genes was performed and drug and disease relationship prediction of DElncRNA was carried out.
Results
A total of 626 DEGs, 26 DElncRNAs, and 18 hub genes were identified. However, only one gene and two lncRNAs were found to be suitable as candidate gene and lncRNAs respectively.
Conclusion
The DEGs, hub genes, candidate gene, and candidate lncRNAs screened out in this context were considered as potential biomarkers for the response to neoadjuvant chemotherapy of osteosarcoma.</description><identifier>ISSN: 2096-5230</identifier><identifier>EISSN: 2523-899X</identifier><identifier>DOI: 10.1007/s11596-021-2430-2</identifier><identifier>PMID: 34671904</identifier><language>eng</language><publisher>Wuhan: Huazhong University of Science and Technology</publisher><subject>Biomarkers, Tumor - genetics ; Bone Neoplasms - drug therapy ; Bone Neoplasms - genetics ; Bone Neoplasms - surgery ; Computational Biology - methods ; Databases, Genetic ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Humans ; Medicine ; Medicine & Public Health ; Neoadjuvant Therapy ; Osteosarcoma - drug therapy ; Osteosarcoma - genetics ; Osteosarcoma - surgery ; Prognosis ; RNA, Long Noncoding - genetics ; Survival Analysis</subject><ispartof>Current medical science, 2021-10, Vol.41 (5), p.916-929</ispartof><rights>Huazhong University of Science and Technology 2021</rights><rights>2021. Huazhong University of Science and Technology.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c332t-102366bb668c3f3f0a8e55f316a2a2c9c6b362c67c6bbc0db66be7cabd4014383</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34671904$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Mi</creatorcontrib><creatorcontrib>Cheng, Wei-ting</creatorcontrib><creatorcontrib>Li, Hao</creatorcontrib><creatorcontrib>Zhang, Zhi</creatorcontrib><creatorcontrib>Lu, Xiao-li</creatorcontrib><creatorcontrib>Deng, Si-si</creatorcontrib><creatorcontrib>Li, Jian</creatorcontrib><creatorcontrib>Yang, Cai-hong</creatorcontrib><title>Comprehensive Analysis of Key mRNAs and lncRNAs in Osteosarcoma Response to Preoperative Chemotherapy with Prognostic Values</title><title>Current medical science</title><addtitle>CURR MED SCI</addtitle><addtitle>Curr Med Sci</addtitle><description>Objective
Osteosarcoma is one of the most common types of bone sarcoma with a poor prognosis. However, identifying the predictive factors that contribute to the response to neoadjuvant chemotherapy remains a significant challenge.
Methods
A public data series (GSE87437) was downloaded to identify differentially expressed genes (DEGs) and differentially expressed lncRNAs (DElncRNAs) between osteosarcoma patients that do and do not respond to preoperative chemotherapy. Subsequently, functional analysis of the transcriptome expression profile, regulatory networks of DEGs and DElncRNAs, competing endogenous RNAs (ceRNA) and protein-protein interaction networks were performed. Furthermore, the function, pathway, and survival analysis of hub genes was performed and drug and disease relationship prediction of DElncRNA was carried out.
Results
A total of 626 DEGs, 26 DElncRNAs, and 18 hub genes were identified. However, only one gene and two lncRNAs were found to be suitable as candidate gene and lncRNAs respectively.
Conclusion
The DEGs, hub genes, candidate gene, and candidate lncRNAs screened out in this context were considered as potential biomarkers for the response to neoadjuvant chemotherapy of osteosarcoma.</description><subject>Biomarkers, Tumor - genetics</subject><subject>Bone Neoplasms - drug therapy</subject><subject>Bone Neoplasms - genetics</subject><subject>Bone Neoplasms - surgery</subject><subject>Computational Biology - methods</subject><subject>Databases, Genetic</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Gene Regulatory Networks</subject><subject>Humans</subject><subject>Medicine</subject><subject>Medicine & Public Health</subject><subject>Neoadjuvant Therapy</subject><subject>Osteosarcoma - drug therapy</subject><subject>Osteosarcoma - genetics</subject><subject>Osteosarcoma - surgery</subject><subject>Prognosis</subject><subject>RNA, Long Noncoding - genetics</subject><subject>Survival Analysis</subject><issn>2096-5230</issn><issn>2523-899X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp9kEtPwzAQhC0EgqrwA7ggH7kE_Ejc5FhVvASiqALEzXLcDQ1K7OBNQZX48bi0cOS0s5rZWekj5JizM87Y6Bw5zwqVMMETkUqWiB0yEJmQSV4UL7tRs-jGnR2QI8S6ZJILJXku9smBTNWIFywdkK-Jb7sAC3BYfwAdO9OssEbqK3oLK9rO7sdIjZvTxtkfXTs6xR48mmB9a-gMsPMOgfaePgTwHQTTr6smC2h9v4hrt6Kfdb-Itn91Hvva0mfTLAEPyV5lGoSj7RySp8uLx8l1cje9upmM7xIrpegTzoRUqiyVyq2sZMVMDllWSa6MMMIWVpVSCatGUZSWzWOwhJE15TxlPJW5HJLTTW8X_Hv82-u2RgtNYxz4JWqR5VmqIjAZo3wTtcEjBqh0F-rWhJXmTK-56w13HbnrNXct4s3Jtn5ZtjD_u_ilHANiE8BouVcI-s0vQ0SN_7R-A6X7j2I</recordid><startdate>20211001</startdate><enddate>20211001</enddate><creator>Li, Mi</creator><creator>Cheng, Wei-ting</creator><creator>Li, Hao</creator><creator>Zhang, Zhi</creator><creator>Lu, Xiao-li</creator><creator>Deng, Si-si</creator><creator>Li, Jian</creator><creator>Yang, Cai-hong</creator><general>Huazhong University of Science and Technology</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>20211001</creationdate><title>Comprehensive Analysis of Key mRNAs and lncRNAs in Osteosarcoma Response to Preoperative Chemotherapy with Prognostic Values</title><author>Li, Mi ; Cheng, Wei-ting ; Li, Hao ; Zhang, Zhi ; Lu, Xiao-li ; Deng, Si-si ; Li, Jian ; Yang, Cai-hong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c332t-102366bb668c3f3f0a8e55f316a2a2c9c6b362c67c6bbc0db66be7cabd4014383</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Biomarkers, Tumor - genetics</topic><topic>Bone Neoplasms - drug therapy</topic><topic>Bone Neoplasms - genetics</topic><topic>Bone Neoplasms - surgery</topic><topic>Computational Biology - methods</topic><topic>Databases, Genetic</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Neoplastic</topic><topic>Gene Regulatory Networks</topic><topic>Humans</topic><topic>Medicine</topic><topic>Medicine & Public Health</topic><topic>Neoadjuvant Therapy</topic><topic>Osteosarcoma - drug therapy</topic><topic>Osteosarcoma - genetics</topic><topic>Osteosarcoma - surgery</topic><topic>Prognosis</topic><topic>RNA, Long Noncoding - genetics</topic><topic>Survival Analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Mi</creatorcontrib><creatorcontrib>Cheng, Wei-ting</creatorcontrib><creatorcontrib>Li, Hao</creatorcontrib><creatorcontrib>Zhang, Zhi</creatorcontrib><creatorcontrib>Lu, Xiao-li</creatorcontrib><creatorcontrib>Deng, Si-si</creatorcontrib><creatorcontrib>Li, Jian</creatorcontrib><creatorcontrib>Yang, Cai-hong</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>Current medical science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Mi</au><au>Cheng, Wei-ting</au><au>Li, Hao</au><au>Zhang, Zhi</au><au>Lu, Xiao-li</au><au>Deng, Si-si</au><au>Li, Jian</au><au>Yang, Cai-hong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comprehensive Analysis of Key mRNAs and lncRNAs in Osteosarcoma Response to Preoperative Chemotherapy with Prognostic Values</atitle><jtitle>Current medical science</jtitle><stitle>CURR MED SCI</stitle><addtitle>Curr Med Sci</addtitle><date>2021-10-01</date><risdate>2021</risdate><volume>41</volume><issue>5</issue><spage>916</spage><epage>929</epage><pages>916-929</pages><issn>2096-5230</issn><eissn>2523-899X</eissn><abstract>Objective
Osteosarcoma is one of the most common types of bone sarcoma with a poor prognosis. However, identifying the predictive factors that contribute to the response to neoadjuvant chemotherapy remains a significant challenge.
Methods
A public data series (GSE87437) was downloaded to identify differentially expressed genes (DEGs) and differentially expressed lncRNAs (DElncRNAs) between osteosarcoma patients that do and do not respond to preoperative chemotherapy. Subsequently, functional analysis of the transcriptome expression profile, regulatory networks of DEGs and DElncRNAs, competing endogenous RNAs (ceRNA) and protein-protein interaction networks were performed. Furthermore, the function, pathway, and survival analysis of hub genes was performed and drug and disease relationship prediction of DElncRNA was carried out.
Results
A total of 626 DEGs, 26 DElncRNAs, and 18 hub genes were identified. However, only one gene and two lncRNAs were found to be suitable as candidate gene and lncRNAs respectively.
Conclusion
The DEGs, hub genes, candidate gene, and candidate lncRNAs screened out in this context were considered as potential biomarkers for the response to neoadjuvant chemotherapy of osteosarcoma.</abstract><cop>Wuhan</cop><pub>Huazhong University of Science and Technology</pub><pmid>34671904</pmid><doi>10.1007/s11596-021-2430-2</doi><tpages>14</tpages></addata></record> |
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| source | Springer Nature |
| subjects | Biomarkers, Tumor - genetics Bone Neoplasms - drug therapy Bone Neoplasms - genetics Bone Neoplasms - surgery Computational Biology - methods Databases, Genetic Gene Expression Profiling Gene Expression Regulation, Neoplastic Gene Regulatory Networks Humans Medicine Medicine & Public Health Neoadjuvant Therapy Osteosarcoma - drug therapy Osteosarcoma - genetics Osteosarcoma - surgery Prognosis RNA, Long Noncoding - genetics Survival Analysis |
| title | Comprehensive Analysis of Key mRNAs and lncRNAs in Osteosarcoma Response to Preoperative Chemotherapy with Prognostic Values |
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