Quantitative proteomics reveals stage-specific protein regulation of triple negative breast cancer
Backgrounds Triple negative breast cancer (TNBC) is a heterogeneous disease with more aggressive clinical courses than other subtypes of breast cancer. In this study, we performed high-resolution mass spectrometry-based quantitative proteomics with TNBC clinical tissue specimens to explore the early...
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Veröffentlicht in: | Breast cancer research and treatment 2021, Vol.185 (1), p.39-52 |
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creator | Lin, Yuxiang Lin, Ling Fu, Fangmeng Wang, Chuan Hu, Anqi Xie, Juanjuan Jiang, Meichen Wang, Zhenxin Yang, Lujie Guo, Rongrong Yang, Pengyuan Shen, Huali |
description | Backgrounds
Triple negative breast cancer (TNBC) is a heterogeneous disease with more aggressive clinical courses than other subtypes of breast cancer. In this study, we performed high-resolution mass spectrometry-based quantitative proteomics with TNBC clinical tissue specimens to explore the early and sensitive diagnostic signatures and potential therapeutic targets for TNBC patients.
Methods
We performed an iTRAQ labeling coupled LC–MS/MS approach to explore the global proteome in tumor tissues and corresponding para-tumor tissues from 24 patients with grade I-II and grade III primary TNBC. Relative peptide quantification and protein identification were performed by Proteome Discoverer™ software with Mascot search engine. Differentially expressed proteins were analyzed by bioinformatic analyses, including GO function classification annotation and KEGG enrichment analysis. Pathway analyses for protein–protein interactions and upstream regulations of differentially expressed candidates were performed by Ingenuity Pathway Analysis (IPA) software.
Results
Totally, 5401 unique proteins were identified and quantified in different stage of TNBCs. 845 proteins were changed in patients with grade I or II TNBC, among which 304 were up-regulated and 541 were down-regulated. Meanwhile, for patients with grade III TNBC, 358 proteins were increased and 651 proteins were decreased. Comparing to para-cancerous tissues, various signaling pathways and metabolic processes, including PPAR pathways, PI3K-Akt pathway, one-carbon metabolism, amino acid synthesis, and lipid metabolism were activated in TNBC cancer tissues. Death receptor signaling was significantly activated in grade I-II TNBCs, however, remarkably inhibited in grade III TNBCs. Western blot experiments were conducted to validate expression levels of CYCS, HMGA1 and XIAP with samples from individual patients.
Conclusions
Overall, our proteomic data presented precise quantification of potential signatures, signaling pathways, regulatory networks, and characteristic differences in each clinicopathological subgroup. The proteome provides complementary information for TNBC accurate subtype classification and therapeutic targets research. |
doi_str_mv | 10.1007/s10549-020-05916-8 |
format | Article |
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Triple negative breast cancer (TNBC) is a heterogeneous disease with more aggressive clinical courses than other subtypes of breast cancer. In this study, we performed high-resolution mass spectrometry-based quantitative proteomics with TNBC clinical tissue specimens to explore the early and sensitive diagnostic signatures and potential therapeutic targets for TNBC patients.
Methods
We performed an iTRAQ labeling coupled LC–MS/MS approach to explore the global proteome in tumor tissues and corresponding para-tumor tissues from 24 patients with grade I-II and grade III primary TNBC. Relative peptide quantification and protein identification were performed by Proteome Discoverer™ software with Mascot search engine. Differentially expressed proteins were analyzed by bioinformatic analyses, including GO function classification annotation and KEGG enrichment analysis. Pathway analyses for protein–protein interactions and upstream regulations of differentially expressed candidates were performed by Ingenuity Pathway Analysis (IPA) software.
Results
Totally, 5401 unique proteins were identified and quantified in different stage of TNBCs. 845 proteins were changed in patients with grade I or II TNBC, among which 304 were up-regulated and 541 were down-regulated. Meanwhile, for patients with grade III TNBC, 358 proteins were increased and 651 proteins were decreased. Comparing to para-cancerous tissues, various signaling pathways and metabolic processes, including PPAR pathways, PI3K-Akt pathway, one-carbon metabolism, amino acid synthesis, and lipid metabolism were activated in TNBC cancer tissues. Death receptor signaling was significantly activated in grade I-II TNBCs, however, remarkably inhibited in grade III TNBCs. Western blot experiments were conducted to validate expression levels of CYCS, HMGA1 and XIAP with samples from individual patients.
Conclusions
Overall, our proteomic data presented precise quantification of potential signatures, signaling pathways, regulatory networks, and characteristic differences in each clinicopathological subgroup. The proteome provides complementary information for TNBC accurate subtype classification and therapeutic targets research.</description><identifier>ISSN: 0167-6806</identifier><identifier>EISSN: 1573-7217</identifier><identifier>DOI: 10.1007/s10549-020-05916-8</identifier><identifier>PMID: 32920739</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>1-Phosphatidylinositol 3-kinase ; AKT protein ; Amino acids ; Breast cancer ; Cancer research ; Computer programs ; Health aspects ; Internet/Web search services ; Lipid metabolism ; Mass spectrometry ; Mass spectroscopy ; Medicine ; Medicine & Public Health ; Metabolism ; Oncology ; Peroxisome proliferator-activated receptors ; Physiological aspects ; Preclinical Study ; Protein interaction ; Protein-protein interactions ; Proteins ; Proteomes ; Proteomics ; Signal transduction ; Synthesis ; Therapeutic applications ; Therapeutic targets ; XIAP protein</subject><ispartof>Breast cancer research and treatment, 2021, Vol.185 (1), p.39-52</ispartof><rights>Springer Science+Business Media, LLC, part of Springer Nature 2020</rights><rights>COPYRIGHT 2021 Springer</rights><rights>Springer Science+Business Media, LLC, part of Springer Nature 2020.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c473t-216d64500aaf3076d2fab0b709a3a24286e96e8327085e80de905646af129d1a3</citedby><cites>FETCH-LOGICAL-c473t-216d64500aaf3076d2fab0b709a3a24286e96e8327085e80de905646af129d1a3</cites><orcidid>0000-0002-6766-5432</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10549-020-05916-8$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10549-020-05916-8$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32920739$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lin, Yuxiang</creatorcontrib><creatorcontrib>Lin, Ling</creatorcontrib><creatorcontrib>Fu, Fangmeng</creatorcontrib><creatorcontrib>Wang, Chuan</creatorcontrib><creatorcontrib>Hu, Anqi</creatorcontrib><creatorcontrib>Xie, Juanjuan</creatorcontrib><creatorcontrib>Jiang, Meichen</creatorcontrib><creatorcontrib>Wang, Zhenxin</creatorcontrib><creatorcontrib>Yang, Lujie</creatorcontrib><creatorcontrib>Guo, Rongrong</creatorcontrib><creatorcontrib>Yang, Pengyuan</creatorcontrib><creatorcontrib>Shen, Huali</creatorcontrib><title>Quantitative proteomics reveals stage-specific protein regulation of triple negative breast cancer</title><title>Breast cancer research and treatment</title><addtitle>Breast Cancer Res Treat</addtitle><addtitle>Breast Cancer Res Treat</addtitle><description>Backgrounds
Triple negative breast cancer (TNBC) is a heterogeneous disease with more aggressive clinical courses than other subtypes of breast cancer. In this study, we performed high-resolution mass spectrometry-based quantitative proteomics with TNBC clinical tissue specimens to explore the early and sensitive diagnostic signatures and potential therapeutic targets for TNBC patients.
Methods
We performed an iTRAQ labeling coupled LC–MS/MS approach to explore the global proteome in tumor tissues and corresponding para-tumor tissues from 24 patients with grade I-II and grade III primary TNBC. Relative peptide quantification and protein identification were performed by Proteome Discoverer™ software with Mascot search engine. Differentially expressed proteins were analyzed by bioinformatic analyses, including GO function classification annotation and KEGG enrichment analysis. Pathway analyses for protein–protein interactions and upstream regulations of differentially expressed candidates were performed by Ingenuity Pathway Analysis (IPA) software.
Results
Totally, 5401 unique proteins were identified and quantified in different stage of TNBCs. 845 proteins were changed in patients with grade I or II TNBC, among which 304 were up-regulated and 541 were down-regulated. Meanwhile, for patients with grade III TNBC, 358 proteins were increased and 651 proteins were decreased. Comparing to para-cancerous tissues, various signaling pathways and metabolic processes, including PPAR pathways, PI3K-Akt pathway, one-carbon metabolism, amino acid synthesis, and lipid metabolism were activated in TNBC cancer tissues. Death receptor signaling was significantly activated in grade I-II TNBCs, however, remarkably inhibited in grade III TNBCs. Western blot experiments were conducted to validate expression levels of CYCS, HMGA1 and XIAP with samples from individual patients.
Conclusions
Overall, our proteomic data presented precise quantification of potential signatures, signaling pathways, regulatory networks, and characteristic differences in each clinicopathological subgroup. The proteome provides complementary information for TNBC accurate subtype classification and therapeutic targets research.</description><subject>1-Phosphatidylinositol 3-kinase</subject><subject>AKT protein</subject><subject>Amino acids</subject><subject>Breast cancer</subject><subject>Cancer research</subject><subject>Computer programs</subject><subject>Health aspects</subject><subject>Internet/Web search services</subject><subject>Lipid metabolism</subject><subject>Mass spectrometry</subject><subject>Mass spectroscopy</subject><subject>Medicine</subject><subject>Medicine & Public Health</subject><subject>Metabolism</subject><subject>Oncology</subject><subject>Peroxisome proliferator-activated receptors</subject><subject>Physiological aspects</subject><subject>Preclinical Study</subject><subject>Protein interaction</subject><subject>Protein-protein interactions</subject><subject>Proteins</subject><subject>Proteomes</subject><subject>Proteomics</subject><subject>Signal transduction</subject><subject>Synthesis</subject><subject>Therapeutic applications</subject><subject>Therapeutic targets</subject><subject>XIAP protein</subject><issn>0167-6806</issn><issn>1573-7217</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNp9klFrFTEQhYMo9nr1D_ggC4L4snWSbJLdx1JsFQoi6HPI7s7epuxNrkm24L93rlutFZE8BDLfOcycDGMvOZxyAPMuc1BNV4OAGlTHdd0-YhuujKyN4OYx2wDXptYt6BP2LOcbAOgMdE_ZiRSdACO7Des_Ly4UX1zxt1gdUiwY937IVcJbdHOucnE7rPMBBz_5YSV8oPJumUkUQxWnqiR_mLEKuFt9-oQul2pwYcD0nD2ZyAlf3N1b9vXi_ZfzD_XVp8uP52dX9dAYWWrB9agbBeDcJMHoUUyuh54adtKJRrQaO42tFAZahS2M2IHSjXYTF93Indyyt6sv9fhtwVzs3ucB59kFjEu2ommEpgxo8C17_Rd6E5cUqDuiWiEVcfqe2rkZrQ9TLMkNR1N7phVvtDJKEnX6D4rOiBRkDDh5en8gePOH4JpSLtc5zssxzPwQFCs4pJhzwskekt-79N1ysMcNsOsGWNoA-3MDbEuiV3ejLf0ex9-SX19OgFyBTKWww3Q_-39sfwAPerlp</recordid><startdate>2021</startdate><enddate>2021</enddate><creator>Lin, Yuxiang</creator><creator>Lin, Ling</creator><creator>Fu, Fangmeng</creator><creator>Wang, Chuan</creator><creator>Hu, Anqi</creator><creator>Xie, Juanjuan</creator><creator>Jiang, Meichen</creator><creator>Wang, Zhenxin</creator><creator>Yang, Lujie</creator><creator>Guo, Rongrong</creator><creator>Yang, Pengyuan</creator><creator>Shen, Huali</creator><general>Springer US</general><general>Springer</general><general>Springer Nature B.V</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TO</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>K9-</scope><scope>K9.</scope><scope>M0R</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>MBDVC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-6766-5432</orcidid></search><sort><creationdate>2021</creationdate><title>Quantitative proteomics reveals stage-specific protein regulation of triple negative breast cancer</title><author>Lin, Yuxiang ; Lin, Ling ; Fu, Fangmeng ; Wang, Chuan ; Hu, Anqi ; Xie, Juanjuan ; Jiang, Meichen ; Wang, Zhenxin ; Yang, Lujie ; Guo, Rongrong ; Yang, Pengyuan ; Shen, Huali</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c473t-216d64500aaf3076d2fab0b709a3a24286e96e8327085e80de905646af129d1a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>1-Phosphatidylinositol 3-kinase</topic><topic>AKT protein</topic><topic>Amino acids</topic><topic>Breast cancer</topic><topic>Cancer research</topic><topic>Computer programs</topic><topic>Health aspects</topic><topic>Internet/Web search services</topic><topic>Lipid metabolism</topic><topic>Mass spectrometry</topic><topic>Mass spectroscopy</topic><topic>Medicine</topic><topic>Medicine & Public Health</topic><topic>Metabolism</topic><topic>Oncology</topic><topic>Peroxisome proliferator-activated receptors</topic><topic>Physiological aspects</topic><topic>Preclinical Study</topic><topic>Protein interaction</topic><topic>Protein-protein interactions</topic><topic>Proteins</topic><topic>Proteomes</topic><topic>Proteomics</topic><topic>Signal transduction</topic><topic>Synthesis</topic><topic>Therapeutic applications</topic><topic>Therapeutic targets</topic><topic>XIAP protein</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lin, Yuxiang</creatorcontrib><creatorcontrib>Lin, Ling</creatorcontrib><creatorcontrib>Fu, Fangmeng</creatorcontrib><creatorcontrib>Wang, Chuan</creatorcontrib><creatorcontrib>Hu, Anqi</creatorcontrib><creatorcontrib>Xie, Juanjuan</creatorcontrib><creatorcontrib>Jiang, Meichen</creatorcontrib><creatorcontrib>Wang, Zhenxin</creatorcontrib><creatorcontrib>Yang, Lujie</creatorcontrib><creatorcontrib>Guo, Rongrong</creatorcontrib><creatorcontrib>Yang, Pengyuan</creatorcontrib><creatorcontrib>Shen, Huali</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</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>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Consumer Health Database (Alumni Edition)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Consumer Health Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Research Library (Corporate)</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 China</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><jtitle>Breast cancer research and treatment</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lin, Yuxiang</au><au>Lin, Ling</au><au>Fu, Fangmeng</au><au>Wang, Chuan</au><au>Hu, Anqi</au><au>Xie, Juanjuan</au><au>Jiang, Meichen</au><au>Wang, Zhenxin</au><au>Yang, Lujie</au><au>Guo, Rongrong</au><au>Yang, Pengyuan</au><au>Shen, Huali</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantitative proteomics reveals stage-specific protein regulation of triple negative breast cancer</atitle><jtitle>Breast cancer research and treatment</jtitle><stitle>Breast Cancer Res Treat</stitle><addtitle>Breast Cancer Res Treat</addtitle><date>2021</date><risdate>2021</risdate><volume>185</volume><issue>1</issue><spage>39</spage><epage>52</epage><pages>39-52</pages><issn>0167-6806</issn><eissn>1573-7217</eissn><abstract>Backgrounds
Triple negative breast cancer (TNBC) is a heterogeneous disease with more aggressive clinical courses than other subtypes of breast cancer. In this study, we performed high-resolution mass spectrometry-based quantitative proteomics with TNBC clinical tissue specimens to explore the early and sensitive diagnostic signatures and potential therapeutic targets for TNBC patients.
Methods
We performed an iTRAQ labeling coupled LC–MS/MS approach to explore the global proteome in tumor tissues and corresponding para-tumor tissues from 24 patients with grade I-II and grade III primary TNBC. Relative peptide quantification and protein identification were performed by Proteome Discoverer™ software with Mascot search engine. Differentially expressed proteins were analyzed by bioinformatic analyses, including GO function classification annotation and KEGG enrichment analysis. Pathway analyses for protein–protein interactions and upstream regulations of differentially expressed candidates were performed by Ingenuity Pathway Analysis (IPA) software.
Results
Totally, 5401 unique proteins were identified and quantified in different stage of TNBCs. 845 proteins were changed in patients with grade I or II TNBC, among which 304 were up-regulated and 541 were down-regulated. Meanwhile, for patients with grade III TNBC, 358 proteins were increased and 651 proteins were decreased. Comparing to para-cancerous tissues, various signaling pathways and metabolic processes, including PPAR pathways, PI3K-Akt pathway, one-carbon metabolism, amino acid synthesis, and lipid metabolism were activated in TNBC cancer tissues. Death receptor signaling was significantly activated in grade I-II TNBCs, however, remarkably inhibited in grade III TNBCs. Western blot experiments were conducted to validate expression levels of CYCS, HMGA1 and XIAP with samples from individual patients.
Conclusions
Overall, our proteomic data presented precise quantification of potential signatures, signaling pathways, regulatory networks, and characteristic differences in each clinicopathological subgroup. The proteome provides complementary information for TNBC accurate subtype classification and therapeutic targets research.</abstract><cop>New York</cop><pub>Springer US</pub><pmid>32920739</pmid><doi>10.1007/s10549-020-05916-8</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0002-6766-5432</orcidid></addata></record> |
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subjects | 1-Phosphatidylinositol 3-kinase AKT protein Amino acids Breast cancer Cancer research Computer programs Health aspects Internet/Web search services Lipid metabolism Mass spectrometry Mass spectroscopy Medicine Medicine & Public Health Metabolism Oncology Peroxisome proliferator-activated receptors Physiological aspects Preclinical Study Protein interaction Protein-protein interactions Proteins Proteomes Proteomics Signal transduction Synthesis Therapeutic applications Therapeutic targets XIAP protein |
title | Quantitative proteomics reveals stage-specific protein regulation of triple negative breast cancer |
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