Identification of Breast Cancer Subtype-Specific Biomarkers by Integrating Copy Number Alterations and Gene Expression Profiles
<i>Background and Objectives</i>: Breast cancer is a heterogeneous disease categorized into four subtypes. Previous studies have shown that copy number alterations of several genes are implicated with the development and progression of many cancers. This study evaluates the effects of DN...
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doaj-5e94e1fddd8c4ff8918fd15b2fc1f7142021-03-13T00:07:18ZengMDPI AGMedicina1010-660X1648-91442021-03-015726126110.3390/medicina57030261Identification of Breast Cancer Subtype-Specific Biomarkers by Integrating Copy Number Alterations and Gene Expression ProfilesClaudia Cava0Mirko Pisati1Marco Frasca2Isabella Castiglioni3Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, Segrate-Milan, 20090 Milan, ItalyInstitute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, Segrate-Milan, 20090 Milan, ItalyDepartment of Computer Science, Università degli Studi di Milano, Via Celoria 18, 20133 Milano, ItalyDepartment of Physics “Giuseppe Occhialini”, University of Milan-Bicocca Piazza dell’Ateneo Nuovo, 20126 Milan, Italy<i>Background and Objectives</i>: Breast cancer is a heterogeneous disease categorized into four subtypes. Previous studies have shown that copy number alterations of several genes are implicated with the development and progression of many cancers. This study evaluates the effects of DNA copy number alterations on gene expression levels in different breast cancer subtypes. <i>Materials and Methods</i>: We performed a computational analysis integrating copy number alterations and gene expression profiles in 1024 breast cancer samples grouped into four molecular subtypes: luminal A, luminal B, HER2, and basal. <i>Results</i>: Our analyses identified several genes correlated in all subtypes such as <i>KIAA1967</i> and <i>MCPH1</i>. In addition, several subtype-specific genes that showed a significant correlation between copy number and gene expression profiles were detected: <i>SMARCB1</i>, <i>AZIN1</i>, <i>MTDH</i> in luminal A, <i>PPP2R5E</i>, <i>APEX1</i>, <i>GCN5</i> in luminal B, <i>TNFAIP1</i>, <i>PCYT2</i>, <i>DIABLO</i> in HER2, and <i>FAM175B</i>, <i>SENP5</i>, <i>SCAF1</i> in basal subtype. <i>Conclusions</i>: This study showed that computational analyses integrating copy number and gene expression can contribute to unveil the molecular mechanisms of cancer and identify new subtype-specific biomarkers.https://www.mdpi.com/1648-9144/57/3/261copy number alterationgene expressionbreast cancer subtypes |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Claudia Cava Mirko Pisati Marco Frasca Isabella Castiglioni |
spellingShingle |
Claudia Cava Mirko Pisati Marco Frasca Isabella Castiglioni Identification of Breast Cancer Subtype-Specific Biomarkers by Integrating Copy Number Alterations and Gene Expression Profiles Medicina copy number alteration gene expression breast cancer subtypes |
author_facet |
Claudia Cava Mirko Pisati Marco Frasca Isabella Castiglioni |
author_sort |
Claudia Cava |
title |
Identification of Breast Cancer Subtype-Specific Biomarkers by Integrating Copy Number Alterations and Gene Expression Profiles |
title_short |
Identification of Breast Cancer Subtype-Specific Biomarkers by Integrating Copy Number Alterations and Gene Expression Profiles |
title_full |
Identification of Breast Cancer Subtype-Specific Biomarkers by Integrating Copy Number Alterations and Gene Expression Profiles |
title_fullStr |
Identification of Breast Cancer Subtype-Specific Biomarkers by Integrating Copy Number Alterations and Gene Expression Profiles |
title_full_unstemmed |
Identification of Breast Cancer Subtype-Specific Biomarkers by Integrating Copy Number Alterations and Gene Expression Profiles |
title_sort |
identification of breast cancer subtype-specific biomarkers by integrating copy number alterations and gene expression profiles |
publisher |
MDPI AG |
series |
Medicina |
issn |
1010-660X 1648-9144 |
publishDate |
2021-03-01 |
description |
<i>Background and Objectives</i>: Breast cancer is a heterogeneous disease categorized into four subtypes. Previous studies have shown that copy number alterations of several genes are implicated with the development and progression of many cancers. This study evaluates the effects of DNA copy number alterations on gene expression levels in different breast cancer subtypes. <i>Materials and Methods</i>: We performed a computational analysis integrating copy number alterations and gene expression profiles in 1024 breast cancer samples grouped into four molecular subtypes: luminal A, luminal B, HER2, and basal. <i>Results</i>: Our analyses identified several genes correlated in all subtypes such as <i>KIAA1967</i> and <i>MCPH1</i>. In addition, several subtype-specific genes that showed a significant correlation between copy number and gene expression profiles were detected: <i>SMARCB1</i>, <i>AZIN1</i>, <i>MTDH</i> in luminal A, <i>PPP2R5E</i>, <i>APEX1</i>, <i>GCN5</i> in luminal B, <i>TNFAIP1</i>, <i>PCYT2</i>, <i>DIABLO</i> in HER2, and <i>FAM175B</i>, <i>SENP5</i>, <i>SCAF1</i> in basal subtype. <i>Conclusions</i>: This study showed that computational analyses integrating copy number and gene expression can contribute to unveil the molecular mechanisms of cancer and identify new subtype-specific biomarkers. |
topic |
copy number alteration gene expression breast cancer subtypes |
url |
https://www.mdpi.com/1648-9144/57/3/261 |
work_keys_str_mv |
AT claudiacava identificationofbreastcancersubtypespecificbiomarkersbyintegratingcopynumberalterationsandgeneexpressionprofiles AT mirkopisati identificationofbreastcancersubtypespecificbiomarkersbyintegratingcopynumberalterationsandgeneexpressionprofiles AT marcofrasca identificationofbreastcancersubtypespecificbiomarkersbyintegratingcopynumberalterationsandgeneexpressionprofiles AT isabellacastiglioni identificationofbreastcancersubtypespecificbiomarkersbyintegratingcopynumberalterationsandgeneexpressionprofiles |
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1724222292617068544 |