PMID- 34282769 OWN - NLM STAT- PubMed-not-MEDLINE VI - 13 IP - 13 TI - Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis. LA - eng PT - Journal Article PL - Switzerland TA - Cancers (basel) JT - Cancers JID - 101526829 IS - 2072-6694 (Print) LID - 3371 [pii] LID - 10.3390/cancers13133371 [doi] FAU - Savino, Aurora AU - Savino A AUID- ORCID: 0000-0002-0783-7191 AD - Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy. FAU - De Marzo, Niccolò AU - De Marzo N AD - Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy. FAU - Provero, Paolo AU - Provero P AUID- ORCID: 0000-0001-8664-8630 AD - Department of Neurosciences "Rita Levi Montalcini", University of Turin, Corso Massimo D'Azeglio 52, 10126 Turin, Italy. AD - Center for Omics Sciences, Ospedale San Raffaele IRCCS, Via Olgettina 60, 20132 Milan, Italy. FAU - Poli, Valeria AU - Poli V AD - Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy. IS - 2072-6694 (Linking) OTO - NOTNLM OT - LCM OT - breast cancer OT - database OT - meta-analysis OT - microarray OT - microdissection OT - transcriptomics OT - tumor microenvironment OT - tumor stroma PMC - PMC8268805 LR - 20231101 DP - 2021 Jul 05 DEP - 20210705 AB - Transcriptome data provide a valuable resource for the study of cancer molecular mechanisms, but technical biases, sample heterogeneity, and small sample sizes result in poorly reproducible lists of regulated genes. Additionally, the presence of multiple cellular components contributing to cancer development complicates the interpretation of bulk transcriptomic profiles. To address these issues, we collected 48 microarray datasets derived from laser capture microdissected stroma or epithelium in breast tumors and performed a meta-analysis identifying robust lists of differentially expressed genes. This was used to create a database with carefully harmonized metadata that we make freely available to the research community. As predicted, combining the results of multiple datasets improved statistical power. Moreover, the separate analysis of stroma and epithelium allowed the identification of genes with different contributions in each compartment, which would not be detected by bulk analysis due to their distinct regulation in the two compartments. Our method can be profitably used to help in the discovery of biomarkers and the identification of functionally relevant genes in both the stroma and the epithelium. This database was made to be readily accessible through a user-friendly web interface.