Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA341348 | ENA |
REPOSITORIES: ENA
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Project description:A microRNA signature identifies four subtypes of triple-negative breast cancer II
| PRJNA341352 | ENA
Project description:Breast cancer is one of the most common cancers in women. Of the different subtypes of breast cancer, the triple negative breast cancer subtype of breast cancer is the most aggressive. A proteomic screen of nucleolar content across breast cancer subtypes found that triple negative breast cancer cell lines have a distinct nucleolar proteome signature in comparison to non-TNBC breast cancer cell lines.
2021-03-05 | PXD021201 | Pride
Project description:Accurate characterization and understanding of the breast cancer subtypes is of crucial clinical importance to the heterogeneity of this disease. Several layers of information, including immunohistochemical markers, mRNA and microRNA expression profiles, and pathway analysis have been used for such purpose in several studies. However, a comprehensively integrative approach is currently missing. This paper provides microRNA and mRNA expression profiles, characterizing four breast tumor subtypes, as defined by four immunohistochemical markers. The defined sets of features were validated in two independent data sets at multiple levels, including unsupervised clustering and supervised classification. Moreover, the gene expression signatures of the tumor subtypes were screened by in-depth analysis of 12 cancer core pathways. We successfully identified and validated a novel breast cancer subtypes gene expression signature composed of 976 mRNAs and 69 miRNAs. Luminal and non-luminal tumors are shown to significantly differ both at the mRNA and miRNA levels. HER2 positive tumors are more closely related to triple negative tumors by mRNA profiling than by miRNA expression. Closely related miRNAs sharing the same targets may exert opposite roles during tumor progression. Besides the core cancer pathways, other pathways such as those controling biomass synthesis are shown to be important to enable the core basal subtype with additional progressive nature compared with the other triple negative tumors. Some therapeutic strategies are proposed for breast cancer treatment, including the combined blockage of MAPK/ERK and PI3K/Pten signalings for tumors with poor clinical outcome, and targeting Wnt and JAK/STAT and/or Hedgehog, depending on tumor subtypes, together with conventional chemotherapy with the purpose of achieving an eradicative outcome. The pathway analysis also reveals that the clinical strategy and pivotal targets need to be tuned according to different tumor subtypes. This study is the first attempt to elucidate breast cancer subtypes by combining microRNA and mRNA expression, immunohistochemical markers, and cancer core pathways. The results can avail the functional studies of the etiology of breast cancer and translated for clinical use given their intrinsic link in terms of immunohistochemistry and survival. This submission consists of microRNA profiles of 115 breast cancer tumors of several subtypes only.
2013-06-01 | E-GEOD-43040 | biostudies-arrayexpress
Project description:Identification of four subtypes of Triple Negative Breast Cancer (TNBC) by genomic profiling
| PRJNA306943 | ENA
Project description:Accurate characterization and understanding of the breast cancer subtypes is of crucial clinical importance to the heterogeneity of this disease. Several layers of information, including immunohistochemical markers, mRNA and microRNA expression profiles, and pathway analysis have been used for such purpose in several studies. However, a comprehensively integrative approach is currently missing. This paper provides microRNA and mRNA expression profiles, characterizing four breast tumor subtypes, as defined by four immunohistochemical markers. The defined sets of features were validated in two independent data sets at multiple levels, including unsupervised clustering and supervised classification. Moreover, the gene expression signatures of the tumor subtypes were screened by in-depth analysis of 12 cancer core pathways. We successfully identified and validated a novel breast cancer subtypes gene expression signature composed of 976 mRNAs and 69 miRNAs. Luminal and non-luminal tumors are shown to significantly differ both at the mRNA and miRNA levels. HER2 positive tumors are more closely related to triple negative tumors by mRNA profiling than by miRNA expression. Closely related miRNAs sharing the same targets may exert opposite roles during tumor progression. Besides the core cancer pathways, other pathways such as those controling biomass synthesis are shown to be important to enable the core basal subtype with additional progressive nature compared with the other triple negative tumors. Some therapeutic strategies are proposed for breast cancer treatment, including the combined blockage of MAPK/ERK and PI3K/Pten signalings for tumors with poor clinical outcome, and targeting Wnt and JAK/STAT and/or Hedgehog, depending on tumor subtypes, together with conventional chemotherapy with the purpose of achieving an eradicative outcome. The pathway analysis also reveals that the clinical strategy and pivotal targets need to be tuned according to different tumor subtypes. This study is the first attempt to elucidate breast cancer subtypes by combining microRNA and mRNA expression, immunohistochemical markers, and cancer core pathways. The results can avail the functional studies of the etiology of breast cancer and translated for clinical use given their intrinsic link in terms of immunohistochemistry and survival.
2013-06-01 | GSE43040 | GEO
Project description:In this study we report the neoantigen landscape, tumor mutational burden and tumor microenvironment of seven breast cancer patients, consisting of three Estrogen receptor (ER) positive and four Triple negative breast cancer (TNBC) subtypes.
2022-03-22 | GSE189191 | GEO
Project description:Methylome sequencing identifies potential epigenetic prognostic biomarker signature that stratifies triple negative breast cancer
| PRJNA248722 | ENA
Project description:Discrepancies in the prognosis of triple negative breast cancer exist between Caucasian and Asian populations. Yet, the gene signature of triple negative breast cancer specifically for Asians has not become available. Therefore, the purpose of this study is to construct a prediction model for recurrence of triple negative breast cancer in Taiwanese patients. Whole genome expression profiling of breast cancers from 185 patients in Taiwan from 1995 to 2008 was performed, and the results were compared to the previously published literature to detect differences between Asian and Western patients. Pathway analysis and Cox proportional hazard models were applied to construct a prediction model for the recurrence of triple negative breast cancer. Most expression data of samples (181/185) were reanalyzed from previous studies already uploaded to GEO (see "reanalysis of" links below). Four additional gene expression profiling data of triple negative breast cancer sample were added to this study.
2012-02-02 | E-GEOD-33095 | biostudies-arrayexpress
Project description:Systems-wide profiling of breast cancer has so far built on RNA and DNA analysis by microarray and sequencing techniques. Dramatic developments in proteomic technologies now enable very deep profiling of clinical samples, with high identification and quantification accuracy. We analyzed 40 estrogen receptor positive (luminal), Her2 positive and triple negative breast tumors and reached a quantitative depth of more than 10,000 proteins. Comparison to mRNA classifiers revealed multiple discrepancies between proteins and mRNA markers of breast cancer subtypes. These proteomic profiles identified functional differences between breast cancer subtypes, related to energy metabolism, cell growth, mRNA translation and cell-cell communication. Furthermore, we derived a 19-protein predictive signature, which discriminates between the breast cancer subtypes, through Support Vector Machine (SVM)-based classification and feature selection. The deep proteome profiles also revealed novel features of breast cancer subtypes, which may be the basis for future development of subtype specific therapeutics.
2016-01-05 | PXD002619 | Pride
Project description:Triple negative breast cancer is a heterogeneous disease with distinct molecular subtypes that differentially respond to chemotherapy and targeted agents. The purpose of this study was to explore the clinical relevance of Lehmann triple negative breast cancer subtypes by identifying any differences in response to neoadjuvant chemotherapy among them.
2017-11-17 | GSE106977 | GEO