Differential expression of neurogenes among breast cancer subtypes identifies high risk patients

Fernández‐Nogueira, Patricia; Bragado, Paloma; Almendro, Vanessa; Ametller, Elisabet; Ríos, José; Choudhury, Sangita; Mancino, Mario; Gascón, Pedro

doi:10.18632/oncotarget.6543

Cited by 31 publications

(41 citation statements)

References 77 publications

(83 reference statements)

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“…Further analysis of the “cell‐cell signaling” pathway (Table ) shows that 78% of the 69 genes in the pathway are hypermethylated in ERpos primary C1 tumors, and of those 69 genes, high expression is associated with increased survival. It is interesting to note that recent literature has focused on the importance of differential expression of neurogenes in breast cancer . Fernández‐Noguiera et al examined six neurogenes that were differentially expressed among breast cancer subtypes and had expression correlated with survival and metastasis (HRH1, NRP2, ENFB1, NGFR, APP, and STX1A).…”

Section: Discussionmentioning

confidence: 99%

DNA methylation in breast cancers: Differences based on estrogen receptor status and recurrence

Williams

Jawale

Schneider

et al. 2018

J of Cellular Biochemistry

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DNA methylation plays a role in the etiology of primary breast cancers. We analyzed paired primary and second breast tumors to elucidate the role of methylation in recurrence. Methylation profiles from paired primary and second breast tumors of 23 women were assessed using the HumanMethylation450 BeadChip. Twelve women had estrogen receptor positive (ERpos) primary and second tumors, five had estrogen receptor negative (ERneg) primary and second tumors, and six had an ERpos primary tumor but an ERneg second tumor. Stratifying tumors by occurrence revealed that the greater methylation previously associated with ERpos tumors, is more pronounced in primary tumors than in second tumors. Further, ERneg second tumors are more methylated than ERpos second tumors among women who had ERpos primary tumors. Pathway analyses using gene lists generated from comparisons of methylation in ERpos primary tumors from the paired sets with ERpos tumors from six women without recurrences, identified differences between groups based on the ER status of the second tumor. Hypermethylated genes of significantly enriched pathways were differentially associated with survival. DNA methylation profiles of ERpos primary breast tumors support the development and use of tumor methylation profiles for stratifying women with breast cancer both for prognosis and therapy.

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Section: Discussionmentioning

confidence: 99%

DNA methylation in breast cancers: Differences based on estrogen receptor status and recurrence

Williams

Jawale

Schneider

et al. 2018

J of Cellular Biochemistry

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“…The GOBO database (version 1.0.3; ) is a user-friendly public database. It allows for rapid assessment of gene expression levels, identification of co-expressed genes and association with outcome for single genes, gene sets or gene signatures in an 1,881-sample breast cancer dataset (21). The most important functionality of the GOBO database is the possibility of investigating gene expression levels in breast cancer subgroups and cell lines for gene sets (22).…”

Section: Methodsmentioning

confidence: 99%

Bioinformatics analysis of the expression of HOXC13 and its role in the prognosis of breast cancer

Cui

Zou

et al. 2019

Oncol Lett

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The homeobox (HOX) genes, a class of transcription factors, are known to promote embryonic development and induce tumor formation. To date, the HOXA and HOXB gene families have been reported to be associated with breast cancer. However, the expression and exact role of homeobox C13 (HOXC13) in breast cancer has not yet been investigated. In the present study, the HOXC13 expression in human breast cancer was evaluated using the Oncomine database and Cancer Cell Line Encyclopedia (CCLE). Next, the Gene expression-based Outcome for Breast cancer online database, cBioportal, University of California Santa Cruz Xena browser and bc-GenExMinerv were used to explore the specific expression of HOXC13 in breast cancer. The methylation and mutation status of HOXC13 in breast cancer was then validated using the CCLE and cBioportal databases. Finally, the co-expression of HOX transcript antisense RNA (HOTAIR) and HOXC13 in breast cancer were analyzed and their impact on clinical prognosis determined. It was found that the expression of HOXC13 was high in breast cancer compared with other types of cancer, such as gastric cancer and colon cancer. Following co-expression analysis, a significant positive association was identified between HOTAIR and HOXC13. An association between HOTAIR and HOXC13, and lymph node and distant metastasis recurrence was also revealed during the development of breast cancer. Of note, survival analysis showed that high expression of HOTAIR and HOXC13 predicted poor prognosis. These findings revealed that HOXC13 plays an important role in the progression of breast cancer. However, the specific mechanism needs to be confirmed by subsequent experiments.

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“…A handful of studies have addressed the gene expression patterns of TEC compared with different control ECs by using two popular high-throughput gene expression technologies, microarray and serial analysis of gene expression (SAGE) [ 21 – 28 ]. Although these valuable studies have shed much light on characterizing gene expression patterns and finding potential biomarkers of TEC, both DNA microarray and SAGE need voluminous mRNA extracted from millions of ECs that is often difficult to attain given limitations of available surgical tissue.…”

Section: Introductionmentioning

confidence: 99%

Single-cell RNA sequencing reveals gene expression signatures of breast cancer-associated endothelial cells

et al. 2017

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Tumor endothelial cells (TEC) play an indispensible role in tumor growth and metastasis although much of the detailed mechanism still remains elusive. In this study we characterized and compared the global gene expression profiles of TECs and control ECs isolated from human breast cancerous tissues and reduction mammoplasty tissues respectively by single cell RNA sequencing (scRNA-seq). Based on the qualified scRNA-seq libraries that we made, we found that 1302 genes were differentially expressed between these two EC phenotypes. Both principal component analysis (PCA) and heat map-based hierarchical clustering separated the cancerous versus control ECs as two distinctive clusters, and MetaCore disease biomarker analysis indicated that these differentially expressed genes are highly correlated with breast neoplasm diseases. Gene Set Enrichment Analysis software (GSEA) enriched these genes to extracellular matrix (ECM) signal pathways and highlighted 127 ECM-associated genes. External validation verified some of these ECM-associated genes are not only generally overexpressed in various cancer tissues but also specifically overexpressed in colorectal cancer ECs and lymphoma ECs. In conclusion, our data demonstrated that ECM-associated genes play pivotal roles in breast cancer EC biology and some of them could serve as potential TEC biomarkers for various cancers.

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Differential expression of neurogenes among breast cancer subtypes identifies high risk patients

Cited by 31 publications

References 77 publications

DNA methylation in breast cancers: Differences based on estrogen receptor status and recurrence

DNA methylation in breast cancers: Differences based on estrogen receptor status and recurrence

Bioinformatics analysis of the expression of HOXC13 and its role in the prognosis of breast cancer

Single-cell RNA sequencing reveals gene expression signatures of breast cancer-associated endothelial cells

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