Gene expression profiling of the 8q22-24 position in human breast cancer: TSPYL5, MTDH, ATAD2 and CCNE2 genes are implicated in oncogenesis, while WISP1 and EXT1 genes may predict a risk of metastasis

Taghavi, Afsoon; Akbari, Mohammad Esmaeil; Hashemi-Bahremani, Mohammad; Nafissi, Nahid; Khalilnezhad, Ahad; Poorhosseini, Seyed Mohammad; Hashemi‐Gorji, Feyzollah; Yassaee, Vahid Reza

doi:10.3892/ol.2016.5218

Cited by 40 publications

(30 citation statements)

References 43 publications

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“…Virtually all tumors with this expression pattern possessed co-amplification of a region on 8q22-24 that includes RPL8, RPL30 and the oncogene MYC. Amplification of this region has been previously described in breast cancers and correlates with chemoresistance and metastasis (Hu et al 2009;Parris et al 2014;Taghavi et al 2016). Our results indicate that this amplification and the ensuing overexpression of RPL8 and RPL30 also occurs in subsets of melanoma, liver, prostate, lung, and head and neck cancers.…”

Section: Discussionsupporting

confidence: 77%

Diagnostic and Prognostic Implications of Ribosomal Protein Transcript Coordination in Human Cancers

Dash

2017

Preprint

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Ribosomes, the organelles responsible for the translation of mRNA, are comprised of rRNA and ~80 ribosomal proteins (RPs). Although canonically assumed to be maintained in equivalent proportions, some RPs have been shown to possess differential expression across tissue types. Dysregulation of RP expression occurs in a variety of human diseases, notably in many cancers, and altered expression of some RPs correlates with different tumor phenotypes and patient survival. To investigate the impact of global RP transcript (RPT) expression patterns on tumor phenotypes, we analyzed RPT expression of ~10,000 human tumors and 700 normal tissues with t-distributed stochastic neighbor embedding (t-SNE). We show here that normal tissues and cancers possess readily discernible RPT expression patterns. In tumors, this patterning is distinct from normal tissues, distinguishes tumor subtypes from one another, and in many cases correlates with molecular, pathological, and clinical features, including survival. Collectively, RPT expression can be used as a powerful and novel method of tumor classification, offering a potential clinical tool for prognosis and therapeutic stratification.

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Section: Discussionsupporting

confidence: 77%

Diagnostic and Prognostic Implications of Ribosomal Protein Transcript Coordination in Human Cancers

Dash

2017

Preprint

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“…Some of these mRNAs including WISP1, S1PR1 and SORBS1 have been characterized as oncogenes or tumor suppressors in various cancers. It has been showed that WISP1 gene might be a predictive marker of breast cancer metastasis [39]. Our data also indicated that WISP1 was inversely related to patients overall survival.…”

Section: Discussionsupporting

confidence: 70%

Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs/mRNAs and miRNAs with Associated ceRNA Networks in Triple-Negative Breast Cancer

Yang

Liu

Wang

et al. 2018

Cell Physiol Biochem

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Background/Aims: Triple-negative breast cancer (TNBC) is a subtype of highly malignant breast cancer with poor prognosis. Growing evidence indicates that Long noncoding RNAs (lncRNAs) play important regulatory roles in the development and progression of a variety of cancers including breast cancer. However, the underlying mechanisms remain largely unknown. Methods: Here, we compared the expression profiles of mRNAs, lncRNAs and miRNAs between 111 TNBC tissues and 104 non-cancerous tissues utilizing RNA-Seq Data from The Cancer Genome Atlas (TCGA). Gene Ontology and KEGG pathway enrichment analyses were executed to investigate the principal functions of the significantly dysregulated mRNAs. Moreover, Kaplan-Meier survival analyses were performed to determine the effects of differentially expressed lncRNAs/mRNAs/miRNAs on overall survival. Subsequently, we constructed a competing endogenous RNA (ceRNA) network, which included 66 dysregulated lncRNAs, 24 miRNAs and 55 mRNAs. The four dysregulated lncRNAs, three aberrantly expressed miRNAs and four mRNAs were confirmed in the ceRNA network by qRT-PCR in 30 pairs of samples, respectively. Results: A total of 1441 lncRNAs, 114 miRNA and 2501 mRNAs were found to be differentially expressed in TNBC tissues compared with controls. 109 lncRNAs and 124 mRNAs might serve as prognostic signature for patients with TNBC according to the survival analysis. Functional analysis revealed that 19 mRNAs in the ceRNA network were enriched in 17 cancer-related pathways. Conclusion: Taken together, we identified novel lncRNAs/miRNAs which may serve as potential biomarkers to predict the survival and therapeutic targets for TNBC patients based on a large-scale sample. More importantly, we constructed the ceRNA network of TNBC, which provides valuable information to further explore the molecular mechanism underlying tumorigenesis and development of TNBC.

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“…Virtually all tumors with this expression pattern possessed co-amplification of a region on 8q22–24 that includes RPL8 , RPL30 , and the oncogenes MYC and PVT1. Amplification of this region has been previously described in breast cancers and correlates with chemoresistance and metastasis [ 36 , 37 , 45 – 47 ]. Our results indicate that this amplification and the ensuing overexpression of RPL8 and RPL30 also occurs in subsets of melanoma, liver, prostate, lung, and head and neck cancers.…”

Section: Discussionmentioning

confidence: 99%

Diagnostic and prognostic implications of ribosomal protein transcript expression patterns in human cancers

2018

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BackgroundRibosomes, the organelles responsible for the translation of mRNA, are comprised of four rRNAs and ~ 80 ribosomal proteins (RPs). Although canonically assumed to be maintained in equivalent proportions, some RPs have been shown to possess differential expression across tissue types. Dysregulation of RP expression occurs in a variety of human diseases, notably in many cancers, and altered expression of some RPs correlates with different tumor phenotypes and patient survival. Little work has been done, however, to characterize overall patterns of RP transcript (RPT) expression in human cancers.MethodsTo investigate the impact of global RPT expression patterns on tumor phenotypes, we analyzed RPT expression of ~ 10,000 human tumors and over 700 normal tissues from The Cancer Genome Atlas (TCGA) using t-distributed stochastic neighbor embedding (t-SNE). Clusters of tumors identified by t-SNE were then analyzed with chi-squared and t-tests to compare phenotypic data, ANOVA to compare individual RPT expression, and Kaplan-Meier curves to assess survival differences.ResultsNormal tissues and cancers possess distinct and readily discernible RPT expression patterns that are independent of their absolute levels of expression. In tumors, RPT patterning is distinct from that of normal tissues, identifies heretofore unrecognized tumor subtypes, and in many cases correlates with molecular, pathological, and clinical features, including survival.ConclusionsRPT expression patterns are both tissue-specific and tumor-specific. These could be used as a powerful and novel method of tumor classification, offering a potential clinical tool for prognosis and therapeutic stratification.Electronic supplementary materialThe online version of this article (10.1186/s12885-018-4178-z) contains supplementary material, which is available to authorized users.

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Gene expression profiling of the 8q22-24 position in human breast cancer: TSPYL5, MTDH, ATAD2 and CCNE2 genes are implicated in oncogenesis, while WISP1 and EXT1 genes may predict a risk of metastasis

Cited by 40 publications

References 43 publications

Diagnostic and Prognostic Implications of Ribosomal Protein Transcript Coordination in Human Cancers

Diagnostic and Prognostic Implications of Ribosomal Protein Transcript Coordination in Human Cancers

Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs/mRNAs and miRNAs with Associated ceRNA Networks in Triple-Negative Breast Cancer

Diagnostic and prognostic implications of ribosomal protein transcript expression patterns in human cancers

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