Transcriptomics-based screening of molecular signatures associated with patients overall survival and their key regulators in subtypes of breast cancer

Eskandari, Elaheh; Motalebzadeh, Jamshid

doi:10.1016/j.cancergen.2019.09.004

Cited by 9 publications

(5 citation statements)

References 45 publications

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“…In addition, this factor plays a role in cell proliferation, migration, and invasion in malignant glioblastoma cells [38]. We previously showed that the nuclear receptor AR is an important factor for breast cancer development and progression [22]. The value of AR has been shown in HCC as a useful molecule in the molecular targeted therapy for hard-totreat cancers [39].…”

Section: Discussionmentioning

confidence: 99%

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Transcription Factors Linked to the Molecular Signatures in the Development of HCC on a Cirrhotic Background

Motalebzadeh

Eskandari

2021

Preprint

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Mechanisms underlying the regulation of gene expression in cancer have been surveyed for decades to find novel prognostic factors and new targets for molecular targeted therapies in cancer. Because most cases of liver cancer are associated with liver cirrhosis, we aimed to analyze the gene expression signatures and the gene regulatory mechanism in hepatocellular carcinoma (HCC) on a cirrhotic background using high-throughput data analysis. In the present study, three valid array-based datasets containing HCC and liver cirrhosis samples were obtained to identify common differentially expressed genes (DEGs). Moreover, a comprehensive data analysis was conducted based on RNA-Seq data and using Kaplan-Meier curve analysis to find molecular signatures that reduce patients' overall survival rate. Furthermore, we proposed a gene regulatory network (GRN) to explore the possible regulatory mechanism of these molecular signatures by transcription factors in HCC progression from cirrhosis. Besides, we analyzed protein-protein interactions, gene ontology (GO), and pathway enrichment to elucidate the cellular and molecular function of the GRN elements in HCC. In this way, we found a list of 231 molecular signatures in HCC derived from cirrhosis. We also found the importance of TCF4, RUNX1, HINFP, KDM2B, MAF, JUN, NR5A2, NFYA, and AR as key differentially expressed transcription factors (DETFs) in the progression of HCC from cirrhosis. In conclusion, the identified molecular signatures and their transcription factors propose candidate prognostic markers and possible molecular targets in the progression of HCC.

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Section: Discussionmentioning

confidence: 99%

“…CytoCtrlAnalyser [21], and Minimum Connected Dominating Set (MCDS) [22] plugins. We created a network that allows us to predict the impact of molecular signatures and their regulatory mechanism by DETFs in HCC on a cirrhotic background.…”

Section: Gene Regulatory Network Analysismentioning

confidence: 99%

Transcription Factors Linked to the Molecular Signatures in the Development of HCC on a Cirrhotic Background

Motalebzadeh

Eskandari

2021

Preprint

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“…Eskandari et al described the characteristics of a gene regulation network based on transcription factors, miRNAs, and their target genes, finding altered key regulators involved in BC subtypes and reducing OSs in each BC subtype. For the BL subtype, nine key regulators were identified including HMGA1, WT1, and FOXM1 adjusted at the top and STAT3 and TP63 at the bottom; mir-19a-3p, mir-106b-5p, mir-20a-5p, and mir-17-5p as key miRNAs were up-adjusted [112].…”

Section: Main Mirnas and Biology Of Tnbc With Basal-like Phenotypementioning

confidence: 99%

Modulatory Role of microRNAs in Triple Negative Breast Cancer with Basal-Like Phenotype

Angius

Cossu-Rocca

Arru

et al. 2020

Cancers

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Development of new research, classification, and therapeutic options are urgently required due to the fact that TNBC is a heterogeneous malignancy. The expression of high molecular weight cytokeratins identifies a biologically and clinically distinct subgroup of TNBCs with a basal-like phenotype, representing about 75% of TNBCs, while the remaining 25% includes all other intrinsic subtypes. The triple negative phenotype in basal-like breast cancer (BLBC) makes it unresponsive to endocrine therapy, i.e., tamoxifen, aromatase inhibitors, and/or anti-HER2-targeted therapies; for this reason, only chemotherapy can be considered an approach available for systemic treatment even if it shows poor prognosis. Therefore, treatment for these subgroups of patients is a strong challenge for oncologists due to disease heterogeneity and the absence of unambiguous molecular targets. Dysregulation of the cellular miRNAome has been related to huge cellular process deregulations underlying human malignancy. Consequently, epigenetics is a field of great promise in cancer research. Increasing evidence suggests that specific miRNA clusters/signatures might be of clinical utility in TNBCs with basal-like phenotype. The epigenetic mechanisms behind tumorigenesis enable progress in the treatment, diagnosis, and prevention of cancer. This review intends to summarize the epigenetic findings related to miRNAome in TNBCs with basal-like phenotype.

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“…Dysregulation of miRNA expression has been associated with a wide range of diseases, including cancer [ [7] , [8] , [9] , [10] , [11] ]. MiRNAs may function as oncogenes (oncomiRs) or tumor suppressors by regulating the expression of corresponding genes.…”

Section: Introductionmentioning

confidence: 99%

miRNAs and related genetic biomarkers according to the WHO glioma classification: From diagnosis to future therapeutic targets

Nikolova,

Laleva,

Milev

et al. 2024

Non-coding RNA Research

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Transcriptomics-based screening of molecular signatures associated with patients overall survival and their key regulators in subtypes of breast cancer

Cited by 9 publications

References 45 publications

Transcription Factors Linked to the Molecular Signatures in the Development of HCC on a Cirrhotic Background

Transcription Factors Linked to the Molecular Signatures in the Development of HCC on a Cirrhotic Background

Modulatory Role of microRNAs in Triple Negative Breast Cancer with Basal-Like Phenotype

miRNAs and related genetic biomarkers according to the WHO glioma classification: From diagnosis to future therapeutic targets

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