Integration analysis of microRNA and mRNA paired expression profiling identifies deregulated microRNA-transcription factor-gene regulatory networks in ovarian endometriosis

Zhao, Lei; Gu, Chenglei; Ye, Mingxia; Zhang, Zhe; Li, Lian; Fan, Wensheng; Meng, Yuanguang

doi:10.1186/s12958-017-0319-5

Cited by 63 publications

(66 citation statements)

References 96 publications

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“…Zhao et al 2018 [198] Endometriosis-associated cancer studies CE, HE and EEC Higher level of expression miR-96 and miR-182 in endometrioid OC. Loss of FOXO1 expression and malignant transformation appeared coinciding with a strong induction of these miRs.…”

Section: Ptenmentioning

confidence: 99%

How Benign is Endometriosis: Multi-Scale Interrogation of Documented Evidence

Ghosh

Anupa

et al. 2019

COGO

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Endometriosis is an inflammatory disease characterized by the presence of endometrium-like tissue outside the uterus primarily on pelvic organs and tissues. It affects up to 15% of women in the reproductive age group and is often associated with pelvic pain and subfertility. Different theories explain how retrograde menstruation gives rise to endometrial deposits at ectopic sites, and how several other factors are involved in the progression of the disease. Its final diagnosis is established through direct visualization at laparoscopy or surgery followed by histological confirmation. Available epidemiological reports along with histopathological observations and molecular studies shed interesting light on the pathogenetic basis of different variants of the disease like deep infiltrating endometriosis and ovarian endometriosis. Evidence also suggests that endometriosis is a neoplastic condition which serves as a precursor of ovarian and endometrial cancers. In the present review, we have attempted to take a stock of the current epidemiological and molecular knowledge regarding endometriosis associated cancers and develop a model of functional network with interactions among critical genomic factors regulating cellular processes leading to fibrotic reaction. It is being conjectured that cyclic bleeding associated with inflammatory and oxidative stress followed by repeated tissue injury and repair along with recurrent estrogenic stimulation and ovulatory events in the pelvic environment bring about the complex phenotype of atypical endometriosis and associated neoplasm with a trade-off malignant transformation in high risk population. Finally, we have presented an algorithm for pre-emptive monitoring and management of endometriosis-associated cancers.

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Section: Ptenmentioning

confidence: 99%

How Benign is Endometriosis: Multi-Scale Interrogation of Documented Evidence

Ghosh

Anupa

et al. 2019

COGO

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“…Considering all training datasets were comprised of microarray data, we intended to validate interested pathways related genes, for example, the most enriched pathway of common DEGs or representative pathways in the certain subtype, in RNA-sequencing datasets. However, due to the lack of PE and DIE RNA-sequencing datasets in searching results, we only performed the validation analysis in an OE RNA-sequencing dataset GSE105764 from the GEO database, which contained 8 paired EC and EU tissue samples based on GPL20301 (Illumina HiSeq 4000) (Zhao et al, 2018). The raw read counts were calculated by the DEseq2 R package (Love, Huber & Anders, 2014) to obtain the DEGs.…”

Section: Validation Of Interested Pathway-related Genes In Gse105764mentioning

confidence: 99%

Common and specific gene signatures among three different endometriosis subtypes

Jiang

Zhang

Wang

et al. 2020

PeerJ

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Aims To identify the common and specific molecular mechanisms of three well-defined subtypes of endometriosis (EMs): ovarian endometriosis (OE), peritoneal endometriosis (PE), and deep infiltrating endometriosis (DIE). Methods Four microarray datasets: GSE7305 and GSE7307 for OE, E-MTAB-694 for PE, and GSE25628 for DIE were downloaded from public databases and conducted to compare ectopic lesions (EC) with eutopic endometrium (EU) from EMs patients. Differentially expressed genes (DEGs) identified by limma package were divided into two parts: common DEGs among three subtypes and specific DEGs in each subtype, both of which were subsequently performed with the Kyoto Encyclopedia of Genes (KEGG) pathway enrichment analysis. The protein-protein interaction (PPI) network was constructed by common DEGs and five hub genes were screened out from the PPI network. Besides, these five hub genes together with selected interested pathway-related genes were further validated in an independent OE RNA-sequencing dataset GSE105764. Results A total of 54 EC samples from three EMs subtypes (OE, PE, DIE) and 58 EU samples were analyzed, from which we obtained 148 common DEGs among three subtypes, and 729 specific DEGs in OE, 777 specific DEGs in PE and 36 specific DEGs in DIE. The most enriched pathway of 148 shared DEGs was arachidonic acid (AA) metabolism, in which most genes were up-regulated in EC, indicating inflammation was the most common pathogenesis of three subtypes. Besides, five hub genes AURKB, RRM2, DTL, CCNB1, CCNB2 identified from the PPI network constructed by 148 shared DEGs were all associated with cell cycle and mitosis, and down-regulated in EC, suggesting a slow and controlled proliferation in ectopic lesions. The KEGG pathway analysis of specific DEGs in each subtype revealed that abnormal ovarian steroidogenesis was a prominent feature in OE; OE and DIE seems to be at more risk of malignant development since both of their specific DEGs were enriched in the pathways in cancer, though enriched genes were different, while PE tended to be more associated with dysregulated peritoneal immune and inflammatory microenvironment. Conclusion By integrated bioinformatic analysis, we explored common and specific molecular signatures among different subtypes of endometriosis: activated arachidonic acid (AA) metabolism-related inflammatory process and a slow and controlled proliferation in ectopic lesions were common features in OE, PE and DIE; OE and DIE seemed to be at more risk of malignant development while PE tended to be more associated with dysregulated peritoneal immune and inflammatory microenvironment, all of which could deepen our perception of endometriosis.

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“…Several researchers have performed a large-scale survey for the identification of differentially expressed genes (DEGs) between the eutopic and ectopic endometrium of women with endometriosis (6)(7)(8)(9)(10)(11). Some studies have examined the global transcriptome of isolated ectopic and eutopic tissues from women with adenomyosis (12)(13)(14).…”

Section: Bioinformatics Strategy For the Screening Of Key Genes To DImentioning

confidence: 99%

“…Recent biological studies have used large-scale datasets combined with bioinformatics to investigate global patterns of gene expression in a group of clinically heterogeneous disorders. The differential gene expression profiles were compared between ectopic and eutopic endometrial tissues of endometriosis via global genomics, transcriptomics and proteomics, coupled with bioinformatics and biostatistics (6)(7)(8)(9)(10)(11)130). Endometriosis is involved in pathways, such as hormonal regulation, proliferation, anti-apoptosis, cell cycle regulation, cytokines, chemokines, (pro)inflammatory and immune response, stress response and detoxification, metabolism, cell adhesion, motility, invasion and survival of endometriotic cells.…”

Section: Conclusion and Future Considerationsmentioning

confidence: 99%