A bioinformatics approach to identify novel long, non-coding RNAs in breast cancer cell lines from an existing RNA-sequencing dataset

Zaheed, Oza; Samson, Julia; Dean, Kellie

doi:10.1016/j.ncrna.2020.02.004

Cited by 14 publications

(10 citation statements)

References 89 publications

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“…In addition to the described LINC00885 gene amplification in multiple tumor types, and likely in part as a consequence of this phenomenon, this lncRNA was recently described as deregulated in transcriptomic studies of hepatocellular, bladder, malignant pleural mesothelioma and breast cancer [ 14 , 26 , 27 , 28 ]. The possibility exists that LINC00885 may behave as ceRNA which could co-drive the oncogenesis process in various tumor types by regulating mRNA expression through the interaction with microRNAs related to cell proliferation, migration and invasion.…”

Section: Resultsmentioning

confidence: 99%

“…Thousands of lncRNAs have been shown to be estrogen-regulated in breast cancer lines, most of them acting in cis as eRNAs increasing the expression of estrogen target genes [ 10 , 11 ]. Various lncRNAs have been identified differentially expressed between normal and breast cancer samples or cell lines [ 12 , 13 , 14 ]. By analyzing breast cancer TCGA RNA-seq datasets subgroups of lncRNAs were identified as associated with prognosis and with specific intrinsic breast cancer subtypes [ 15 , 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

LINC00885 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression

Abba

Canzoneri

Gurruchaga

et al. 2020

IJMS

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Long intergenic non-protein coding RNA 885 (LINC00885) was identified as significantly upregulated in breast ductal carcinoma in situ (DCIS). The aim of this study was to characterize the phenotypic effects and signaling pathways modulated by LINC00885 in non-invasive and invasive breast cancer models. We determined that LINC00885 induces premalignant phenotypic changes by increasing cell proliferation, motility, migration and altering 3D growth in normal and DCIS breast cell lines. Transcriptomic studies (RNA-seq) identified the main signaling pathways modulated by LINC00885, which include bioprocesses related to TP53 signaling pathway and proliferative signatures such as activation of EREG, EGFR and FOXM1 pathways. LINC00885 silencing in breast cancer lines overexpressing this lncRNA leads to downregulation of proliferation related transcripts such as EREG, CMYC, CCND1 and to significant decrease in cell migration and motility. TCGA-BRCA data analyses show an association between high LINC00885 expression and worse overall survival in patients with primary invasive breast carcinomas (p = 0.024), suggesting that the pro-tumorigenic effects of LINC00885 overexpression persist post-invasion. We conclude that LINC00885 behaves as a positive regulator of cell growth both in normal and DCIS breast cells possibly operating as a ceRNA and representing a novel oncogenic lncRNA associated with early stage breast cancer progression.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

LINC00885 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression

Abba

Canzoneri

Gurruchaga

et al. 2020

IJMS

View full text Add to dashboard Cite

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“…LINC00885 is a newly discovered lncRNA with few relevant studies, and its abnormal expression has been observed only in human breast and bladder cancer (10,11). To the best of our knowledge, the present study was the first to show the increased expression of LINC00885 in CC and its crucial role in the acquisition of a malignant phenotype in CC cells.…”

Section: Discussionmentioning

confidence: 50%

“…Recent studies have reported that dysregulated expression of lncRNAs are likely pervasive in human cancer types, and can drive cancer development and progression of several types of cancer, such as colorectal, breast and gastric cancer (7)(8)(9). LINC00885, a novel oncogenic lncRNA type, was upregulated in breast cancer cell lines (10). LINC00885 may also serve roles in preventing the progression and metastasis of bladder cancer (11).…”

Section: Introductionmentioning

confidence: 99%

FOXP3‑induced LINC00885 promotes the proliferation and invasion of cervical cancer cells

Liu

Zhang

et al. 2021

Mol Med Rep

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Cervical cancer (CC) is the fourth most common type of cancer in women worldwide. LINC00885, a novel oncogenic type of long non-coding RNA, is upregulated in various types of cancer, but its expression in CC remains unknown. The aim of the present study was to investigate the expression of LINC00885 in CC, and its effect on the proliferation and invasion of CC cells in vitro. The expression levels of LINC00885 and forkhead box protein 3 (FOXP3) from The Cancer Genome Atlas (TCGA) were selected to analyze the differences between CC tissues and normal cervical tissues using bioinformatics analyses. Reverse transcription-quantitative (RT-q)PCR was used to detect the relative expression of LINC00885 in CC cell lines, and its expression was knocked down. Cell Counting Kit-8 assays and EdU staining were used to detect the changes in cell proliferative capacity of cells. Transwell experiments were used to examine cell invasion. Dual-luciferase reporter and chromatin immunoprecipitation assays were performed to examine the interactions between LINC00885 and FOXP3. FOXP3 and epithelial-mesenchymal transition (EMT)-related proteins were detected using western blotting. The expression of LINC00885 and FOXP3 in CC tissues and CC cells was significantly higher compared with the normal cervical tissues and normal cervical epithelial cells. FOXP3 could specifically interact with the promoter of LINC00885 and activate LINC00885 transcription. Knockdown of LINC00885 and silencing of FOXP3 significantly inhibited proliferation, invasion and EMT of CC cells. Overexpression of LINC00885 reversed the inhibitory effects of FOXP3 knockdown on the proliferation and invasion of CC cells. Collectively, LINC00885 and FOXP3 may serve as biomarkers for the early diagnosis of CC and as a potential therapeutic target for reversing the malignant phenotype of CC.

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“…Breast cancer remains the most frequently diagnosed malignancy and leading cause of cancer-associated deaths among females worldwide [1,2]. Despite significant declines in mortality, the incidence of breast cancer has risen more than 30% in the last 25 years [3,4].…”

Section: Introductionmentioning

confidence: 99%

Emerging nanomedicines for effective breast cancer immunotherapy

2020

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Breast cancer continues to be the most frequently diagnosed malignancy among women, putting their life in jeopardy. Cancer immunotherapy is a novel approach with the ability to boost the host immune system to recognize and eradicate cancer cells with high selectivity. As a promising treatment, immunotherapy can not only eliminate the primary tumors, but also be proven to be effective in impeding metastasis and recurrence. However, the clinical application of cancer immunotherapy has faced some limitations including generating weak immune responses due to inadequate delivery of immunostimulants to the immune cells as well as uncontrolled modulation of immune system, which can give rise to autoimmunity and nonspecific inflammation. Growing evidence has suggested that nanotechnology may meet the needs of current cancer immunotherapy. Advanced biomaterials such as nanoparticles afford a unique opportunity to maximize the efficiency of immunotherapy and significantly diminish their toxic side-effects. Here we discuss recent advancements that have been made in nanoparticle-involving breast cancer immunotherapy, varying from direct activation of immune systems through the delivery of tumor antigens and adjuvants to immune cells to altering immunosuppression of tumor environment and combination with other conventional therapies.

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A bioinformatics approach to identify novel long, non-coding RNAs in breast cancer cell lines from an existing RNA-sequencing dataset

Cited by 14 publications

References 89 publications

LINC00885 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression

LINC00885 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression

FOXP3‑induced LINC00885 promotes the proliferation and invasion of cervical cancer cells

Emerging nanomedicines for effective breast cancer immunotherapy

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