Copy number analysis identifies tumor suppressive lncRNAs in human osteosarcoma

Xie, Jian‐Jun; Lin, De–Chen; Lee, Dhong Hyun Tony; Akunowicz, Jennifer; Hansen, Marc F.; Miller, Carl W.; Sanada, Masashi; Kato, Motohiro; Akagi, Tadayuki; Kawamata, Norihiko; Ogawa, Seishi; Koeffler, H. Phillip

doi:10.3892/ijo.2017.3864

Cited by 14 publications

(12 citation statements)

References 28 publications

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“…Loc285194, also named LSAMP antisense RNA3, is a 2105-bp lncRNA encoded on chromosomal locus 3q13.31, also called as osteo3q13.31, a locus with frequent copy number alterations and loss of heterozygocity in osteosarcoma [171,172]. Loc285194 is downregulated in osteosarcoma cell lines and tissue specimens.…”

Section: Tumor Suppression Lncrnasmentioning

confidence: 99%

Long Noncoding RNAs in Osteosarcoma: Mechanisms and Potential Clinical Implications

Valavanis¹,

Stanc²

2019

Osteosarcoma – Diagnosis, Mechanisms, and Translational Developments

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Long noncoding RNAs (lncRNAs) are noncoding transcripts consisting of a diverse class of long RNAs of more than 200 nucleotides in length. Recent studies have shown that lncRNAs are involved in cell signal transduction pathways, cell cycle and cell death regulation, chromatin remodeling, and gene expression regulation at the transcriptional and posttranscriptional levels. They are also involved in the metastatic process of different types of tumors, such as urothelial carcinoma, colon carcinoma, breast carcinoma, lung carcinoma, and hepatocellular carcinoma. In addition, lncRNAs demonstrate precise expression patterns in specific tissues and cells and therefore play important roles in cell differentiation and tissue development. In this chapter, we review the molecular mechanisms of lncRNA cell functions and their involvement in the pathogenesis, progression, and metastasis of osteosarcoma, a rare bone tumor of childhood and adolescence. We also review emerging clinical implications of lncRNA use as potential prognostic biomarkers and therapeutic targets, as well as their putative involvement in drug resistance, in osteosarcoma progression, and in therapeutic interventions.

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Section: Tumor Suppression Lncrnasmentioning

confidence: 99%

Long Noncoding RNAs in Osteosarcoma: Mechanisms and Potential Clinical Implications

Valavanis¹,

Stanc²

2019

Osteosarcoma – Diagnosis, Mechanisms, and Translational Developments

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“…The lncRNA HOTAIR is a prognostic biomarker in chondrosarcoma [59] . lncRNAs are commonly identified via microarrays, RNA-Seq or quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis [60][61][62][63] . A recent study described two novel and possibly tumor suppressor lncRNAs, LOC285194 and BC040587, whose expressions are either lost or mutated in osteosarcoma [63] .…”

Section: Transcriptomic Analysismentioning

confidence: 99%

The advancements of genomics and data integration in sarcoma research

et al. 2017

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Abstract:In the age of big data, genomics and clinical research have reached a crossroads. A wealth of data is being generated, but it is becoming increasingly complicated to analyze these data to extract meaningful results. The ability to understand biological systems holistically has unprecedented potential to transform how cancers are treated. Recent major advances leading biomedical research towards "systems medicine" have been fueled by high-throughput platforms, such as microarrays and next-generation sequencing, which can capture vast amounts of data in different genomic spaces. Unfortunately, because of high dimensionality and complex relationships among these data, inferring comprehensive and useful biological models has proven computationally and statistically challenging. However, novel bioinformatic methods for data integration of cancer genomic datasets have been developed. In this review, we will describe the applications of various genomic approaches in sarcoma research and introduce bioinformatic methods for data integration. With the continuing evolution of technological and bioinformatic methodologies, the application of big data within clinics and hospitals will ultimately result in significant improvements on how cancers are detected and treated.Keywords: omics; genomics; sarcomas; sequencing; microarray; data integration; bioinformatics; big data

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“…BC040587 (also known as Linc00901) is one of the most important LncRNAs which have not been featured. BC040587, which locates in chromosome 3q13, harbors various copy number alterations, therefore it suggests BC040587 could be of vital importance in oncogenesis [10,11]. Moreover, dysregulation of BC040587 expression could be a critical step in sarcoma, suggesting an example in tumorigenesis [12] MDM2/P53 negative feedback pathway is notable in cancer research, and it is mainly related to apoptosis as well as proliferation [13].…”

Section: Introductionmentioning

confidence: 99%

Long Non-Coding RNA BC040587 is Required in Cell Invasion of Renal Cancer Induced by Acidosis

Zhou

Dong

Yao

et al. 2020

Preprint

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Background: It is well known that aggressive growth and metastasis of tumors are strengthened in acidic environments of cancer. Whether Long non-coding RNA (LncRNA) is involved in this process is still unknown and has never been reported in renal cell cancer(RCC).Methods: We determined the invasion ability of 786-O and 769P cells upon acidosis. Then LncRNA profiling was used to figure out the potential acidosis-related LncRNAs. We then knocked out the LncRNA (BC040587) to investigate its role in acidosis-induced cell invasion. AKT/mTOR ,MEK/ERK pathway as well as pMDM2 were analyzed to uncover the cell signaling induced by BC040587 upon acidosis. Clinical features were also carefully analyzed.Results: Acidosis elevated the level of Snail and induced cell invasions in RCC. BC040587 was required in this process as the increased cell invasion could be abolished by knockout of BC040587. Acidosis activated AKT/mTOR and MEK/ERK pathway in a BC040587-dependent manner. MDM2 could be the downstream of BC040587, which implicated poorer prognosis in RCC based on the clinical features.Conclusions: BC040587 is required in cell invasion of renal cancer induced by acidosis. The BC040587-AKT/ERK-pMDM2-Snail axis is of vital importance in the development of RCC and is likely to be potential therapeutic target in RCC.

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Copy number analysis identifies tumor suppressive lncRNAs in human osteosarcoma

Cited by 14 publications

References 28 publications

Long Noncoding RNAs in Osteosarcoma: Mechanisms and Potential Clinical Implications

Long Noncoding RNAs in Osteosarcoma: Mechanisms and Potential Clinical Implications

The advancements of genomics and data integration in sarcoma research

Long Non-Coding RNA BC040587 is Required in Cell Invasion of Renal Cancer Induced by Acidosis

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Copy number analysis identifies tumor suppressive lncRNAs in human osteosarcoma

Cited by 14 publications

References 28 publications

Long Noncoding RNAs in Osteosarcoma: Mechanisms and Potential Clinical Implications

Long Noncoding RNAs in Osteosarcoma: Mechanisms and Potential Clinical Implications

The advancements of genomics and data integration in sarcoma research

Long Non-Coding RNA BC040587 is Required in&nbsp;Cell Invasion of Renal Cancer Induced by Acidosis

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Long Non-Coding RNA BC040587 is Required in Cell Invasion of Renal Cancer Induced by Acidosis