Identification and validation of a novel long non-coding RNA (LINC01465) in ovarian cancer

Malgundkar, Shika Hanif; Hassan, Nada Abdullah; Badi, Hala Al; Gupta, Ishita; Burney, Ikram A.; Hashami, Zainab Al; Barwani, Hamida Al; Riyami, Hamad Al; Kalbani, Moza Al; Lakhtakia, Ritu; Okamoto, Aikou; Tamimi, Yahya

doi:10.1007/s13577-022-00842-x

Cited by 7 publications

(3 citation statements)

References 38 publications

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“…In a previous study using ChIP to study downstream genes regulated by E2F5, a transcription factor overexpressed during the early EOC stages (Malgundkar et al, 2022, Kothandaraman et al, 2010, we identified 145 E2F5 targets. These included FBXW7 and a few ncRNAs (four miRNAs and twenty lncRNAs, including LINC01588), which might themselves have a role as a biological marker in EOC.…”

Section: Discussionmentioning

confidence: 99%

“…Based on the list of genes identified, using previously performed ChIP as actual targets regulated by E2F5 (Malgundkar et al 2022) (Supplementary file, S1: Tables 1-4), a gene panel including FBXW7 was designed using the online custom panel Ion AmpliSeq Designer (ThermoFisher Scientific, USA). Pre-capture libraries were constructed using Ion AmpliSeq Library Kit 2.0-96V for the Ion Torrent system (ThermoFisher Scientific, USA), following the manufacturer's guidelines.…”

Section: Gene Panel Exome Sequencingmentioning

confidence: 99%

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Epigenetic status of FBXW7 gene and its role in Ovarian cancer pathogenesis

Hinai

Malgundkar

Gupta

et al. 2023

Asian Pac J Cancer Prev

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Background: Chromatin immunoprecipitation (ChIP) analysis revealed that the FBXW7 gene and the long non-coding RNA (LINC01588) are potential candidates in epithelial ovarian cancer (EOC) pathogenesis. However, their exact role in EOC is not yet known. Thus, the present study sheds light on the impact of the mutations/ methylation status of the FBXW7 gene. Materials and Methods: We used public databases to assess the correlation between mutations/ methylation status and the FBXW7 expression. Furthermore, we performed Pearson’s correlation analysis between the FBXW7 gene and LINC01588. We performed gene panel exome sequencing and Methylation-speciﬁc PCR (MSP) in HOSE 6-3, MCAS, OVSAHO, and eight EOC patients’ samples to validate the bioinformatics results. Results: The FBXW7 gene was less expressed in EOC, particularly in stages III and IV, compared to healthy tissues. Furthermore, bioinformatics analysis, gene panel exome sequencing, and MSP revealed that the FBXW7 gene is neither mutated nor methylated in EOC cell lines and tissues, suggesting alternative mechanisms for FBXW7 gene regulation. Interestingly, Pearson’s correlation analysis showed an inverse, significant correlation between the FBXW7 gene and LINC01588 expression, suggesting a potential regulatory role of LINC01588. Conclusion: Neither mutations nor methylation is the causative mechanism for the FBXW7 downregulation in EOC, suggesting alternative means involving the lncRNA LINC01588.

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Section: Discussionmentioning

confidence: 99%

Section: Gene Panel Exome Sequencingmentioning

confidence: 99%

Epigenetic status of FBXW7 gene and its role in Ovarian cancer pathogenesis

Hinai

Malgundkar

Gupta

et al. 2023

Asian Pac J Cancer Prev

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“…Overexpression of SPACA6P-AS regulates onco-suppressive mir-125a, resulting in upregulation of oncogenic mir-125a targets [47]. LINC01465 is located on chromosome 12q14.1 and is suggested to have a potential role in cell migration of epithelial ovarian cancer (EOC) cells [48]. The sequence of mir-let-7i is complementary to the beginning of the exon sequences of an isoform (ENST00000408887.3) of this lncRNA (Figure 2).…”

Section: Spaca6p-as (Spaca6 Antisense Rna 1)mentioning

confidence: 99%

Crosstalk between Long Non-Coding RNA and Spliceosomal microRNA as a Novel Biomarker for Cancer

Arafat,

Sperling

2023

ncRNA

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Non-coding RNAs (ncRNAs) play diverse roles in regulating cellular processes and have been implicated in pathological conditions, including cancer, where interactions between ncRNAs play a role. Relevant here are (i) microRNAs (miRNAs), mainly known as negative regulators of gene expression in the cytoplasm. However, identification of miRNAs in the nucleus suggested novel nuclear functions, and (ii) long non-coding RNA (lncRNA) regulates gene expression at multiple levels. The recent findings of miRNA in supraspliceosomes of human breast and cervical cancer cells revealed new candidates of lncRNA targets. Here, we highlight potential cases of crosstalk between lncRNA and supraspliceosomal miRNA expressed from the same genomic region, having complementary sequences. Through RNA:RNA base pairing, changes in the level of one partner (either miRNA or lncRNA), as occur in cancer, could affect the level of the other, which might be involved in breast and cervical cancer. An example is spliceosomal mir-7704 as a negative regulator of the oncogenic lncRNA HAGLR. Because the expression of spliceosomal miRNA is cell-type-specific, the list of cis-interacting lncRNA:spliceosomal miRNA presented here is likely just the tip of the iceberg, and such interactions are likely relevant to additional cancers. We thus highlight the potential of lncRNA:spliceosomal miRNA interactions as novel targets for cancer diagnosis and therapies.

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The pivotal role of long non-coding RNAs as potential biomarkers and modulators of chemoresistance in ovarian cancer (OC)

Malgundkar,

Tamimi

2024

Hum. Genet.

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Identification and validation of a novel long non-coding RNA (LINC01465) in ovarian cancer

Cited by 7 publications

References 38 publications

Epigenetic status of FBXW7 gene and its role in Ovarian cancer pathogenesis

Epigenetic status of FBXW7 gene and its role in Ovarian cancer pathogenesis

Crosstalk between Long Non-Coding RNA and Spliceosomal microRNA as a Novel Biomarker for Cancer

The pivotal role of long non-coding RNAs as potential biomarkers and modulators of chemoresistance in ovarian cancer (OC)

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