Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches. (November 2022)

• Record Type: Journal Article
• Authors: Shaath, Hibah; Vishnubalaji, Radhakrishnan; Elango, Ramesh; Kardousha, Ahmed; Islam, Zeyaul; Qureshi, Rizwan; Alam, Tanvir; Kolatkar, Prasanna R.; Alajez, Nehad M.
• Is Part Of: Seminars in cancer biology. Volume 86(2023)Part 3
• Page Start: 325
• Page End: 345
• Publication Date: 2022-11
• Subjects: lncRNA long non-coding RNA -- RBP RNA-binding protein -- m6A N6-methyladenosine -- LPI lncRNA-protein interaction -- ncRNAs non-coding RNAs -- miRNAs microRNAs -- tRNAs transfer RNAs -- rRNAs ribosomal RNAs -- siRNAs small interfering RNAs -- CLIP cross-linking immunoprecipitation -- RIP RNA immunoprecipitation -- HuR human antigen R -- SRSF1 serine/arginine-rich splicing factor 1 -- ML machine learning -- DL deep learning -- PUP polyU polymerase -- ChIRP-MS comprehensive identification of RBPs by mass spectrometry -- RCC renal cell carcinoma -- PTEN phosphatase and tensin homolog -- Lnc-DILC long non-coding RNA downregulated in liver cancer stem cells -- CRC colorectal cancer -- WWP2 ww domain containing E3 ubiquitin protein ligase 2 -- OCC-1 overexpressed in colon carcinoma-1 -- TrCP1 transducin repeat-containing protein 1 -- DUXAP9 double homeobox A pseudogene 9 -- EMT epithelial-mesenchymal transition -- IGF2BP2 insulin like growth factor 2 mRNA binding protein 2 -- IGF2BP1 insulin like growth factor 2 mRNA binding protein 1 -- PI3K/AKT phosphoinositide 3-kinase/ serine/threonine-protein kinase -- HULC highly up-regulated in liver cancer -- HCC hepatocellular carcinoma -- CNOT1 CCR4-NOT transcription complex subunit 1 -- NEAT1 nuclear enriched abundant transcript 1 -- LSCC laryngeal squamous cell carcinoma -- METTL methyltransferase-like -- RBM RNA binding motif -- ZC3H3 zinc finger CCCH-type containing 3 -- VIRMA vir like m6A methyltransferase associated -- YTHDF YTH N6-methyladenosine RNA binding protein -- SPTBN2 spectrin beta, non-erythrocytic 2 -- LCAT3 lung cancer associated transcript 3 -- FENDRR FOXF1 adjacent non-coding developmental regulatory RNA -- SOX4 SRY-box transcription factor 4 -- EEC endometrioid endometrial carcinoma -- hnRNPM heterogeneous nuclear ribonucleoprotein M -- RRM RNA recognition motif -- PCGEM1 prostate cancer specific transcript 1 lncRNA -- U2AF65 U2 snRNP auxiliary factor large subunit 65 -- AR3 androgen receptor 3 -- SF3B3 splicing factor 3b subunit 3 -- EZH2 enhancer of zeste homolog 2 -- SNAI1 snail family transcriptional repressor 1 -- TPM1-AS tropomyosin 1 antisense RNA -- RBM4 RNA-binding motif protein 4 -- EPB41L4A-AS1 erythrocyte membrane protein band 4.1 like 4A anti-sense 1 -- HDAC2 histone deacetylase 2 -- NPM1 nucleophosmin 1 -- GRSF1 G-rich RNA sequence-binding factor 1 -- XIST X-inactive specific transcript -- PRC2 polycomb repressive complex 2 -- H3K27me3 trimethylates histone H3 at lysine 27 -- BRCA1 breast cancer gene 1 -- BC breast cancer -- ANCR anti-differentiation non-coding RNA -- CDK1 cyclin-dependent kinase 1 -- TUG1 taurine upregulated 1 -- ChIP chromatin immunoprecipitation -- BCL2 B-cell lymphoma 2 -- BAX BCL2 associated X, apoptosis regulator -- NSCLC non-small cell lung cancer -- CELF1 CUGBP elav-like family member 1 -- WDR5 WD repeat domain 5 -- VEGFC vascular endothelial growth factor C -- MLL mixed lineage leukemia -- HOTAIR HOX antisense intergenic RNA -- SAV1 salvador homolog 1 -- CDDP cisplatin -- lnc-LBCS lncRNA bladder and prostate cancer suppressor -- hnRNPK heterogeneous nuclear ribonucleoprotein K -- SOX2 SRY box 2 -- AFAP1-AS1 actin filament associated protein 1, antisense RNA 1 -- H3K27ac H3K27 acetylation -- AUF1 AU-rich element RNA binding protein 1 -- ERBB2 Erb-B2 receptor tyrosine kinase 2 -- PiHL p53 inHibiting lncRNA -- 5-FU 5-Fluorouracil -- RPL11 ribosomal protein L11 -- MDM2 mouse double minute 2 homolog -- GRWD1 glutamate rich WD repeat containing 1 -- FOXD3-AS1 forkhead box D3 antisense RNA 1 -- TINCR terminal differentiation‐induced non‐coding RNA -- NPC nasopharyngeal carcinoma -- ACLY ATP citrate Lyase -- PADI1 peptidyl arginine deiminase 1 -- SNHG12 small nucleolar RNA host gene 12 -- CDCA3 cell division cycle associated 3 -- SP1 specificity protein 1 -- RBDs RNA-binding domains -- NMR nuclear magnetic resonance -- ZnFs zinc fingers -- qRRM quasi-RRM -- ΨRRM pseudo-RRM -- UHM U2AF homology motifs -- PTB polypyrimidine tract binding protein -- TFIIIA transcription factor IIIA -- ZRANB2 zinc finger RANBP2-type containing 2 -- PUF-HD pumilio homology domain -- SAXS small angle scattering -- MALAT1 metastasis associated lung adenocarcinoma transcript 1 -- CLIP-seq cross-linking and immunoprecipitation-seq -- MD molecular docking -- PDB protein data bank -- RPISeq RNA-protein interaction prediction -- CTF conjoint triad feature -- SVM support vector machine -- RF random forest -- SFPEL-LPI sequence-based feature projection ensemble learning for LPI -- PseDNC pseudo dinucleotide composition -- PseAAC pseudo amino acid composition -- LPI-BLS lncRNA–protein interactions-broad learning system -- GPLPI graph-based deep learning for lncRNA-protein interaction prediction -- LSTM long short-term memory -- MIL multiple instance learning -- AUC area under the curve -- AUPRC area under the precision-recall curve; Long non-coding RNA -- LncRNA, RNA-binding protein -- RBP, lncRNA-protein interaction (LPI) -- Cancer -- Mechanisms of action -- Structural and functional domains -- Machine learning -- Deep learning; Cancer -- Periodicals; Neoplasms -- Periodicals; Review Literature; Cancer -- Périodiques; Electronic journals; 616.994
• DOI: 10.1016/j.semcancer.2022.05.013
• Languages: English
• ISSNs: 1044-579X

Abstract

Abstract: Understanding the complex and specific roles played by non-coding RNAs (ncRNAs), which comprise the bulk of the genome, is important for understanding virtually every hallmark of cancer. This large group of molecules plays pivotal roles in key regulatory mechanisms in various cellular processes. Regulatory mechanisms, mediated by long non-coding RNA (lncRNA) and RNA-binding protein (RBP) interactions, are well documented in several types of cancer. Their effects are enabled through networks affecting lncRNA and RBP stability, RNA metabolism including N 6 -methyladenosine (m 6 A) and alternative splicing, subcellular localization, and numerous other mechanisms involved in cancer. In this review, we discuss the reciprocal interplay between lncRNAs and RBPs and their involvement in epigenetic regulation via histone modifications, as well as their key role in resistance to cancer therapy. Other aspects of RBPs including their structural domains, provide a deeper knowledge on how lncRNAs and RBPs interact and exert their biological functions. In addition, current state-of-the-art knowledge, facilitated by machine and deep learning approaches, unravels such interactions in better details to further enhance our understanding of the field, and the potential to harness RNA-based therapeutics as an alternative treatment modality for cancer are discussed.