Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches

Seminars in Cancer Biology, Journal Year: 2022, Volume and Issue: 86, P. 325 - 345

Published: May 25, 2022

Understanding the complex and specific roles played by non-coding RNAs (ncRNAs), which comprise bulk of genome, is important for understanding virtually every hallmark cancer. This large group molecules plays pivotal in key regulatory mechanisms various cellular processes. Regulatory mechanisms, mediated long RNA (lncRNA) RNA-binding protein (RBP) interactions, are well documented several types Their effects enabled through networks affecting lncRNA RBP stability, metabolism including N6-methyladenosine (m6A) alternative splicing, subcellular localization, numerous other involved In this review, we discuss reciprocal interplay between lncRNAs RBPs their involvement epigenetic regulation via histone modifications, as role resistance to cancer therapy. Other aspects structural domains, provide a deeper knowledge on how interact exert biological functions. addition, current state-of-the-art knowledge, facilitated machine deep learning approaches, unravels such interactions better details further enhance our field, potential harness RNA-based therapeutics an treatment modality discussed.

Language: Английский

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A narrative review of epigenetic marker in H3K27ac and its emerging potential as a therapeutic target in cancer

Epigenomics, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 17

Published: Feb. 21, 2025

Histone acetylation, particularly H3 K27 acetylation (H3K27ac), is a critical post-translational modification that regulates chromatin structure and gene expression, which plays significant role in various cancers, including breast, colon, lung, hepatocellular, prostate cancer. However, the mechanisms of H3K27ac tumorigenesis are not yet comprehensive, especially its epigenetic mechanisms. This review endeavors to discuss findings on involvement carcinogenesis within past 5 years through literature search using academic databases such as Web Science. Firstly, we provide an overview diverse landscape histone modifications, emphasizing distinctive characteristics significance H3K27ac. Secondly, summarize compare advanced high-throughput sequencing technologies have been utilized construction map. Thirdly, elucidate mediating transcription. Fourthly, venture into potential molecular mechanism cancer development. Finally, engage discussing future therapeutic approaches oncology, with spotlight strategies harness H3K27 modifications. In conclusion, this comprehensively summarizes underscores pivotal cancer, providing valuable insights target for intervention.

Language: Английский

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Colon cancer transcriptome

Progress in Biophysics and Molecular Biology, Journal Year: 2023, Volume and Issue: 180-181, P. 49 - 82

Published: April 13, 2023

Language: Английский

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The Prognostic Significance of TRs in Hepatocellular Carcinoma: Insights from TCGA and GEO Databases

Biomarker Insights, Journal Year: 2025, Volume and Issue: 20

Published: Jan. 1, 2025

Reduced expression of thyroid hormone receptors (TRs) has been observed in various human malignancies, though its predictive value hepatocellular carcinoma (HCC) remains uncertain. To explore the TRs patients with carcinoma. The design was bioinformatic analysis combined experimental study. This study utilized Kaplan-Meier TR profiles from Cancer Genome Atlas (TCGA). Expression levels HCC and immune single cells were assessed using datasets Gene Omnibus (GEO) TCGA, analyzed R software. Cox logistic regression analyses also conducted. Functional assays, including wound healing, CCK-8, Transwell migration employed to investigate role THRB gene. revealed that low significantly associated reduced overall survival (OS), 5-year OS disease-specific (DSS) (P < 0.05), while no significant association found THRA expression. Both identified as an independent risk factor for HCC. downregulated tumor tissues compared non-tumorous 3 GEO TCGA profile. assays confirmed inhibited cell proliferation migration. Additionally, single-cell RNA sequencing primarily expressed CD16+ monocytes within a poor rate. expression, but not THRA, correlated decreased patients.

Language: Английский

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Overview of the interplay between m6A methylation modification and non-coding RNA and their impact on tumor cells

Translational Cancer Research, Journal Year: 2024, Volume and Issue: 13(6), P. 3106 - 3125

Published: June 1, 2024

: N6-methyladenosine (m6A) is one of the most common internal modifications in eukaryotic RNA. The presence m6A on transcripts can affect a series fundamental cellular processes, including mRNA splicing, nuclear transportation, stability, and translation. modification introduced by methyltransferases (writers), removed demethylases (erasers), recognized m6A-binding proteins (readers). Current research has demonstrated that methylation involved regulation malignant phenotypes tumors controlling expression cancer-related genes. Non-coding RNAs (ncRNAs) are diverse group RNA molecules do not encode widely present human genome. This includes microRNAs (miRNAs), long non-coding (lncRNAs), circular (circRNAs), PIWI interaction (piRNAs). They function as oncogenes or tumor suppressors through various mechanisms, regulating initiation progression cancer. Previous studies primarily focused coding RNAs, but recent discoveries have revealed significant regulatory role ncRNAs. Simultaneously, ncRNAs also exert their influence modulating translation, other biological processes m6A-related enzymes. interplay between collectively contributes to occurrence humans. review provides an overview interactions factors impact tumors.

Language: Английский

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The Interaction Between N6-Methyladenosine Modification and Non-Coding RNAs in Gastrointestinal Tract Cancers

Frontiers in Oncology, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 7, 2022

N 6 -methyladenosine (m A) is the most common epigenetic modification of eukaryotic RNA, which can participate in growth and development body a variety physiological disease processes by affecting splicing, processing, localization, transport, translation, degradation RNA. Increasing evidence shows that non-coding RNAs, particularly microRNA, long circular also regulate RNA m A process expression A-related enzymes. The interaction between RNAs provides new perspective for exploration potential mechanism tumor genesis development. In this review, we summarize mechanisms effects gastrointestinal tract cancers.

Language: Английский

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Decreased SPTBN2 expression regulated by the ceRNA network is associated with poor prognosis and immune infiltration in low‑grade glioma

Experimental and Therapeutic Medicine, Journal Year: 2023, Volume and Issue: 25(6)

Published: April 18, 2023

The majority of low‑grade gliomas (LGGs) in adults invariably progress to glioblastoma over time. Spectrin β non‑erythrocytic 2 (SPTBN2) is detected numerous tumors and involved tumor occurrence metastasis. However, the specific roles detailed mechanisms SPTBN2 LGG are largely unknown. present study performed pan‑cancer analysis for expression prognosis SPTBN2 using Cancer Genome Atlas Genotype‑Tissue Expression. Western blotting was used detect amount between glioma tissues normal brain tissues. Subsequently, based on expression, prognosis, correlation immune infiltration, non‑coding RNAs (ncRNAs) were identified that regulated expression. Finally, infiltrates associated with performed. Lower correlated an unfavorable outcome LGG. A significant low mRNA poor clinicopathological features observed, including wild‑type isocitrate dehydrogenase status (P<0.001), 1p/19q non‑codeletion (P<0.001) elders (P=0.019). western results revealed that, compared tissues, significantly lower (P=0.0266). Higher five microRNAs (miRs/miRNAs), hsa‑miR‑15a‑5p, hsa‑miR‑15b‑5p, hsa‑miR‑16‑5p, hsa‑miR‑34c‑5p hsa‑miR‑424‑5p, by targeting four long ncRNAs (lncRNAs) [ARMCX5‑GPRASP2, BASP1‑antisense RNA 1 (AS1), EPB41L4A‑AS1 LINC00641] observed regulation via miRNAs. Moreover, checkpoint biomarkers cells. In conclusion, lowly expressed total six miRNAs lncRNAs as being able modulate a lncRNA‑miRNA‑mRNA network Furthermore, current findings also indicated possessed anti‑tumor regulating infiltration

Language: Английский

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SPTBN2 regulates endometroid ovarian cancer cell proliferation, invasion and migration via ITGB4‑mediated focal adhesion and ECM receptor signalling pathway

Experimental and Therapeutic Medicine, Journal Year: 2023, Volume and Issue: 25(6)

Published: April 24, 2023

Ovarian cancer is as a major contributor to gynaecologic death globally. The present study aimed investigate the regulatory role of spectrin β non-erythrocytic 2 gene (SPTBN2) in endometroid ovarian and its mechanism action. According Gene Expression Profiling Interactive Analysis (GEPIA) database, SPTBN2 expression elevated tissues higher indicated worse prognosis. assessed mRNA protein levels by reverse transcription-quantitative PCR western blotting, respectively. Cell viability, proliferation, migration invasion were with Counting Kit-8, 5-ethynyl-2'-deoxyuridine incorporation, wound healing Transwell assays, was notably enhanced cell lines, especially A2780 cells compared HOSEPiC (P<0.001). Following transfection small interfering (si)RNA targeting SPTBN2, decreased those transfected siRNA-NC Set Enrichment database revealed that primarily enriched 'focal adhesion' 'extracellular matrix (ECM)-receptor interaction', whereas significantly associated integrin β4 (ITGB4) GEPIA database. In addition, rescue experiments performed determine cancer. ITGB4 overexpression reversed inhibitory effects knockdown on (P<0.05). impacts focal adhesion downstream ECM receptor signalling-related proteins, including Src p-FAK/FAK, (P<0.01). Collectively, may regulate through ITGB4-mediated signalling pathway.

Language: Английский

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The bidirectional interplay between ncRNAs and methylation modifications in gastrointestinal tumors

International Journal of Biological Sciences, Journal Year: 2023, Volume and Issue: 19(15), P. 4834 - 4848

Published: Jan. 1, 2023

The aberrant expression of methylation and ncRNAs, two crucial regulators epigenetic modifications, has been widely demonstrated in cancer.The complex interplay between them is essential promoting malignant phenotype, poor prognosis, drug resistance GI tumors (including esophageal, gastric, colorectal, liver, pancreatic cancers).Therefore, we summarize the interrelation process ncRNAs modifications tumors, including detailed mechanism enzyme regulation molecular correlation interactions clinical features tumors.Finally, discuss potential value diagnosis therapy.

Language: Английский

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SPTBN2 Promotes the Progression of Thyroid Cancer by Accelerating G1/S Transition and Inhibiting Apoptosis

Disease Markers, Journal Year: 2022, Volume and Issue: 2022, P. 1 - 16

Published: Aug. 3, 2022

Thyroid carcinoma (TC) is an increasingly common malignancy of endocrine organs, and its most frequently encountered histotype papillary thyroid cancer (PTC). Identifying new potential gene alterations important for completely elucidating the mechanism PTC initiation progression. Thus, we performed whole transcriptome sequence analysis (RNA-seq) on 79 tissue samples paired adjacent nontumor to study molecular TC tumorigenesis progression further. The results RNA-seq showed that spectrin beta, nonerythrocytic 2 (SPTBN2), was markedly overexpressed in tissues relative tissues. Additionally, 502 58 from Cancer Genome Atlas dataset were consistent with our results. However, mechanisms function SPTBN2 remain unknown. We examined expression 48 tumor normal by using qRT-PCR. cell lines silenced small interfering RNA. Then, transfected cells used investigate vitro SPTBN2. significantly upregulated cohort, local validated TCGA cohort. experiment revealed lines, downregulation considerably suppressed proliferation, cycle, migration, colony formation, invasion induced apoptosis. Furthermore, protein levels CCNE2, CDK2, CDK4, Bcl-2 downregulated, those P21, Bax, cleaved caspase-8, caspase-3 had increased control cells. caused apoptosis retarded G1/S cycle transition may be a good candidate diagnosis therapy.

Language: Английский

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