Cancer-related molecular mechanisms research

Competing endogenous RNA networks reveal long non-coding RNAs as potential prognostic biomarkers in gastric cancer: A systematic review and meta-analysis

This study performs a systematic review and meta-analysis of lncRNAs as prognostic biomarkers in gastric cancer through ceRNA network studies, identifying two lncRNAs with significant prognostic value.

Frequent functional orthology of long noncoding RNAs and genomic loci associated with complex traits and disorders

The paper links GWAS-associated haplotype blocks to lncRNAs and their mammalian orthologs, showing strong functional associations with complex traits.

CRISPRi Screen Identifies a Novel Growth Suppressor lncRNA, INSTAR, in Human Monocytes

The paper identifies INSTAR, a novel lncRNA, as a growth suppressor in human monocytes through a CRISPRi screen, showing it regulates SFMBT2 expression to control proliferation.

LncRNA YIYA enhances pancreatic cancer proliferation under high-glucose conditions through RAS and PKM2 mediated metabolic reprogramming that reinforces the Warburg phenotype

This study identifies lncRNA YIYA as a glucose-responsive factor in pancreatic cancer that promotes proliferation via RAS and PKM2-mediated metabolic reprogramming, enhancing the Warburg effect.

Cell-Type-Specific Transcriptomic Signatures in Prefrontal Cortex Reveal lncRNA-mediated Gene Silencing and Enhancer Activities Contributing to the Pathophysiology of Major Depressive Disorder

The paper identifies cell-type-specific lncRNA-mediated gene silencing and enhancer activities in MDD, linking them to disrupted neuron-glia interactions and Hippo signaling.

The long non-coding RNA, CyKILRb, augments oncogenic phenotypes via induction of PIK3R2 and activation of the PI3K/AKT axis

This study identifies CyKILRb as an oncogenic long non-coding RNA that promotes tumorigenesis by upregulating PIK3R2 and activating the PI3K/AKT pathway.

SURFR: genome-free discovery of cancer-unique small RNAs from cohort sequencing data

The paper introduces a reference-free computational method to discover cancer-unique small RNAs from sequencing data, identifying 1211 novel oncRNAs with potential clinical relevance.

Promoter hijacking by primate LINC00473 disrupts an ancestral CREB-PDE10A feedback loop

The paper investigates how the primate-specific lncRNA LINC00473 disrupts an ancestral CREB-PDE10A feedback loop by hijacking its promoter.

A Bioinformatics-Driven ceRNA Network in Stomach Adenocarcinoma: Identification of Novel Prognostic mRNA-miRNA-lncRNA Interactions

The paper identifies novel prognostic mRNA-miRNA-lncRNA interactions in stomach adenocarcinoma through bioinformatics analysis.

CDH3-AS1 antisense RNA enhances P-cadherin translation and acts as a tumor suppressor in melanoma

A proteogenomic approach to discover novel lncRNA-derived peptides and their potential clinical utility in hepatocellular carcinoma

The paper discovers novel lncRNA-derived peptides in hepatocellular carcinoma using proteogenomic approaches and shows their potential as biomarkers.

Integrative multi-modal analysis reveals the contribution of noncoding RNAs to post-treatment progression of IDH-mutant astrocytomas

The paper identifies progression-related noncoding RNAs in IDH-mutant astrocytomas after treatment, linking them to cell cycle, ECM, and neural differentiation processes.

LncRNA LINC00941 Links Oncogenic KRAS Signaling to Aggressiveness and Chemoresistance in Pancreatic Cancer

This study identifies LINC00941 as a KRAS-regulated lncRNA that promotes aggressiveness and chemoresistance in pancreatic cancer, with prognostic significance.

Gain-of-function mutant p53 regulates long-noncoding RNA LINC00643 to modulate HIF1α in glioblastoma

This study identifies LINC00643 as a target of GOF-MUT-p53 in glioblastoma, showing it suppresses tumor growth by repressing HIF1α under hypoxia.

Using Deep Learning with Different Architectures to Recognize RNA:DNA Triplex Structures from Histone Modification Features

This study develops four deep learning models to predict RNA:DNA triplex formation potential using histone modification features, identifying novel lncRNAs and DNA sites.

Long non-coding RNA-3'UTR interactions coordinate GABA signaling in the brain

The paper shows that a long non-coding RNA, Gul, coordinates GABAergic gene expression by interacting with 3'UTR sites of target mRNAs in Drosophila neurons.

Deciphering the role of the lncRNA TRIBAL in hepatocyte models

The paper validates HepaRG cells as a model for studying TRIBAL, showing functional overlap with hepatocytes and highlighting TRIBAL's role in metabolic regulation.

JMJD6 and YBX1 physically interact and regulate HOTAIR proximal promoter

The paper shows JMJD6 and YBX1 physically interact and regulate HOTAIR promoter activity through a positive feedback loop, contributing to tumor progression.

Robust CRISPR Screens Identify TPL1 as a Novel Long Noncoding RNA Driving Triple-Negative Breast Cancer Hallmarks

The paper identifies TPL1 as a novel long noncoding RNA that drives triple-negative breast cancer hallmarks through multiple molecular mechanisms.

Cancer Driver Topologically Associated Domains identify oncogenic and tumor suppressive lncRNAs

The paper identifies cancer driver lncRNAs by analyzing their association with cancer driver genes and topologically associated domains, revealing 256 oncogenic, 177 tumor suppressive, and 75 dual-function lncRNAs.

LncCE: Landscape of Cellular-Elevated LncRNAs in Single Cells Across Normal and Cancer Tissues

LncCE identifies and characterizes cellular-elevated lncRNAs across normal and cancer tissues using single-cell RNA sequencing data, providing expression patterns and clinical associations.

Investigating the role of long non-coding RNA in hypertrophic cardiomyopathy

This study identifies differentially expressed lncRNAs in a mouse HCM model and prioritizes them using cross-species conservation and micropeptide coding potential.

PVT1 splicing activity predicts genome-wide gene expression with miRNA regulatory signatures

The paper identifies PVT1 splicing activity as a predictor of gene expression signatures enriched in miR-200/205 targets in breast cancer.

A shared RNA structural element mediates hnRNP K binding by two divergent lncRNAs in the DNA damage response

The paper identifies a conserved RNA structural element in lincRNA-p21 that mediates hnRNP K binding, enabling Cdkn1a activation in DNA damage response across species.

LncRNA SChLAP1 promotes cancer cell proliferation and invasion via its distinct structural domains and conserved regions

This study identifies functionally important structural modules of SChLAP1 that drive cancer cell proliferation and invasion in prostate cancer.

Correlated protein-RNA associations and a requirement for HNRNPU in long-range Polycomb recruitment by the lncRNAs Airn and Kcnq1ot1

The paper compares RNA-protein associations across lncRNAs Airn, Kcnq1ot1, and Xist, identifying HNRNPU's role in long-range Polycomb recruitment by Airn and Kcnq1ot1.

MACGA: Multi-scale Adaptive Convolution with Graph Attention for LncRNA-Disease Association Prediction

MACGA predicts lncRNA-disease associations using a graph attention network with multi-scale adaptive convolution, outperforming existing methods in cross-validation and validated by case studies.

Coordinated regulation by lncRNAs results in tight lncRNA-target couplings

The paper identifies lncRNAs that coordinately regulate both transcription and post-transcriptional processing of their targets, showing tight coupling between lncRNA and target abundance, with implications for cancer gene regulation.

LncPTPred: Predicting lncRNA-Protein Interaction based on Crosslinking and Immunoprecipitation (CLIP-Seq) Data

LncPTPred predicts lncRNA-protein interactions using CLIP-Seq data, outperforming existing tools and providing interaction segments for validation experiments.

Long Noncoding RNAs Preserve Pancreatic Cancer Identity and Resist Cell Fate Conversion

This study identifies long noncoding RNAs as key regulators of pancreatic cancer identity and resistance to reprogramming.