Emerging Roles of Long Noncoding RNAs in Breast Cancer Epigenetics and Epitranscriptomics

Suppression of HIV-1 transcription and latency reversal via ectopic expression of the viral antisense transcript AST

The mechanisms that regulate HIV-1 latency are not fully elucidated. Our previous studies showed that an HIV-1 antisense transcript (AST) promotes the deposition of histone modifications at the HIV-1 5' long terminal repeat, causing a closed chromatin state that suppresses viral transcription. Here, we report that ectopic expression of AST in CD4+ T cells from people living with HIV-1 undergoing antiretroviral therapy hinders the reactivation of viral transcription in response to ex vivo stimulation with pharmacologic and T cell receptor agonists, thus preventing the reversal of latency. We defined the structural domains and sequence motifs of AST that contribute to its latency-promoting functions. Last, we carried out an unbiased proteomic screen of AST interactors that revealed an array of host factors both previously known and not known to suppress HIV-1 expression. Our studies identify AST as a first-in-class biological molecule that is capable of enforcing HIV-1 latency and with actionable curative potential.

Epigenetic and epitranscriptomic role of lncRNA in carcinogenesis (Review)

Long non‑coding RNAs (lncRNAs) are key players in the regulation of gene expression by mediating epigenetic and epitranscriptomic modification. Dysregulation of lncRNAs is implicated in tumor initiation, progression and metastasis. lncRNAs modulate chromatin structure and gene transcription by recruiting epigenetic regulators, including DNA‑ or histone‑modifying enzymes. Additionally, lncRNAs mediate chromatin remodeling and enhancer‑promoter long‑range chromatin interactions to control oncogene expression by recruiting chromatin organization‑associated proteins, thereby promoting carcinogenesis. Furthermore, lncRNAs aberrantly induce oncogene expression by mediating epitranscriptomic modifications, including RNA methylation and RNA editing. The present study aimed to summarize the regulatory mechanisms of lncRNAs in cancer to unravel the complex interplay between lncRNAs and epigenetic/epitranscriptomic regulators in carcinogenesis. The present review aimed to provide a novel perspective on the epigenetic and epitranscriptomic roles of lncRNAs in carcinogenesis to facilitate identification of potential biomarkers and therapeutic targets for cancer diagnosis and treatment.

LINC00899 suppresses the progression of triple-negative breast cancer via the miRNA-425/PTEN axis and is a biomarker for neoadjuvant chemotherapy efficacy

Background: Close clinical attention has been paid to triple-negative breast cancer (TNBC) due to its poor prognosis, high recurrence and mortality rates and rapid invasion and metastasis. The present study aimed to explore the potential mechanism of LINC00899 in the progression of TNBC and its effect on the proliferation and migration of TNBC cells via the microRNA (miR)-425/phosphatase and tensin homolog (PTEN) axis. Methods: For this purpose, plasma exosomes and related clinical data from 119 patients with breast cancer receiving neoadjuvant chemotherapy (59 patients with TNBC, 32 with HER2+ and with 28 luminal-type) and 20 healthy women were collected. Functional assays were then used to verify the role of the LINC00899/miR-425/PTEN axis in the proliferation and migration of TNBC cells. Results: The results showed that the expression of LINC00899 was reduced in plasma exosomes and breast cancer cell lines, which was associated with the Ki-67 index, tumor size and the presence or absence of lymph node metastasis but was not associated with patient age, androgen receptor expression or cholangiocarcinoma thrombus. The receiver operating characteristic curve results showed that LINC00899 had a high predictive value for the pathological outcome of patients with TNBC receiving neoadjuvant treatment. The results of the functional experiments also showed that LINC00899 targeted and regulated miR-425 in TNBC, and miR-425 negatively regulated the expression of PTEN. Conclusions: In conclusion, the results of the present indicated that LINC00899 may predict neoadjuvant chemotherapy efficacy in patients with TNBC and that LINC00899 inhibited the proliferation and migration of MDA-MB-231 cells via the miR-425/PTEN axis.

Early Detection, Precision Treatment, Recurrence Monitoring: Liquid Biopsy Transforms Colorectal Cancer Therapy

Colorectal cancer (CRC) is a significant global health concern. We need ways to detect it early and determine the best treatments. One promising method is liquid biopsy, which uses cancer cells and other components in the blood to help diagnose and treat the disease. Liquid biopsies focus on three key elements: circulating tumor DNA (ctDNA), circulating microRNA (miRNA), and circulating tumor cells (CTC). By analyzing these elements, we can identify CRC in its early stages, predict how well a treatment will work, and even spot signs of cancer returning. This study investigates the world of liquid biopsy, a rapidly growing field. We want to understand how it can help us better recognize the molecular aspects of cancer, improve and diagnostics, tailor treatments to individual patients, and keep track of the disease over the long-term. We explored specific components of liquid biopsy, like extracellular vesicles and cell-free DNA, and how they are used to detect CRC. This review sheds light on the current state of knowledge and the many ways a liquid biopsy can be used in treating colorectal cancer. It can transform patient care, disease management, and clinical outcomes by offering non-invasive cancer-targeting solutions.

New insights of LncRNAs fingerprints in breast cancer progression: Tumorigenesis, drug resistance, and therapeutic opportunities

Breast cancer (BC) is one of the common female cancers and it is characterized by considerable problems regarding its development and therapy. Long non-coding RNAs (lncRNAs) have been identified as significant modulators in BC development, especially, in tumorigenicity and chemoresistance. We therefore endeavor to present an up-to-date understanding of lncRNAs and their impact on BC progression and treatment, concerning molecular processes, treatment options, and use as a therapeutic opportunity. LncRNAs are novel regulators of genes that cause therapeutic resistance and directly impact the functioning of both coding and non-coding genes in BC patients, but little is known about their mechanisms of actions. Thus, additional study is required to have a deeper understanding of their modes of action and possible roles in BC disease. This study aims to investigate the functions of lncRNAs in the development of BC, with particular attention to their role in tumorigenesis, drug resistance mechanisms, and therapeutic targets. This will help to identify novel therapeutic targets and improve the effectiveness of BC treatment.

Epitranscriptomic orchestrations: Unveiling the regulatory paradigm of m6A, A-to-I editing, and m5C in breast cancer via long noncoding RNAs and microRNAs

Breast cancer (BC) poses a persistent global health challenge, particularly in countries with elevated human development indices linked to factors such as increased life expectancy, education, and wealth. Despite therapeutic progress, challenges persist, and the role of epitranscriptomic RNA modifications in BC remains inadequately understood. The epitranscriptome, comprising diverse posttranscriptional modifications on RNA molecules, holds the potential to intricately modulate RNA function and regulation, implicating dysregulation in various diseases, including BC. Noncoding RNAs (ncRNAs), acting as posttranscriptional regulators, influence physiological and pathological processes, including cancer. RNA modifications in long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) add an extra layer to gene expression control. This review delves into recent insights into epitranscriptomic RNA modifications, such as N-6-methyladenosine (m6A), adenine-to-inosine (A-to-I) editing, and 5-methylcytosine (m5C), specifically in the context of lncRNA and miRNAs in BC, highlighting their potential implications in BC development and progression. Understanding this intricate regulatory landscape is vital for deciphering the molecular mechanisms underlying BC and identifying potential therapeutic targets.

Cuproptosis-related lncRNAs potentially predict prognosis and therapy sensitivity of breast cancer

Background: Cuproptosis-related lncRNAs regulate the biological functions of various cancers. However, the role of cuproptosis-related lncRNAs in breast cancer remains unclear. In this study, we investigated the biological functions and clinical applications of cuproptosis-related lncRNAs in breast cancer. Methods: The Cancer Genome Atlas (TCGA) database and the GSE20685 dataset were used for screening cuproptosis-related lncRNAs. Colony formation and CCK-8 kit assays were performed for detecting the proliferative function of cuproptosis-related lncRNAs, whereas wound healing, migration, and invasion assays were performed for detecting the metastatic regulation of cuproptosis-related lncRNAs in breast cancer. Finally, a prognostic cuproptosis-related lncRNA model was constructed using LASSO Cox regression analysis for detecting survival and sensitivity to conventional treatment (endocrine therapy, chemotherapy, and radiotherapy) and novel therapy (PARP and CDK4/6 inhibitors). Results: In this study, we screened six cuproptosis-related lncRNAs associated with the survival of patients with breast cancer. Biofunctional experiments indicated that cuproptosis-related lncRNAs play essential roles in regulating the proliferation and metastasis of breast cancer cells. Finally, we applied a model of six cuproptosis-related lncRNAs to classify the patients into high- and low-risk groups. High-risk group patients exhibited worse survival rates (p < 0.001) and lower sensitivity to chemotherapy, endocrine therapy, and radiation therapy. Compared with high-risk patients, low-risk patients exhibited a lower expression of CDK4/6 inhibitor-resistant biomarkers (CCNE1, E2F1, and E2F2) and PARP inhibitor-resistant biomarkers (BRCA1/BRCA2), indicating that patients in the low-risk group were more suitable for PARP inhibitor and CDK4/6 inhibitor application. Conclusion: Cuproptosis-related lncRNAs are essential for regulating the biological functions of breast cancer, and they have the potential to predict prognosis and sensitivity of breast cancer to various therapies.