LncRNA TMPO-AS1 promotes esophageal squamous cell carcinoma progression by forming biomolecular condensates with FUS and p300 to regulate TMPO transcription

In smokers, the axis NCAPG/hsa-let-7b-5p/TMPO-AS1 promotes lung adenocarcinoma

Background

Smoking is linked to high morbidity and mortality rates of lung cancer, emphasizing the need for a better understanding of prognosis-related mRNA/miRNA/lncRNA-ceRNA networks.

Materials and methods

The study utilized databases like OncoMX, The University of ALabama at Birmingham CANcer data (UALCAN), OncoDB, ENCORI, Kaplan-Meier (KM) Plotter, miRNet, CancerMIRNome, TISIDB, and TIMER2.0 to analyze NCAPG/miRNA and LncRNA expression in lung cancer tumors and healthy tissues.

Results

The NCAPG gene is overexpressed in lung cancer cells. High NCAPG expression is associated with adenocarcinoma patients with a log fold change of 8.7 in case of tumor vs. normal samples (t = 515, n = 59). Overexpression of NCAPG indicates poor overall survivability in lung adenocarcinoma (LUAD) patients [hazard ratio (HR) = 1.6, confidence interval (CI) = 1.34-1.9, p = 9.9e-08] and those with a smoking history (HR = 1.44, CI = 1.11-1.87, p = 0.0062), but not significantly associated with lung squamous cell carcinoma (LUSC). miRNA hsa-let-7b-5p negatively correlates (R = -0.348) with NCAPG expression, with its down expression associated with poor survivability (HR = 0.71), while lncRNA TMPO-AS1 positively correlates (R = 0.575) with the NCAPG axis, with its overexpression associated with poor survivability (HR = 2.16).

Conclusion

Elevated levels of NCAPG and TMPO-AS1 in lung adenocarcinoma patients lead to aggressive growth and poor prognosis. miRNA hsa-let-7b-5p, a key miRNA, may inhibit these factors, potentially improving patient prognosis. Further research and clinical trials are needed to validate this targeted therapy.

New mechanism of LncRNA: In addition to act as a ceRNA

Long non-coding RNAs (LncRNAs) are a class of RNA molecules with nucleic acid lengths ranging from 200 bp to 100 kb that cannot code for proteins, which are diverse and widely expressed in both animals and plants. Scholars have found that lncRNAs can regulate human physiological processes at the gene and protein levels, mainly through the regulation of epigenetic, transcriptional and post-transcriptional levels of genes and proteins, as well as in the immune response by regulating the expression of immune cells and inflammatory factors, and thus participate in the occurrence and development of a variety of diseases. From the downstream targets of lncRNAs, we summarize the new research progress of lncRNA mechanisms other than miRNA sponges in recent years, aiming to provide new ideas and directions for the study of lncRNA mechanisms.

Epigenetic modifications involving ncRNAs in digestive system cancers: focus on histone modification

In recent years, epigenetic modifications have been strongly linked to tumor development, with histone modifications representing a key epigenetic mechanism. In addition, non-coding RNAs (ncRNAs) play a critical role in regulating cancer-related pathways. The abnormal interaction between histone modifications and ncRNAs, both pivotal epigenetic regulators, has been widely observed across various cancer types. Here, we systematically explore the molecular mechanisms through which histone modifications and ncRNAs contribute in the pathogenesis of digestive system cancers, and aberrant ncRNA-mediated histone modifications manipulate various biological behaviors of tumor cells including proliferation, migration, angiogenesis, etc. In addition, we provide new insights into diagnostic, prognostic markers, therapeutic targets and chemoradiation resistance for digestive system cancers from the epigenetic perspective.

AP001885.4 promotes the proliferation of esophageal squamous cell carcinoma cells by histone lactylation- and NF-κB (p65)-dependent transcription activation and METTL3-mediated mRNA stability of c-myc

Esophageal squamous cell carcinoma (ESCC) is an aggressive malignant neoplasm, and up to now, the role of long non-coding RNA (lncRNA) AP001885.4 in cancer, including ESCC, is absolutely unclear. The GEPIA database was applied to identify differentially expressed and prognosis-associated genes in esophageal cancer (ESCA). CCK-8, colony formation, Western blot, and qRT-PCR methods were harnessed to investigate the role and mechanism of AP001885.4 in esophageal carcinogenesis. By analyzing TCGA data in the GEPIA database, two lncRNAs were selected. AP001885.4 was overexpressed and positively associated with the unfavorable outcome of ESCC patients, and LINC001786 was under-expressed and negatively linked with the poor prognosis. Knockdown of AP001885.4 suppressed the proliferation and colony formation of ESCC cells. Importantly, the silence of AP001885.4 downregulated c-myc. Mechanically, the knockdown of AP001885.4 reduced METTL3 expression and m6A modification in c-myc mRNA, and METTL3 positively regulated c-myc. Furthermore, the knockdown of AP001885.4 diminished histone lactylation and NF-κB (p65) expression, and the protein lactylation inhibitors (2-DG, 2-deoxy-D-glucose and oxamate) and the NF-κB inhibitor (JSH-23) also lessened c-myc expression. Consequently, our findings suggested that AP001885.4 promoted the proliferation of esophageal squamous cell carcinoma cells by histone lactylation- and NF-κB (p65)-dependent transcription activation and METTL3-mediated mRNA stability of c-myc.

CXCR4 up-regulation mediated by USP1 deubiquitination promotes the tumorigenesis and immune escape in esophageal squamous-cell carcinoma

CXC chemokine receptor 4 (CXCR4) and ubiquitin specific protease 1 (USP1) have been reported to involve in the tumorigenesis of esophageal squamous-cell carcinoma (ESCC). Here, we investigated whether USP1 induced CXCR4 deubiquitination in regulating ESCC progression. MTT assay, 5-ethynyl-2'-deoxyuridine assay, flow cytometry, transwell assay and ELISA analysis were used to detect cell oncogenic phenotypes, macrophage phenotypes, inflammatory cytokines production, the cytotoxicity of cytokine-induced killer (CIK) cells and CD8 + T cell apoptosis. Protein interaction was determined by immunoprecipitation assay. Cellular ubiquitination detected the ubiquitination effect on CXCR4. A mouse xenograft model was established for in vivo experiments. CXCR4 was highly expressed in ESCC tissues and cells. Functionally, CXCR4 silencing suppressed ESCC cell proliferation, invasion, and induced cell apoptosis. Moreover, CXCR4 deficiency suppressed cancer cell immune escape by suppressing macrophage M2 polarization, elevating inflammatory cytokines produced by PBMCs, enhancing the cytotoxicity of CIK cells, and suppressing CD8 + T cell apoptosis. A high USP1 expression was observed in ESCC, USP1 interacted with CXCR4 and enhanced its protein stability through deubiquitination. USP1 silencing suppressed ESCC cell proliferation, invasion, and immune escape, which were reversed by CXCR4 overexpression. In vivo assay showed that USP1 deficiency impeded tumor growth by regulating CXCR4. Besides, fused in sarcoma (FUS) was confirmed to bind to USP1 and stabilized its mRNA expression, and could regulate CXCR4 via USP1. In conclusion, USP1 stabilized CXCR4 by removing ubiquitination on CXCR4, thereby promoting ESCC cell proliferation, invasion, and immune escape in vitro, and tumor growth in vivo.

Construction of machine learning models of lipid metabolism-related long non-coding RNA in lung adenocarcinoma is associated with microenvironmental heterogeneity and immunotherapy

Using various bioinformatics tools, we constructed a prognostic model integrating the expression profiles of lipid metabolization-related lncRNAs and clinical features. Our study discovered that various lipid metabolism-related lncRNAs were linked to the prognosis of lung adenocarcinoma. The link between immune cell infiltration in the tumour microenvironment and the expression level of lncRNAs involved with lipid metabolism was also investigated. Our findings suggest that there is a complex interplay between lipid metabolism, microenvironmental heterogeneity, and immunotherapy in lung adenocarcinoma. Furthermore, the study has significant clinical implications for the development of effective therapies for patients with lung adenocarcinoma by investigating the potential of these lncRNAs as biomarkers for anticipating the response to immunotherapy. Finally, our study emphasises the significance of continued analysis of lncRNAs associated with lipid metabolism in tumours to better understand the mechanisms behind the incidence and progression of lung adenocarcinoma. Several of the strengths of our work are the extensive analysis of the relationship between lipid metabolism and lncRNAs in lung adenocarcinoma and the utilization of a sizable sample size from the TCGA-LUAD cohort. However, there are also some limitations. Firstly, the mechanisms of how these lncRNAs interact with lipid metabolism pathways and immune response require further investigation. Secondly, our study was based on bioinformatics analysis and lacked experimental verification. Finally, our study was limited to the TCGA-LUAD cohort and further validation using other independent cohorts is required. In conclusion, our study provides a comprehensive and systematic analysis of lncRNAs associated with lipid metabolism in lung adenocarcinoma. Lung cancer patients may benefit from using identified lncRNAs as therapeutic targets and prognostic biomarkers. Validating these findings and confirming the potential therapeutic applications of these lncRNAs will require more mechanistic research.

Competing Endogenous TMPO-AS1-let-7c-5p- LDHA RNA Network Predicts the Prognosis of Lung Adenocarcinoma Patients

OBJECTIVE

Lactate dehydrogenase is dysregulated in several cancer types. However, the mechanism of its dysregulation in lung cancer is not fully understood. We utilized web-based computational databases to conduct gene expression analysis on LDHA, identified its regulator, and explored their role in the prognosis of lung cancer.

METHODS

We used various web-based computational tools, including the UALCAN, TIMER2.0, ENCORI, TCGA Portal, OncoDB, and GEPIA2 datasets for lung cancer analysis in this study. We also performed survival, biological processes, and metastasis analysis using various computational tools. We also carried out co-expression functional enrichment analysis using the Enrichr and TIMER databases, multivariate analysis of survival and pathological stage, and transcriptional regulation analysis using the ENCORI and OncoDB datasets. Furthermore, LDHA inhibitor binding of withanolides was analyzed using Auto Dock Tools 1.5.6, LigPlot+, and Pymol.

RESULTS

The study found that the higher levels of LDHA gene expression were associated with poor prognosis and overall survival in lung cancer patients. We identified 11 key genes co-expressed with LDHA; out of them, two genes, MKI67 and PGK1, showed a strong positive correlation with LDHA and associated poor survival outcomes in LUAD patients. Furthermore, we also identified hsa-let-7c-5p and TMPO-AS1 as potential regulators of LDHA in LUAD. It might be possible that the TMPO-AS1- hsa-let-7c-5p-LDHA ceRNA network could serve as a potential regulator of aerobic glycolysis in LUAD and can serve as prognostic biomarkers. Further, Withanolides can inhibit the activity of LDHA and can be tested as an adjuvant treatment.

CONCLUSION

We conclude that LDHA is overexpressed in LUAD, and the patients with high expression of LDHA exhibit poor prognosis. Further, the TMPO-AS1-hsa-let-7c-5p-LDHA ceRNA network can regulate aerobic glycolysis, thereby facilitating tumor growth in lung cancer.

Roles of long non‑coding RNAs in esophageal cell squamous carcinoma (Review)

Esophageal squamous cell carcinoma (ESCC) is a prevalent and deadly malignancy of the digestive tract. Recent research has identified long non‑coding RNAs (lncRNAs) as crucial regulators in the pathogenesis of ESCC. These lncRNAs, typically exceeding 200 nucleotides, modulate gene expression through various mechanisms, including the competing endogenous RNA (ceRNA) pathway and RNA‑protein interactions. The current study reviews the multifaceted roles of lncRNAs in ESCC, highlighting their involvement in processes such as proliferation, migration, invasion, epithelial‑mesenchymal transition, cell cycle progression, resistance to radiotherapy and chemotherapy, glycolysis, apoptosis, angiogenesis, autophagy, tumor growth, metastasis and the maintenance of cancer stem cells. Specific lncRNAs like HLA complex P5, LINC00963 and non‑coding repressor of NFAT have been shown to enhance resistance to radio‑ and chemotherapy by modulating pathways such as AKT signaling and microRNA interaction, which promote cell survival and proliferation under therapeutic stress. Furthermore, lncRNAs like family with sequence similarity 83, member A antisense RNA 1, zinc finger NFX1‑type containing 1 antisense RNA 1 and taurine upregulated gene 1 are implicated in enhancing invasive and proliferative capabilities of ESCC cells through the ceRNA mechanism, while interactions with RNA‑binding proteins further influence cancer cell behavior. The comprehensive analysis underscores the potential of lncRNAs as biomarkers for prognosis and therapeutic targets in ESCC, suggesting avenues for future research focused on elucidating the detailed molecular mechanisms and clinical applications of lncRNAs in ESCC management.

Non‑coding RNA: A promising diagnostic biomarker and therapeutic target for esophageal squamous cell carcinoma (Review)

Esophageal cancer (EC) is a common form of malignant tumor in the digestive system that is classified into two types: Esophageal squamous cell carcinomas (ESCC) and esophageal adenocarcinoma. ESCC is known for its early onset of symptoms, which can be difficult to identify, as well as its rapid progression and tendency to develop drug resistance to chemotherapy and radiotherapy. These factors contribute to the high incidence of disease and low cure rate. Therefore, a diagnostic biomarker and therapeutic target need to be identified for ESCC. Non-coding RNAs (ncRNAs) are a class of molecules that are transcribed from DNA but do not encode proteins. Initially, ncRNAs were considered to be non-functional segments generated during transcription. However, with advancements in high-throughput sequencing technologies in recent years, ncRNAs have been associated with poor prognosis, drug resistance and progression of ESCC. The present study provides a comprehensive overview of the biogenesis, characteristics and functions of ncRNAs, particularly focusing on microRNA, long ncRNAs and circular RNAs. Furthermore, the ncRNAs that could potentially be used as diagnostic biomarkers and therapeutic targets for ESCC are summarized to highlight their application value and prospects in ESCC.

Deciphering the oncogenic landscape: Unveiling the molecular machinery and clinical significance of LncRNA TMPO-AS1 in human cancers

The in-depth exploration of long non-coding RNAs (lncRNAs) reveals their pivotal and diverse roles in various disorders, particularly cancer. Within this intricate landscape, thymopoietin-antisense RNA-1 (TMPO-AS1) emerges as a noteworthy instigator of oncogenesis in humans. This exhaustive review seeks to intricately unravel the present understanding of TMPO-AS1, emphasizing its molecular foundations and highlighting its clinical applications in the realm of cancer research. TMPO-AS1 consistently exhibits heightened expression across a spectrum of cancer types, encompassing lung, colorectal, breast, cervical, bladder, pancreatic, hepatocellular, gastric, ovarian, and osteosarcoma. Elevated levels of TMPO-AS1 are intricately linked to unfavorable prognoses, accompanied by distinctive clinical and pathological characteristics. Functionally, TMPO-AS1 showcases its prowess in enhancing cancer cell migration, invasion, proliferation, and orchestrating epithelial-mesenchymal transition (EMT) through a myriad of molecular mechanisms. These mechanisms entail intricate interactions with proteins, microRNAs, and intricate signaling pathways. Furthermore, TMPO-AS1 is intricately involved in regulating critical cellular processes, including apoptosis and the cell cycle. The mounting evidence converges towards the potential of TMPO-AS1 serving as a diagnostic and prognostic biomarker, further entwined with its potential role in influencing chemoresistance in cancer. This potential is underscored by its consistent associations with clinical outcomes and treatment responses. This comprehensive investigation not only consolidates our existing knowledge of TMPO-AS1's multifaceted roles but also sheds illuminating insights on its profound significance in the intricate landscape of cancer biology, paving the way for potential applications in clinical practice.

27-Hydroxycholesterol induces liver fibrosis via down-regulation of trimethylation of histone H3 at lysine 27 by activating oxidative stress; effect of nutrient interventions

BACKGROUND

Chronic liver injury caused by activation of hepatic stellate cells (HSCs) is a key event in the development of liver fibrosis (LF). A high-cholesterol diet can prompt accumulation of free cholesterol in HSCs, which promotes HSC activation and progression of LF.

OBJECTIVE

27-Hydroxycholesterol (27HC) is the most abundant cholesterol metabolite. Here, we investigated whether the HSC activation and LF induced by high cholesterol is caused by its metabolite 27HC, and whether TGFβ classical signaling were involved in these processes.

METHODS

In vitro, LX2 and HSC-T6 cells were used to explore the effects of 27HC on activation of HSCs, while LSECs were used to observe the effects of 27HC on capillarization. In vivo, zebrafish were used to assess the effect of 27HC on LF.

RESULTS

The cholesterol metabolite 27HC promoted the proliferation of HSCs and up-regulated expression of COL-1 and α-SMA as well as CTGF and TIMP1. Also, 27HC up-regulated expression of Smad2/3 and phosphorylated Smad2/3 in HSCs. Furthermore, 27HC-induced up-regulation of COL-1, α-SMA, CTGF, and TIMP1 protein levels was inhibited by Smad2/3 knockout. In addition, 27HC down-regulated H3K27me3 by inhibition of EZH2 and promotion of UTX and JMJD3 expression via the TGFβ signaling, thereby inducing activation of HSCs. Notably, 27HC significantly aggravated the pathological damage induced by DEN, and induced deposition of collagen fibers in zebrafish liver. Folic acid (FA) and resveratrol (RES) both reduced 27HC-induced production of reactive oxygen species (ROS) and inhibited the effects of TGFβ signaling on EZH2, UTX, and JMJD3, thereby increasing H3K27me3, and finally jointly inhibiting LF.

CONCLUSION

Cholesterol is metabolized to 27HC, which mediates activation of HSCs and onset of LF. Reduced expression of H3k27me3 by TGFβ signaling is crucial to 27HC-induced LF. FA and RES ameliorated activation of HSCs and LF by reducing 27HC-induced production of ROS and regulating of H3K27me3.

Lymph node metastasis-related lncRNA GAS6-AS1 facilitates the progression of esophageal squamous cell carcinoma

Background

Lymph node metastasis is the main type of metastasis in esophageal squamous cell carcinoma (ESCC), especially when the primary tumor invasion depth reaches above the adventitia layer (T3 stage), the incidence of lymph node metastasis increases sharply. Abnormal expression of long non-coding RNAs (lncRNAs) has been confirmed in ESCC, but there are still many unknown connections between lncRNAs and lymph node metastasis.

Methods

We used transcriptome sequencing (RNA-seq) to analyze 10 pairs of ESCC tissues with primary tumor stage T3 and their paired normal epithelium. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to further verify the sequencing results, and survival curve analysis, logistic regression analysis, and receiver operating characteristic (ROC) curve analysis were used to investigate its clinical application value. We investigated the growth and metastasis effects of lncRNA GAS6-AS1 on ESCC cell lines TE-1 and KYSE410 in vitro and in vivo. Other functional experiments included cell apoptosis and cell cycle experiments.

Results

Based on our RNA-seq data, lncRNA GAS6-AS1 is highly expressed in ESCC tissues, especially in cancer tissues with lymph node metastasis. The qRT-PCR experiment analysis showed that high expression of GAS6-AS1 was related to poor tumor differentiation and tumor stage. Logistic regression analysis showed that it was an independent risk factor for lymph node metastasis, and ROC analysis validated that it could predict lymph node metastasis. Further survival analysis suggested that high expression of GAS6-AS1 was associated with patients' poor prognosis. In vitro experiments, knocking down GAS6-AS1 inhibited the growth and metastasis of ESCC cells and inhibited tumor growth in vivo. In addition, knocking down GAS6-AS1 can inhibit cell cycle and promote cell apoptosis.

Conclusions

Our results revealed that lncRNA GAS6-AS1 obtained from RNA-seq can be used as an independent risk factor for ESCC lymph node metastasis and an effective biomarker to predict, and that it was related to the growth and metastasis of ESCC. It may represent a new biomarker to aid in the assessment of the lymph node metastasis of ESCC.

Targeting epigenetic deregulations for the management of esophageal carcinoma: recent advances and emerging approaches

Ranking from seventh in incidence to sixth in mortality, esophageal carcinoma is considered a severe malignancy of food pipe. Later-stage diagnosis, drug resistance, and a high mortality rate contribute to its lethality. Esophageal squamous cell carcinoma and esophageal adenocarcinoma are the two main histological subtypes of esophageal carcinoma, with squamous cell carcinoma alone accounting for more than eighty percent of its cases. While genetic anomalies are well known in esophageal cancer, accountability of epigenetic deregulations is also being explored for the recent two decades. DNA methylation, histone modifications, and functional non-coding RNAs are the crucial epigenetic players involved in the modulation of different malignancies, including esophageal carcinoma. Targeting these epigenetic aberrations will provide new insights into the development of biomarker tools for risk stratification, early diagnosis, and effective therapeutic intervention. This review discusses different epigenetic alterations, emphasizing the most significant developments in esophageal cancer epigenetics and their potential implication for the detection, prognosis, and treatment of esophageal carcinoma. Further, the preclinical and clinical status of various epigenetic drugs has also been reviewed.

Patient-derived tumor models: a suitable tool for preclinical studies on esophageal cancer

Esophageal cancer (EC) is the tenth most common cancer worldwide and has high morbidity and mortality. Its main subtypes include esophageal squamous cell carcinoma and esophageal adenocarcinoma, which are usually diagnosed during their advanced stages. The biological defects and inability of preclinical models to summarize completely the etiology of multiple factors, the complexity of the tumor microenvironment, and the genetic heterogeneity of tumors severely limit the clinical treatment of EC. Patient-derived models of EC not only retain the tissue structure, cell morphology, and differentiation characteristics of the original tumor, they also retain tumor heterogeneity. Therefore, compared with other preclinical models, they can better predict the efficacy of candidate drugs, explore novel biomarkers, combine with clinical trials, and effectively improve patient prognosis. This review discusses the methods and animals used to establish patient-derived models and genetically engineered mouse models, especially patient-derived xenograft models. It also discusses their advantages, applications, and limitations as preclinical experimental research tools to provide an important reference for the precise personalized treatment of EC and improve the prognosis of patients.

Non-coding RNAs' function in cancer development, diagnosis and therapy

While previous research on cancer biology has focused on genes that code for proteins, in recent years it has been discovered that non-coding RNAs (ncRNAs)play key regulatory roles in cell biological functions. NcRNAs account for more than 95% of human transcripts and are an important entry point for the study of the mechanism of cancer development. An increasing number of studies have demonstrated that ncRNAs can act as tumor suppressor genes or oncogenes to regulate tumor development at the epigenetic level, transcriptional level, as well as post-transcriptional level. Because of the importance of ncRNAs in cancer, most clinical trials have focused on ncRNAs to explore whether ncRNAs can be used as new biomarkers or therapies. In this review, we focus on recent studies of ncRNAs including microRNAs (miRNAs), long ncRNAs (lncRNAs), circle RNAs (circRNAs), PIWI interacting RNAs (piRNAs), and tRNA in different types of cancer and explore the application of these ncRNAs in the development of cancer and the identification of relevant therapeutic targets and tumor biomarkers. Graphical abstract drawn by Fidraw.

LncRNA AC142119.1 facilitates the progression of neuroblastoma by epigenetically initiating the transcription of MYCN

BACKGROUND

Oncogene MYCN is closely related with malignant progression and poor prognosis of neuroblastoma (NB). Recently, long non-coding RNAs (lncRNAs) have been recognized as crucial regulators in various cancers. However, whether lncRNAs contribute to the overexpression of MYCN in NB is unclear.

METHODS

Microarray analysis were applied to analyze the differentially expressed lncRNAs between MYCN-amplified and MYCN-non-amplified NB cell lines. Bioinformatic analyses were utilized to identify lncRNAs nearby MYCN locus. qRT-PCR was used to detect the expression level of lncRNA AC142119.1 in NB cell lines and tissues. Gain- and loss-of-function assays were conducted to investigate the biological effect of AC142119.1 in NB. Fluorescence in situ hybridization, RNA pull-down, RNA immunoprecipitation, mass spectrometry, RNA electrophoretic mobility shift, chromatin immunoprecipitation and chromatin isolation by RNA purification assays were performed to validate the interaction between AC142119.1 and WDR5 protein as well as MYCN promoter.

RESULTS

AC142119.1 was significantly elevated in NB tissues with MYCN amplification, advanced INSS stage and high risk, and associated with poor survival of NB patients. Moreover, enforced expression of AC142119.1 reinforced the proliferation of NB cells in vitro and in vivo. Additionally, AC142119.1 specifically recruited WDR5 protein to interact with MYCN promoter, further initiating the transcription of MYCN and accelerating NB progression.

CONCLUSIONS

We identified a novel lncRNA AC142119.1, which promoted the progression of NB through epigenetically initiating the transcription of MYCN via interacting with both WDR5 protein and the promoter of MYCN, indicating that AC142119.1 might be a potential diagnostic biomarker and therapeutic target for NB.

Long noncoding RNA Regulating ImMune Escape regulates mixed lineage leukaemia protein-1-H3K4me3-mediated immune escape in oesophageal squamous cell carcinoma

BACKGROUND

Predictive biomarkers for oesophageal squamous cell carcinoma (ESCC) immunotherapy are lacking, and immunotherapy resistance remains to be addressed. The role of long noncoding RNA (lncRNA) in ESCC immune escape and immunotherapy resistance remains to be elucidated.

METHODS

The tumour-associated macrophage-upregulated lncRNAs and the exosomal lncRNAs highly expressed in ESCC immunotherapy nonresponders were identified by lncRNA sequencing and polymerase chain reaction assays. CRISPR-Cas9 was used to explore the functional roles of the lncRNA. RNA pull-down, MS2-tagged RNA affinity purification (MS2-TRAP) and RNA-binding protein immunoprecipitation (RIP) were performed to identify lncRNA-associated proteins and related mechanisms. In vivo, the humanized PBMC (hu-PBMC) mouse model was established to assess the therapeutic responses of specific lncRNA inhibitors and their combination with programmed cell death protein 1 (PD-1) monoclonal antibody (mAb). Single-cell sequencing, flow cytometry, and multiplex fluorescent immunohistochemistry were used to analyze immune cells infiltrating the tumour microenvironment.

RESULTS

We identified a lncRNA that is involved in tumour immune evasion and immunotherapy resistance. High LINC02096 (RIME) expression in plasma exosomes correlates with a reduced response to PD-1 mAb treatment and poor prognosis. Mechanistically, RIME binds to mixed lineage leukaemia protein-1 (MLL1) and prevents ankyrin repeat and SOCS box containing 2 (ASB2)-mediated MLL1 ubiquitination, improving the stability of MLL1. RIME-MLL1 increases H3K4me3 levels in the promoter regions of programmed death-ligand 1 (PD-L1) and indoleamine 2,3-dioxygenase 1 (IDO-1), constitutively increasing the expression of PD-L1/IDO-1 in tumour cells and inhibiting CD8+ T cells infiltration and activation. RIME depletion in huPBMC-NOG mice significantly represses tumour development and improves the effectiveness of PD-1 mAb treatment by activating T-cell-mediated antitumour immunity.

CONCLUSIONS

This study reveals that the RIME-MLL1-H3K4me3 axis plays a critical role in tumour immunosuppression. Moreover, RIME appears to be a potential prognostic biomarker for immunotherapy and developing drugs that target RIME may be a new therapeutic strategy that overcomes immunotherapy resistance and benefits patients with ESCC.

The long transcript of lncRNA TMPO-AS1 promotes bone metastases of prostate cancer by regulating the CSNK2A1/DDX3X complex in Wnt/β-catenin signaling

The second most common male cancer is prostate cancer (PCa), which has a high tendency for bone metastasis. Long non-coding RNAs, including TMPO-AS1, play a crucial role in PCa progression. However, TMPO-AS1's function in PCa bone metastasis (BM) and its underlying molecular mechanisms are unclear. Herein, we found that the long transcript of TMPO-AS1 (TMPO-AS1L) was upregulated in PCa tissues with bone metastasis, and overexpression of TMPO-AS1L correlated with advanced clinicopathological features and reduced BM-free survival in patients with PCa. Upregulated TMPO-AS1L promoted, whereas downregulated TMPO-AS1L inhibited, the PCa cell bone metastatic capacity in vitro and in vivo. Mechanistically, TMPO-AS1L was demonstrated to act as a scaffold, that strengthened the interaction of casein kinase 2 alpha 1 (CSNK2A1) and DEAD-box helicase 3 X-linked (DDX3X), and activated the Wnt/β-catenin signaling pathway, thus promoting BM of PCa. Moreover, upregulation of TMPO-AS1L in PCa resulted from transcription elongation modulated by general transcription factor IIF subunit 2 (GTF2F2). Collectively, our study provides critical insights into the role of TMPO-AS1L in PCa BM via Wnt/β-catenin signaling, identifying TMPO-AS1L as a candidate marker of PCa bone metastasis prognosis and therapeutic target.

Comparative transcriptome characterization of esophageal squamous cell carcinoma and adenocarcinoma

Background

Esophageal cancers are primarily categorized as esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). While various (epi) genomic alterations associated with tumor development in ESCC and EAC have been documented, a comprehensive comparison of the transcriptomes in these two cancer subtypes remains lacking.

Methods

We collected 551 gene expression profiles from publicly available sources, including normal, ESCC, and EAC tissues or cell lines. Subsequently, we conducted a systematic analysis to compare the transcriptomes of these samples at various levels, including gene expression, promoter activity, alternative splicing (AS), alternative polyadenylation (APA), and gene fusion.

Results

Seven distinct cluster gene expression patterns were identified among the differentially expressed genes in normal, ESCC, and EAC tissues. These patterns were enriched in the PI3K-Akt signaling pathway and the activation of extracellular matrix organization and exhibited repression of epidermal development. Notably, we observed additional genes or unique expression levels enriched in these shared pathways and biological processes related to tumor development and immune activation. In addition to the differentially expressed genes, there was an enrichment of lncRNA co-expression networks and downregulation of promoter activity associated with the repression of epidermal development in both ESCC and EAC. This indicates a common feature between these two cancer subtypes. Furthermore, differential AS and APA patterns in ESCC and EAC appear to partially affect the expression of host genes associated with bacterial or viral infections in these subtypes. No gene fusions were observed between ESCC and EAC, thus highlighting the distinct molecular mechanisms underlying these two cancer subtypes.

Conclusions

We conducted a comprehensive comparison of ESCC and EAC transcriptomes and uncovered shared and distinct transcriptomic signatures at multiple levels. These findings suggest that ESCC and EAC may exhibit common and unique mechanisms involved in tumorigenesis.

m6A-enriched lncRNA LINC00839 promotes tumor progression by enhancing TAF15-mediated transcription of amine oxidase AOC1 in nasopharyngeal carcinoma

Dysregulation of long non-coding RNAs (lncRNAs) contributes to tumorigenesis by modulating specific cancer-related pathways, but the roles of m6A-enriched lncRNAs and underlying mechanisms remain elusive in nasopharyngeal carcinoma (NPC). Here, we reanalyzed the previous genome-wide analysis of lncRNA profiles in 18 pairs of NPC and normal tissues, as well as in 10 paired samples from NPC with or without posttreatment metastases. We discerned that an oncogenic m6A-enriched lncRNA, LINC00839, which was substantially upregulated in NPC and correlated with poor clinical prognosis, promoted NPC growth and metastasis both in vitro and in vivo. Mechanistically, by using RNA pulldown assay combined with mass spectrometry, we found that LINC00839 interacted directly with the transcription factor, TATA-box binding protein associated factor (TAF15). Besides, ChIP and dual-luciferase report assays demonstrated that LINC00839 coordinated the recruitment of TAF15 to the promoter region of amine oxidase copper-containing 1 (AOC1), which encodes a secreted glycoprotein playing vital roles in various cancers, thereby activating AOC1 transcription in trans. In this study, potential effects of AOC1 in NPC progression were first proposed. Moreover, ectopic expression of AOC1 partially rescued the inhibitory effect of downregulation of LINC00839 in NPC. Furthermore, we showed that silencing vir-like m6A methyltransferase-associated (VIRMA) and insulin-like growth factor 2 mRNA-binding proteins 1 (IGF2BP1) attenuated the expression level and RNA stability of LINC00839 in an m6A-dependent manner. Taken together, our study unveils a novel oncogenic VIRMA/IGF2BP1-LINC00839-TAF15-AOC1 axis, and highlights the significance and prognostic value of LINC00839 expression in NPC carcinogenesis.

In Silico and Experimental Analyses of Long Non-coding RNA TMPO-AS1 Expression in Iranian Patients with Gastric Cancer

Background: In recent decades, many long non-coding RNAs (lncRNAs) have been reported to play a prominent role in tumorigenesis and the progression of human cancers, including gastric cancer (GC), a leading cause of cancer death in Iranian men and women. Studies have demonstrated that thymopoietin antisense transcript 1 (TMPO-AS1) was upregulated in different cancers by acting as an oncogenic lncRNA. Objectives: This study aimed to evaluate the expression of lncRNA TMPO-AS1 in Iranian patients with GC. Methods: In order to conduct the present study, 40 gastric tumor samples and 40 marginal noncancerous counterparts were collected. The characteristics of patients’ samples were recorded, and the TMPO-AS1 expression levels were evaluated by qRT-PCR analysis. The Cancer Genome Atlas (TCGA) data for TMPO-AS1 were used and analyzed through GEPIA and TANRIC online tools. Receiver operating characteristic (ROC) curve analysis was used to estimate the diagnostic value. Student t-test, one-way ANOVA, and chi-square test were accomplished via SPSS software. Results: Our data demonstrated that TMPO-AS1 was overexpressed in cancerous tissues compared to adjacent nonmalignant ones (P = 0.0076). None of the demographic and clinicopathological data were associated with TMPO-AS1 expression levels. The TCGA data demonstrated that TMPO-AS1 was upregulated in GC tissues in comparison to adjacent nonmalignant ones (P = 0.001). ROC curve analysis suggested that TMPO-AS1 expression levels could discriminate GC tumor tissues from normal ones (AUC = 0.699, P = 0.001). Conclusions: Altogether, in our study, we demonstrated that lncRNA TMPO-AS1 may be considered a biomarker in Iranian patients with GC. However, further investigations are required to confirm the potential application of this lncRNA in diagnosis, prognosis, and therapeutic applications of GC.

Long noncoding RNA HAND2-AS1: A crucial regulator of malignancy

Long non-coding RNAs (LncRNAs) are single-stranded RNAs over 200 nucleotides in length that have no protein-coding function and have long been considered non-functional by-products of transcription. Recent studies have shown that dysregulation of lncRNAs may be involved in the malignant biological behavior of tumors. Targeted regulation of lncRNAs has become a research focus of anti-tumor treatment. LncRNAs heart and neural crest derivatives expressed 2 antisense RNA 1 (HAND2-AS1) was down-regulated in various tumors and can be used as a critical tumor regulator to modulate tumor cells proliferation, apoptosis, metastasis, invasion, metabolism and drug resistance. Additionally, aberrantly expressed HAND2-AS1 was closely related to the clinical pathological characteristics of cancer patients and serve as a promising tumor diagnostic and prognostic biomarker. This article aims to review the roles of HAND2-AS1 in tumorigenesis and development, as well as the underlying molecular mechanisms and clinical significance.

Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls

Introduction

Long non-coding ribonucleic acids (lncRNAs) are involved in the cellular damage response following exposure to ionizing radiation as applied in radiotherapy. However, the role of lncRNAs in radiation response concerning intrinsic susceptibility to late effects of radiation exposure has not been examined in general or in long-term survivors of childhood cancer with and without potentially radiotherapy-related second primary cancers, in particular.

Methods

Primary skin fibroblasts (n=52 each) of long-term childhood cancer survivors with a first primary cancer only (N1), at least one second primary neoplasm (N2+), as well as tumor-free controls (N0) from the KiKme case-control study were matched by sex, age, and additionally by year of diagnosis and entity of the first primary cancer. Fibroblasts were exposed to 0.05 and 2 Gray (Gy) X-rays. Differentially expressed lncRNAs were identified with and without interaction terms for donor group and dose. Weighted co-expression networks of lncRNA and mRNA were constructed using WGCNA. Resulting gene sets (modules) were correlated to the radiation doses and analyzed for biological function.

Results

After irradiation with 0.05Gy, few lncRNAs were differentially expressed (N0: AC004801.4; N1: PCCA-DT, AF129075.3, LINC00691, AL158206.1; N2+: LINC02315). In reaction to 2 Gy, the number of differentially expressed lncRNAs was higher (N0: 152, N1: 169, N2+: 146). After 2 Gy, AL109976.1 and AL158206.1 were prominently upregulated in all donor groups. The co-expression analysis identified two modules containing lncRNAs that were associated with 2 Gy (module1: 102 mRNAs and 4 lncRNAs: AL158206.1, AL109976.1, AC092171.5, TYMSOS, associated with p53-mediated reaction to DNA damage; module2: 390 mRNAs, 7 lncRNAs: AC004943.2, AC012073.1, AC026401.3, AC092718.4, MIR31HG, STXBP5-AS1, TMPO-AS1, associated with cell cycle regulation).

Discussion

For the first time, we identified the lncRNAs AL158206.1 and AL109976.1 as involved in the radiation response in primary fibroblasts by differential expression analysis. The co-expression analysis revealed a role of these lncRNAs in the DNA damage response and cell cycle regulation post-IR. These transcripts may be targets in cancer therapy against radiosensitivity, as well as provide grounds for the identification of at-risk patients for immediate adverse reactions in healthy tissues. With this work we deliver a broad basis and new leads for the examination of lncRNAs in the radiation response.

A long non-coding RNA with important roles in the carcinogenesis

Long non-coding RNAs are demonstrated to contribute to carcinogenesis. TMPO Antisense RNA 1 (TMPO-AS1) is an example of lncRNAs with crucial roles in this process. This lncRNA serves as a sponge for miR-320a, miR-383-5p, miR-329-3p, miR-126, miR-329, miR-199a-5p, miR-577, miR-4731-5p, miR-140-5p, miR-1179, miR-143-3p, miR-326, miR-383-5p, let-7c-5p, let-7g-5p, miR-199a-5p, miR-200c, miR-204-3p, miR-126-5p, miR-383-5p, miR-498, miR-143-3p, miR-98-5p, miR-140 and miR-143. It can also affect activity of PI3K/Akt/mTOR pathway. The current review summarizes the role of TMPO-AS1 in the carcinogenesis and assessment of its potential as a marker for certain types of cancers.