Mitotically associated long non-coding RNA is a tumor promoter in anaplastic thyroid cancer

Long Non-Coding RNAs as Determinants of Thyroid Cancer Phenotypes: Investigating Differential Gene Expression Patterns and Novel Biomarker Discovery

Thyroid Cancer (TC) is the most common endocrine malignancy, with increasing incidence globally. Papillary thyroid cancer (PTC), a differentiated form of TC, accounts for approximately 90% of TC and occurs predominantly in women of childbearing age. Although responsive to current treatments, recurrence of PTC by middle age is common and is much more refractive to treatment. Undifferentiated TC, particularly anaplastic thyroid cancer (ATC), is the most aggressive TC subtype, characterized by it being resistant and unresponsive to all therapeutic and surgical interventions. Further, ATC is one of the most aggressive and lethal malignancies across all cancer types. Despite the differences in therapeutic needs in differentiated vs. undifferentiated TC subtypes, there is a critical unmet need for the identification of molecular biomarkers that can aid in early diagnosis, prognosis, and actionable therapeutic targets for intervention. Advances in the field of cancer genomics have enabled for the elucidation of differential gene expression patterns between tumors and healthy tissue. A novel category of molecules, known as non-coding RNAs, can themselves be differentially expressed, and extensively contribute to the up- and downregulation of protein coding genes, serving as master orchestrators of regulated and dysregulated gene expression patterns. These non-coding RNAs have been identified for their roles in driving carcinogenic patterns at various stages of tumor development and have become attractive targets for study. The identification of specific genes that are differentially expressed can give insight into mechanisms that drive carcinogenic patterns, filling the gaps of deciphering molecular and cellular processes that modulate TC subtypes, outside of well-known driver mutations.

The Expression Patterns and Implications of MALAT1, MANCR, PSMA3-AS1 and miR-101 in Esophageal Adenocarcinoma

Esophageal adenocarcinoma (EAC) is a malignant tumor with poorly understood molecular mechanisms. This study endeavors to elucidate how the long non-coding RNAs (lncRNAs) MALAT1, MANCR and PSMA3-AS1, as well as the microRNA miR-101, exhibit specific expression patterns in the pathogenesis and prognosis of EAC. A total of 50 EAC tissue samples (tumors and lymph nodes) and a control group comprising 26 healthy individuals were recruited. The samples underwent quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analyses. The relative expression levels of MALAT1, MANCR, PSMA3-AS1, and miR-101 were ascertained and correlated with various clinicopathological parameters including TNM staging, tumor characteristics (size and grade of the tumor) lymphatic invasion, disease-free (DFS) and overall survival (OS) of EAC patients. Quantitative analyses revealed that MALAT1 and MANCR were significantly upregulated in EAC tumors and positive lymph nodes when compared to control tissues (p < 0.05). Such dysregulations correlated positively with advanced lymphatic metastases and a higher N stage. DFS in the subgroup of patients with negative lymph nodes was higher in the setting of low-MANCR-expression patients compared to patients with high MANCR expression (p = 0.02). Conversely, miR-101 displayed a significant downregulation in EAC tumors and positive lymph nodes (p < 0.05), and correlated negatively with advanced tumor stage, lymphatic invasion and the grade of the tumor (p = 0.006). Also, patients with low miR-101 expression showed a tendency towards inferior overall survival. PSMA3-AS1 did not demonstrate statistically significant alterations (p > 0.05). This study reveals MALAT1, MANCR, and miR-101 as putative molecular markers for prognostic evaluation in EAC and suggests their involvement in EAC progression.

Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease

The largest solid organ in humans, the liver, performs a variety of functions to sustain life. When damaged, cells in the liver can regenerate themselves to maintain normal liver physiology. However, some damage is beyond repair, which necessitates liver transplantation. Increasing rates of obesity, Western diets (i.e., rich in processed carbohydrates and saturated fats), and cardiometabolic diseases are interlinked to liver diseases, including non-alcoholic fatty liver disease (NAFLD), which is a collective term to describe the excess accumulation of fat in the liver of people who drink little to no alcohol. Alarmingly, the prevalence of NAFLD extends to 25% of the world population, which calls for the urgent need to understand the disease mechanism of NAFLD. Here, we performed secondary analyses of published RNA sequencing (RNA-seq) data of NAFLD patients compared to healthy and obese individuals to identify long non-coding RNAs (lncRNAs) that may underly the disease mechanism of NAFLD. Similar to protein-coding genes, many lncRNAs are dysregulated in NAFLD patients compared to healthy and obese individuals, suggesting that understanding the functions of dysregulated lncRNAs may shed light on the pathology of NAFLD. To demonstrate the functional importance of lncRNAs in the liver, loss-of-function experiments were performed for one NAFLD-related lncRNA, LINC01639, which showed that it is involved in the regulation of genes related to apoptosis, TNF/TGF, cytokine signaling, and growth factors as well as genes upregulated in NAFLD. Since there is no lncRNA database focused on the liver, especially NAFLD, we built a web database, LiverDB, to further facilitate functional and mechanistic studies of hepatic lncRNAs.

Long-Noncoding RNA MANCR is Associated With Head and Neck Squamous Cell Carcinoma Malignant Development and Immune Infiltration

Recent studies have demonstrated an important role for mitotically associated long non-coding RNA (MANCR) in carcinogenesis and cancer progression, but its function has not been elucidated in head and neck squamous cell carcinoma (HNSCC). In this study, we identified differentially expressed MANCR from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases across 24 cancer types and included 546 HNSCC patients. Furthermore, high expression of MANCR was verified in HNSCC cell lines and tissue by using real-time quantitative PCR (RT-qPCR) analysis. The Kaplan–Meier analysis showed a worse prognosis with higher levels of MANCR for HNSCC. The univariate Cox regression and multivariate Cox regression analyses revealed that MANCR was a high-risk factor in patients with HNSCC. Thereafter, we carried out the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. It was indicated that MANCR participates in axonogenesis and ECM-receptor interaction. Further enrichment analysis demonstrated that the expression of MANCR was positively correlated with the T gamma delta (tgd) cells, neutrophils, and Th1 cells, and negatively correlated with the infiltration of B cells, CD8 T cells, and T cells in HNSCC. In addition, in vitro experiments showed that knockdown of MANCR in HNSCC cells markedly inhibited cell proliferation, migration, and invasion. We find that MANCR was elevated in HNSCC and promoted the malignant progression of HNSCC. MANCR may serve as a potential biomarker in prognostic implications for HNSCC patients. The positive correlation between MANCR and immune infiltration cells may provide novel therapeutic targets and personalized immune-based cancer therapy for HNSCC.

LINC00704 contributes to the proliferation and accelerates the cell cycle of nasopharyngeal carcinoma cells via regulating ETS1/CDK6 axis

This study is aimed at exploring the biological functions and related mechanism of long noncoding RNA 704 (LINC00704) in the proliferation and cell cycle progression of nasopharyngeal carcinoma (NPC) cells. The expression of LINC00704 in NPC tissues and cells was quantified by quantitative real-time polymerase chain reaction (qRT-PCR). After LINC00704 was overexpressed or knocked down in NPC cell lines, cell counting kit-8 (CCK-8) assay, 5-bromo-2'-deoxyuridine assay, flow cytometry assay, and Transwell assay were adopted to detect the proliferation, cell cycle progression, migration, and invasion of NPC cells. The interaction between LINC00704 and ETS proto-oncogene 1 (ETS1) was verified by bioinformatics analysis, RNA pull-down assay, and RNA immunoprecipitation assay. Dual-luciferase reporter gene assay and chromatin immunoprecipitation followed by qPCR analysis were used to verify the binding status between ETS1 and the promoter region of cyclin-dependent kinase 6 (CDK6). The regulatory effects of LINC00704 and ETS1 on CDK6 expression were detected by Western blot. LINC00704 expression was elevated in NPC tissues and cells, which was significantly correlated with the advanced TNM stage and poor differentiation. LINC00704 overexpression promoted the multiplication, migration, and invasion of NPC cells and blocked the cell cycle progression while knocking down LINC00704 worked oppositely. LINC00704 could bind to ETS1, thus promoting CDK6 transcription. Knocking down LINC00704 inhibited the CDK6 expression in NPC cells. LINC00704 promotes CDK6 transcription by recruiting ETS1 to the promoter region of CDK6, thus promoting the malignant progression of NPC.

Long Non-coding RNA RP11-395G23.3 Acts as a Competing Endogenous RNA of miR-124-3p to Regulate ROR1 in Anaplastic Thyroid Carcinoma

Anaplastic thyroid carcinoma (ATC) is one of the most aggressive human malignancies with poor prognosis. However, the underlying mechanisms of ATC remain to be elucidated. Recently, increasing studies have focused on competitive endogenous RNA (ceRNA) to discover valuable biomarkers for the diagnosis of ATC. The present study identified 705 differentially expressed mRNAs and 47 differentially expressed lncRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were also conducted. Additionally, an lncRNA/miRNA/mRNA network was constructed which included 1103 regulatory relations. The upregulation of RP11-395G23.3 in ATC cells was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). In the loss of function assays, results suggested silencing of RP11-395G23.3 inhibited cell proliferation and induced cell apoptosis. Mechanically, RP11-395G23.3 could increase ROR1 via sponging miR-124-3p as a ceRNA. Moreover, ROR1 expression was decreased with the downregulation of RP11-395G23.3, but was rescued by the co-transfection of the miR-124-3p inhibitor in ATC cells. Our research suggested that the RP11-395G23.3/miR-124-3p/ROR1 axis potentially acted as a potential target for the diagnosis of ATC.

LncRNA MANCR positively affects the malignant progression of lung adenocarcinoma

BACKGROUND

LncRNA MANCR (mitosis-related lncRNA, LINC00704) is deemed as a pivotal regulator in various cancers, yet the biological function it performs in lung adenocarcinoma (LUAD) was rarely reported. We made an in-depth study to clarify its effect during the progression of this cancer.

METHODS

Expression data and clinical information were first accessed from TCGA LUAD dataset ( https://portal.gdc.cancer.gov/repository ). Differentially expressed lncRNAs were identified. R package "survival" determined the survival significance of the lncRNA MANCR. GSEA software was applied to conduct single sample enrichment analysis. qRT-PCR was used to examine MANCR expression. The expression levels of related proteins were tested using Western blot assay. The impact of MANCR on cancer cell biological behaviors was investigated via cell function experiments.

RESULTS

MANCR was significantly upregulated in LUAD cells. It also resulted in a poor prognosis. When MANCR expression was down-regulated, the expression of proteins related to invasion and migration, cell cycle and proliferation was decreased, while the expression of proteins associated with apoptosis was elevated. Furthermore, in vitro experiments revealed that silencing MANCR inhibited cancer cell functions, blocked cell cycle progression while promoting cell apoptosis.

CONCLUSION

LncRNA MANCR can lead to enhanced proliferative, invasive and migratory abilities of cancer cells while reducing cell apoptosis. Hence, MANCR might be a novel biomarker of LUAD.

Role of Non-coding RNAs on the Radiotherapy Sensitivity and Resistance of Head and Neck Cancer: From Basic Research to Clinical Application

Head and neck cancers (HNCs) rank as the sixth common and the seventh leading cause of cancer-related death worldwide, with an estimated incidence of 600,000 cases and 40-50% mortality rate every year. Radiotherapy is a common local therapeutic modality for HNC mainly through the function of ionizing radiation, with approximately 60% of patients treated with radiotherapy or chemoradiotherapy. Although radiotherapy is more advanced and widely used in clinical practice, the 5-year overall survival rates of locally advanced HNCs are still less than 40%. HNC cell resistance to radiotherapy remains one of the major challenges to improve the overall survival in HNC patients. Non-coding RNAs (ncRNAs) are newly discovered functional small RNA molecules that are different from messenger RNAs, which can be translated into a protein. Many previous studies have reported the dysregulation and function of ncRNAs in HNC. Importantly, researchers reported that several ncRNAs were also dysregulated in radiotherapy-sensitive or radiotherapy-resistant HNC tissues compared with the normal cancer tissues. They found that ectopically elevating or knocking down expression of some ncRNAs could significantly influence the response of HNC cancer cells to radiotherapy, indicating that ncRNAs could regulate the sensitivity of cancer cells to radiotherapy. The implying mechanism for ncRNAs in regulating radiotherapy sensitivity may be due to its roles on affecting DNA damage sensation, inducing cell cycle arrest, regulating DNA damage repair, modulating cell apoptosis, etc. Additionally, clinical studies reported that in situ ncRNA expression in HNC tissues may predict the response of radiotherapy, and circulating ncRNA from body liquid serves as minimally invasive therapy-responsive and prognostic biomarkers in HNC. In this review, we aimed to summarize the current function and mechanism of ncRNAs in regulating the sensitivity of HNC cancer cells to radiotherapy and comprehensively described the state of the art on the role of ncRNAs in the prognosis prediction, therapy monitoring, and prediction of response to radiotherapy in HNC.