Gene Signature and Identification of Clinical Trait-Related m6 A Regulators in Pancreatic Cancer

Palmatine inhibits expression fat mass and obesity associated protein (FTO) and exhibits a curative effect in dextran sulfate sodium (DSS)-induced experimental colitis

BACKGROUND

Ulcerative colitis (UC) is an inflammatory disease whose pathogenesis and mechanisms have not been fully described. The m6A methylation modification is a general mRNA modification in mammalian cells and is closely associated with the onset and progression of inflammatory bowel disease (IBD). Palmatine (PAL) is a biologically active alkaloid with anti-inflammatory and protective effects in animal models of colitis. Accordingly, we examined the role of PAL on colitis by regulating N6-methyladenosine (m6A) methylation.

METHODS

A rat experimental colitis model was established by 5 % dextran sulfate sodium (DSS) in drinking water for seven days, then PAL treatment was administered for seven days. The colonic tissue pathology was assessed using hematoxylin-eosin (HE) and disease activity index (DAI). In in vitro studies, a human, spontaneously immortalized non-cancerous colon mucosal epithelial cell line (NCM460) was exposed to 2 % DSS and treated with PAL and cell viability was assayed using Cell Counting Kit-8 (CCK-8). The levels of tumor necrosis factor α (TNF-α), interleukin (IL)-1β, IL-6, and IL-8 were detected by enzyme-linked immunosorbent assay (ELISA) kits. The level of Zonula occludens-1 (ZO-1) was dectected by immunofluorescence. Transepithelial electrical resistance (TEER) of cells was also assessed. The methyltransferase-like 3 (METTL3), METTL14, AlkB homologate 5 (ALKBH5), and fat mass and obesity-associated protein (FTO) expression levels were assessed by western blotting. The localized expression of m6A was measured by immunofluorescence.

RESULTS

PAL significantly prevented bodyweight loss and shortening of the colon in experimental colitis rats, as well as decreasing the DAI and histological damage scores. Furthermore, PAL inhibited the levels of inflammatory factors (TNF-α, IL-6, IL-8, and IL-1β) in both DSS treated rats and NCM460 cells. In addition, PAL enhanced the expression level of ZO-1, and increased the transepithelial electrical resistance to repaire intestinal barrier dysfunction. Colitis occurred due to decreased m6A levels, and the increased FTO expression led to a colitis phenotype. PAL markedly enhanced the METTL3 and METTL14 expression levels while decreasing ALKBH5 and FTO expression levels.

CONCLUSIONS

The findings demonstrated that PAL improved DSS-induced experimental colitis. This effect was associated with inhibiting FTO expression and regulating m6A methylation.

Silencing long noncoding RNA LINC01133 suppresses pancreatic cancer through regulation of microRNA-1299-dependent IGF2BP3

The deregulation of long noncoding RNAs (lncRNAs) holds great potential in the treatment of multiple cancers, including pancreatic cancer (PC). However, the specific molecular mechanisms by which LINC01133 contributes to pancreatic cancer remain unknown. Subsequent to bioinformatics analysis, we predicted and analyzed differentially expressed lncRNAs, microRNAs, and genes in pancreatic cancer. We determined the expression patterns of LINC01133, miR-1299, and insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) in pancreatic cancer cells, and validated their interactions through luciferase reporter and RNA immunoprecipitation assays. We implemented loss-of-function and gain-of-function experiments for LINC01133, miR-1299, and IGF2BP3 to assay their potential effects on pancreatic cancer cell functions. We observed high expression of LINC01133 and IGF2BP3, but low expression of miR-1299, in pancreatic cancer cells. Furthermore, we found that LINC01133 enhances IGF2BP3 through binding with miR-1299. Silencing LINC01133 or IGF2BP3 and/or overexpressing miR-1299 limited pancreatic cancer cell proliferation, invasion, epithelial-mesenchymal transition, and suppressed tumorigenic abilities in mice lacking T cells (nude mice). Overall, our findings identified that silencing LINC01133 downregulates IGF2BP3 by upregulating miR-1299 expression, ultimately leading to the prevention of pancreatic cancer.

FTO plays a crucial role in gastrointestinal cancer and may be a target for immunotherapy: an updated review

Gastrointestinal cancer is a common malignancy with high mortality and poor prognosis. Therefore, developing novel effective markers and therapeutic targets for gastrointestinal cancer is currently a challenging and popular topic in oncology research. Accumulating studies have reported that N6-methyladenosine is the most abundant epigenetic modification in eukaryotes. N6-methyladenosine plays an essential role in regulating RNA expression and metabolism, including splicing, translation, stability, decay, and transport. FTO, the earliest demethylase discovered to maintain the balance of N6-adenosine methylation, is abnormally expressed in many tumors. In this review, we discuss the molecular structure and substrate selectivity of FTO. we focus on the role of FTO in gastrointestinal tumor proliferation, migration, invasion, apoptosis, autophagy, immune microenvironment, and its molecular mechanisms. We also discuss its potential in the treatment of gastrointestinal cancers.

Expression of m6A Methylation Regulator in Osteoarthritis and Its Prognostic Markers

OBJECTIVE

Osteoarthritis (OA) is a multifactorial disorder, in which genetic factors are strongly associated with its development. However, the pathogenesis of OA is still unclear, and recently it has been observed that epigenetic modifications are also involved in the pathogenesis of OA. This study aims to study the potential role of m6A-related genes in the occurrence and development of OA.

DESIGN

We downloaded the OA expression profile data (GSE55235) from the Gene Expression Omnibus database. First, function enrichment analysis of 17 representative m6A methylation regulatory factors was performed using the DAVID database and Metascape online tool. Then, we analyzed the expression of 17 m6A methylation regulatory factors in OA and the correlation between regulatory factors using Perl software. Finally, receiver operating characteristic (ROC) curve analysis and the area under the ROC curve were used to evaluate the diagnostic effectiveness of m6A-related genes for discriminating patients with OA and healthy.

RESULTS

We first identified that 12 of the 17 genes were differentially expressed in OA. ALKBH1, EIF3, IGF2BP3, WTAP, and YTHDC1 were associated with early diagnosis and prognosis of OA.

CONCLUSIONS

m6A RNA methylation regulator factors are key players in the progression of OA and have potential role in the stratification of prognosis and the formulation of treatment strategies.

Role of RNA methylation in the regulation of pancreatic cancer stem cells (Review)

Pancreatic cancer stem cells (CSCs) play a key role in the initiation and progression of pancreatic adenocarcinoma (PDAC). CSCs are responsible for resistance to chemotherapy and radiation, and for cancer metastasis. Recent studies have indicated that RNA methylation, a type of RNA modification, predominantly occurring as m6A methylation, plays an important role in controlling the stemness of cancer cells, therapeutic resistance against chemotherapy and radiation therapy, and their overall relevance to a patient's prognosis. CSCs regulate various behaviors of cancer through cell-cell communication by secreting factors, through their receptors, and through signal transduction. Recent studies have shown that RNA methylation is involved in the biology of the heterogeneity of PDAC. The present review provides an update on the current understanding of RNA modification-based therapeutic targets against deleterious PDAC. Several key pathways and agents that can specifically target CSCs have been identified, thus providing novel insights into the early diagnosis and efficient treatment of PDAC.

m6A regulators are differently expressed and correlated with immune response of pancreatic adenocarcinoma

BACKGROUND

N6 methyladenosine (m6A) RNA methylation regulators play a key role in the occurrence and development of many tumors. However, the function of N6 methyladenosine (m6A) RNA methylation regulators in pancreatic adenocarcinoma (PAAD) has not been fully clarified.

METHODS

We used data set from GEPIA 2, UALCAN, TIMER, TISIDB, CBioPortal database to analyze the gene expression of 20 major m6A RNA methylation regulators.

RESULTS

Our study revealed that the irregularity of m6A regulators were associated with poor prognosis in PAAD. Meantime, 13 m6A regulators showed high expression in PAAD samples (ALKBH5, ELAVL1, FTO, HNRNPC, IGF2BP2, METTL14, METTL16 (METT10D), RBM15, VIRMA (KIAA1429), YTHDF1, YTHDF2, YTHDF3 and ZC3H13). In these regulators, we evaluated HNRNPC and IGF2BP2 were significantly correlated with worse outcomes and ALKBH5, IGF2BP2, METTL16 (METT10D), RBM15 were significantly correlated with PAAD in advanced stage. Moreover, we showed m6A regulators is correlated with Immuno-regulators' (Immunoinhibitors, Immunostimulators and MHC molecules) expression and levels of immune infiltration in PAAD. Bioinformatics further demonstrate m6A regulators were participated in revising in RNA processing.

CONCLUSIONS

Our study investigated that the m6A regulatory factors may serve as a biomarker and a potential target of immunotherapy for PAAD.

Understanding the Epitranscriptome for Avant-Garde Brain Tumour Diagnostics

RNA modifications are diverse, dynamic, and reversible transcript alterations rapidly gaining attention due to their newly defined RNA regulatory roles in cellular pathways and pathogenic mechanisms. The exciting emerging field of 'epitranscriptomics' is predominantly centred on studying the most abundant mRNA modification, N6-methyladenine (m⁶A). The m⁶A mark, similar to many other RNA modifications, is strictly regulated by so-called 'writer', 'reader', and 'eraser' protein species. The abundance of genes coding for the expression of these regulator proteins and m⁶A levels shows great potential as diagnostic and predictive tools across several cancer fields. This review explores our current understanding of RNA modifications in glioma biology and the potential of epitranscriptomics to develop new diagnostic and predictive classification tools that can stratify these highly complex and heterogeneous brain tumours.

Transcriptome-wide m6A methylome analysis uncovered the changes of m6A modification in oral pre-malignant cells compared with normal oral epithelial cells

As the most common post-transcriptional RNA modification, m⁶A methylation extensively regulates the structure and function of RNA. The dynamic and reversible modification of m⁶A is coordinated by m⁶A writers and erasers. m⁶A reader proteins recognize m⁶A modification on RNA, mediating different downstream biological functions. mRNA m⁶A modification and its corresponding regulators play an important role in cancers, but its characteristics in the precancerous stage are still unclear. In this study, we used oral precancerous DOK cells as a model to explore the characteristics of transcriptome-wide m⁶A modification and major m⁶A regulator expression in the precancerous stage compared with normal oral epithelial cell HOEC and oral cancer cell SCC-9 through MeRIP-seq and RT-PCR. Compared with HOEC cells, we found 1180 hyper-methylated and 1606 hypo-methylated m⁶A peaks and 354 differentially expressed mRNAs with differential m⁶A peaks in DOK cells. Although the change of m⁶A modification in DOK cells was less than that in SCC-9 cells, mRNAs with differential m⁶A in both cell lines were enriched into many identical GO terms and KEGG pathways. Among the 20 known m⁶A regulatory genes, FTO, ALKBH5, METTL3 and VIRMA were upregulated or downregulated in DOK cells, and the expression levels of 10 genes such as METTL14/16, FTO and IGF2BP2/3 were significantly changed in SCC-9 cells. Our data suggest that precancerous cells showed, to some extent, changes of m⁶A modification. Identifying some key m⁶A targets and corresponding regulators in precancerous stage may provide potential intervention targets for the prevention of cancer development through epigenetic modification in the future.

The Emerging Role of RNA N6-Methyladenosine Modification in Pancreatic Cancer

Pancreatic cancer (PC) is one of the most common malignant cancers, ranking the seventh highest causes of cancer-related deaths globally. Recently, RNA N6-methyladenosine (m6A) is emerging as one of the most abundant RNA modifications in eukaryote cells, involved in multiple RNA processes including RNA translocation, alternative splicing, maturation, stability, and degradation. As reported, m6A was dynamically and reversibly regulated by its “writers”, “erasers”, and “readers”, Increasing evidence has revealed the vital role of m6A modification in the development of multiple types of cancers including PC. Currently, aberrant m6A modification level has been found in both PC tissues and cell lines. Moreover, abnormal expressions of m6A regulators and m6A-modified genes have been reported to contribute to the malignant development of PC. Here in this review, we will focus on the function and molecular mechanism of m6A-modulated RNAs including coding RNAs as well as non-coding RNAs. Then the m6A regulators will be summarized to reveal their potential applications in the clinical diagnosis, prognosis, and therapeutics of PC.

The Potential Value of m6A RNA Methylation in the Development of Cancers Focus on Malignant Glioma

N6-methyladenosine (m6A) RNA methylation is an epigenetic modification that has emerged in the last few years and has received increasing attention as the most abundant internal RNA modification in eukaryotic cells. m6A modifications affect multiple aspects of RNA metabolism, and m6A methylation has been shown to play a critical role in the progression of multiple cancers through a variety of mechanisms. This review summarizes the mechanisms by which m6A RNA methylation induced peripheral cancer cell progression and its potential role in the infiltration of immune cell of the glioblastoma microenvironment and novel immunotherapy. Assessing the pattern of m6A modification in glioblastoma will contribute to improving our understanding of microenvironmental infiltration and novel immunotherapies, and help in developing immunotherapeutic strategies.

Development and validation of prognostic and diagnostic model for pancreatic ductal adenocarcinoma based on scRNA-seq and bulk-seq datasets

The 5-year overall survival (OS) of pancreatic ductal adenocarcinoma (PDAC) is only 10%, partly owing to the lack of reliable diagnostic and prognostic biomarkers. The raw gene-cell matrix for single-cell RNA-seq (scRNA-seq) analysis was downloaded from the GSA database. We drew cell atlas for PDAC and normal pancreatic tissues. The inferCNV analysis was used to distinguish tumor cells from normal ductal cells. We identified differential expression genes (DEGs) by comparing tumor cells and normal ductal cells. The common DEGs were used to conduct prognostic and diagnostic model using univariate and multivariate Cox or logistic regression analysis. Four genes, MET, KLK10, PSMB9 and ITGB6, were utilized to create risk score formula to predict OS and to establish diagnostic model for PDAC. Finally, we drew an easy-to-use nomogram to predict 2-year and 3-year OSs. In conclusion, we developed and validated the prognostic and diagnostic model for PDAC based on scRNA-seq and bulk-seq datasets.

Essential m6A Methylation Regulator HNRNPC Serves as a Targetable Biomarker for Papillary Renal Cell Carcinoma

m6A RNA modification is a common abundant posttranscriptional modification of mRNAs occurring in cancer growth and progression. Accumulated evidence has proved that HNRNPC, which acts as a m6A reader, plays an essential role in the promotion of cancer occurrence and development; nevertheless, the role of HNRNPC in papillary renal cell carcinoma remained to be discovered. In this study, we comprehensively identified HNRNPC as a hub gene involved in m6A modification in pRCC. Then, the expression level, survival outcomes, PPI network, function enrichment, immune cell infiltration, and single-cell analysis were performed. Finally, we found that HNRNPC significantly promoted renal cell carcinoma proliferation and migration in vitro. In conclusion, our work proved that HNRNPC may act as a momentous m6A regulator, as well as a potential targetable biomarker for pRCC.

An analysis of the role of HnRNP C dysregulation in cancers

Heterogeneous nuclear ribonucleoproteins C (HnRNP C) is part of the hnRNP family of RNA-binding proteins. The relationship between hnRNP C and cancers has been extensively studied, and dysregulation of hnRNP C has been found in many cancers. According to existing public data, hnRNP C could promote the maturation of new heterogeneous nuclear RNAs (hnRNA s, also referred to as pre-mRNAs) into mRNAs and could stabilize mRNAs, controlling their translation. This paper reviews the regulation and dysregulation of hnRNP C in cancers. It interacts with some cancer genes and other biological molecules, such as microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and double-stranded RNAs (dsRNAs). Even directly binds to them. The effects of hnRNP C on biological processes such as alternative cleavage and polyadenylation (APA) and N6-methyladenosine (m6A) modification differ among cancers. Its main function is regulating stability and level of translation of cancer genes, and the hnRNP C is regarded as a candidate biomarker and might be valuable for prognosis evaluation.

Identification and Validation of a Prognostic Prediction Model of m6A Regulator-Related LncRNAs in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a highly invasive malignancy prone to recurrence, and patients with HCC have a low 5-year survival rate. Long non-coding RNAs (lncRNAs) play a vital role in the occurrence and development of HCC. N6-methyladenosine methylation (m6A) is the most common modification influencing cancer development. Here, we used the transcriptome of m6A regulators and lncRNAs, along with the complete corresponding clinical HCC patient information obtained from The Cancer Genome Atlas (TCGA), to explore the role of m6A regulator-related lncRNA (m6ARlnc) as a prognostic biomarker in patients with HCC. The prognostic m6ARlnc was selected using Pearson correlation and univariate Cox regression analyses. Moreover, three clusters were obtained via consensus clustering analysis and further investigated for differences in immune infiltration, immune microenvironment, and prognosis. Subsequently, nine m6ARlncs were identified with Lasso-Cox regression analysis to construct the prognostic signature m6A-9LPS for patients with HCC in the training cohort (n = 226). Based on m6A-9LPS, the risk score for each case was calculated. Patients were then divided into high- and low-risk subgroups based on the cutoff value set by the X-tile software. m6A-9LPS showed a strong prognosis prediction ability in the validation cohort (n = 116), the whole cohort (n = 342), and even clinicopathological stratified survival analysis. Combining the risk score and clinical characteristics, we established a nomogram for predicting the overall survival (OS) of patients. To further understand the mechanism underlying the m6A-9LPS-based classification of prognosis differences, KEGG and GO enrichment analyses, competitive endogenous RNA (ceRNA) network, chemotherapeutic agent sensibility, and immune checkpoint expression level were assessed. Taken together, m6A-9LPS could be used as a precise prediction model for the prognosis of patients with HCC, which will help in individualized treatment of HCC.

The roles and mechanisms of the m6A reader protein YTHDF1 in tumor biology and human diseases

YTHDF1 is the most versatile and powerful reader protein of N⁶-methyladenosine (m6A)-modified RNA, and it can recognize both G(m6A)C and A(m6A)C RNAs as ligands without sequence selectivity. YTHDF1 regulates target gene expression by different mechanisms, such as promoting translation or regulating the stability of mRNA. Numerous studies have shown that YTHDF1 plays an important role in tumor biology and nontumor lesions by mediating the protein translation of important genes or by affecting the expression of key factors involved in many important cell signaling pathways. Therefore, in this review we focus on some of the roles of YTHDF1 in tumor biology and diseases.

Comprehensive Analysis of m6A RNA Methylation Regulators and the Immune Microenvironment to Aid Immunotherapy in Pancreatic Cancer

Pancreatic cancer (PAAD) is one of the most malignant cancers and immune microenvironment has been proved to be involved in pathogenesis of PAAD. m6A modification, related to the expression of m6A regulators, participates in the development of multiple cancers. However, the correlation between m6A regulators and immune microenvironment was largely unknown in PAAD. And because of the small sample size of pancreatic cancer in the TCGA database, it is not enough to draw a convincing conclusion. In the present study, we downloaded seven pancreatic cancer datasets with survival data and removed batch effects among these datasets to be used as the PAAD cohort to analyze the immune landscape of PAAD and the expression pattern of m6A regulators and divided the integrated dataset into cluster 1 and cluster 2 by consensus clustering for m6A regulators. Lower m6A regulators were found to be related to higher immune cell infiltration and a better survival. Moreover, we identified six m6A regulators and constructed the prognostic signature of m6A regulators. Patients with low-risk score had a higher response to immune checkpoint inhibitor and a longer overall survival. To figure out the underlying mechanism, we analyzed the cancer immunity cycle, most altered genes, gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) in risk subtypes. In summary, the present study proved m6A regulators modulated the PAAD immune microenvironment. And risk scores served as predictive indicator for immunotherapy and played a prognostic role for PAAD patients. Our study provided novel therapeutic targets to improve immunotherapy efficacy.

EGFR Pathway-Based Gene Signatures of Druggable Gene Mutations in Melanoma, Breast, Lung, and Thyroid Cancers

EGFR, BRAF, PIK3CA, and KRAS genes play major roles in EGFR pathway, and accommodate activating mutations that predict response to many targeted therapeutics. However, connections between these mutations and EGFR pathway expression patterns remain unexplored. Here, we investigated transcriptomic associations with these activating mutations in three ways. First, we compared expressions of these genes in the mutant and wild type tumors, respectively, using RNA sequencing profiles from The Cancer Genome Atlas project database (n = 3660). Second, mutations were associated with the activation level of EGFR pathway. Third, they were associated with the gene signatures of differentially expressed genes from these pathways between the mutant and wild type tumors. We found that the upregulated EGFR pathway was linked with mutations in the BRAF (thyroid cancer, melanoma) and PIK3CA (breast cancer) genes. Gene signatures were associated with BRAF (thyroid cancer, melanoma), EGFR (squamous cell lung cancer), KRAS (colorectal cancer), and PIK3CA (breast cancer) mutations. However, only for the BRAF gene signature in the thyroid cancer we observed strong biomarker diagnostic capacity with AUC > 0.7 (0.809). Next, we validated this signature on the independent literature-based dataset (n = 127, fresh-frozen tissue samples, AUC 0.912), and on the experimental dataset (n = 42, formalin fixed, paraffin embedded tissue samples, AUC 0.822). Our results suggest that the RNA sequencing profiles can be used for robust identification of the replacement of Valine at position 600 with Glutamic acid in the BRAF gene in the papillary subtype of thyroid cancer, and evidence that the specific gene expression levels could provide information about the driver carcinogenic mutations.

Characterization of Modification Patterns, Biological Function, Clinical Implication, and Immune Microenvironment Association of m6A Regulators in Pancreatic Cancer

Objective: N⁶-methyladenosine (m⁶A) modification may modulate various biological processes. Nonetheless, clinical implications of m⁶A modification in pancreatic cancer are undefined. Herein, this study comprehensively characterized the m⁶A modification patterns in pancreatic cancer based on m⁶A regulators. Methods: Genetic mutation and expression pattern of 21 m⁶A regulators and their correlations were assessed in pancreatic cancer from TCGA dataset. m⁶A modification patterns were clustered using unsupervised clustering analysis in TCGA and ICGC datasets. Differences in survival, biological functions and immune cell infiltrations were assessed between modification patterns. A m⁶A scoring system was developed by principal component analysis. Genetic mutations and TIDE scores were compared between high and low m⁶A score groups. Results: ZC3H13 (11%), RBM15B (9%), YTHDF1 (8%), and YTHDC1 (6%) frequently occurred mutations among m⁶A regulators. Also, most of regulators were distinctly dysregulated in pancreatic cancer. There were tight crosslinks between regulators. Two m⁶A modification patterns were constructed, with distinct prognoses, immune cell infiltration and biological functions. Furthermore, we quantified m⁶A score in each sample. High m⁶A scores indicated undesirable clinical outcomes. There were more frequent mutations in high m⁶A score samples. Lower TIDE score was found in high m⁶A score group, with AUC = 0.61, indicating that m⁶A scores might be used for predicting the response to immunotherapy. Conclusion: Collectively, these data demonstrated that m⁶A modification participates pancreatic cancer progress and ornaments immune microenvironment, providing an insight into pancreatic cancer pathogenesis and facilitating precision medicine development.

Quantification of m6A RNA methylation modulators pattern was a potential biomarker for prognosis and associated with tumor immune microenvironment of pancreatic adenocarcinoma

BACKGROUND

m6A is the most prevalent and abundant form of mRNA modifications and is closely related to tumor proliferation, differentiation, and tumorigenesis. In this study, we try to conduct an effective prediction model to investigated the function of m6A RNA methylation modulators in pancreatic adenocarcinoma and estimated the potential association between m6A RNA methylation modulators and tumor microenvironment infiltration for optimization of treatment.

METHODS

Expression of 28 m6A RNA methylation modulators and clinical data of patients with pancreatic adenocarcinoma and normal samples were obtained from TCGA and GTEx database. Differences in the expression of 28 m6A RNA methylation modulators between tumour (n = 40) and healthy (n = 167) samples were compared by Wilcoxon test. LASSO Cox regression was used to select m6A RNA methylation modulators to analyze the relationship between expression and clinical characteristics by univariate and multivariate regression. A risk score prognosis model was conducted based on the expression of select m6A RNA methylation modulators. Bioinformatics analysis was used to explore the association between the m6Ascore and the composition of infiltrating immune cells between high and low m6Ascore group by CIBERSORT algorithm. Evaluation of m6Ascore for immunotherapy was analyzed via the IPS and three immunotherapy cohort. Besides, the biological signaling pathways of the m6A RNA methylation modulators were examined by gene set enrichment analysis (GSEA).

RESULTS

Expression of 28 m6A RNA methylation modulators were upregulated in patients with PAAD except for MTEEL3. An m6Ascore prognosis model was established, including KIAA1429, IGF2BP2, IGF2BP3, METTL3, EIF3H and LRPPRC was used to predict the prognosis of patients with PAAD, the high risk score was an independent prognostic indicator for pancreatic adenocarcinoma, and a high risk score presented a lower overall survival. In addition, m6Ascore was related with the immune cell infiltration of PAAD. Patients with a high m6Ascore had lower infiltration of Tregs and CD8+T cells but a higher resting CD4+ T infiltration. Patients with a low m6Ascore displayed a low abundance of PD-1, CTLA-4 and TIGIT, however, the IPS showed no difference between the two groups. The m6Ascore applied in three immunotherapy cohort (GSE78220, TCGA-SKCM, and IMvigor210) did not exhibit a good prediction for estimating the patients' response to immunotherapy, so it may need more researches to figure out whether the m6A modulator prognosis model would benefit the prediction of pancreatic patients' response to immunotherapy.

CONCLUSION

Modulators involved in m6A RNA methylation were associated with the development of pancreatic cancer. An m6Ascore based on the expression of IGF2BP2, IGF2BP3, KIAA1429, METTL3, EIF3H and LRPPRC is proposed as an indicator of TME status and is instrumental in predicting the prognosis of pancreatic cancer patients.

Function and clinical significance of N6-methyladenosine in digestive system tumours

RNA modification, like DNA methylation, histone modification, non-coding RNA modification and chromatin rearrangement, plays an important role in tumours. N6-methyladenosine (m6A) is the most abundant RNA modification in cells, and it regulates RNA transcription, processing, splicing, degradation, and translation. m6A-associated proteins have been used as new biomarkers and therapeutic targets for tumour prediction and monitoring. There are three main types of proteins involved in m6A methylation: methyltransferases (METTL3, METTL14, WTAP, RBM15, ZC3H13 and KIAA1429), demethylases (FTO, ALKBH5 and ALKBH3) and RNA-binding proteins (YTHDF1-3, YTHDC1-2, IGF2BPs and HNRNPs). This article reviews the origins, characteristics and functions of m6A and its relationship with digestive system tumours based on recent research. The expression of m6A regulators can be used as an evaluation indicator of tumour growth and progression and as a prognostic indicator. In-depth research on m6A methylation in digestive system tumours may provide new directions for clinical prediction and further treatment.

Genes involved in the epithelial-mesenchymal transition in oral cancer: A systematic review

OBJECTIVE

Epithelial-mesenchymal transition (EMT) is considered the initial step in the invasion-metastasis cascade. The aim of this systematic review was to study the signature of genes involved in the EMT process in oral cancer (OC) confirmed by protein expression and its possible relationship with oral squamous cell carcinoma (OSCC) prognostic variables.

MATERIALS AND METHODS

A search of the scientific literature was carried out with no start date restriction until 17 September 2020 in the electronic databases Pubmed/MEDLINE, Web of Science, Cochrane Library and Scopus, following specific eligibility criteria. The methodological quality of the included studies was assessed using the Newcastle-Ottawa tool.

RESULTS

A total of 8 retrospective cohort studies were included, all of them performed in China and with low risk of bias. Overexpression of the genes HNRNPC, ITGA5, HMGA2 and SRSF3, and low expression of ALDH3A1 and ARID2 promote EMT in OC. The more advanced clinical stages of the TNM classification were significantly associated with overexpression of HNRNPC, ITGA5, HMGA2 and SRSF3, and low expression of ARID2.

CONCLUSIONS

HNRNPC, ITGA5, HMGA2, SRSF3, ALDH3A1 and ARID2 genes were associated with EMT process. Over- or under-expression of these genes is associated with worse stages of OSCC and/or worse prognosis of the tumor. Further studies on this topic are needed in different countries to be able to confirm these results, since the detection of these genes can help to know which tumors have a worse prognosis.

N6 -methyladenosine Steers RNA Metabolism and Regulation in Cancer

As one of the most studied ribonucleic acid (RNA) modifications in eukaryotes, N⁶ -methyladenosine (m⁶ A) has been shown to play a predominant role in controlling gene expression and influence physiological and pathological processes such as oncogenesis and tumor progression. Writer and eraser proteins, acting opposite to deposit and remove m⁶ A epigenetic marks, respectively, shape the cellular m⁶ A landscape, while reader proteins preferentially recognize m⁶ A modifications and mediate fate decision of the methylated RNAs, including RNA synthesis, splicing, exportation, translation, and stability. Therefore, RNA metabolism in cells is greatly influenced by these three classes of m⁶ A regulators. Aberrant expression of m⁶ A regulators has been widely reported in various types of cancer, leading to cancer initiation, progression, and drug resistance. The close links between m⁶ A and cancer shed light on the potential use of m⁶ A methylation and its regulators as prognostic biomarkers and drug targets for cancer therapy. Given the notable effects of m⁶ A in reversing chemoresistance and enhancing immune therapy, it is a promising target for combined therapy. Herein, we summarize the recent discoveries on m⁶ A and its regulators, emphasizing their influences on RNA metabolism, their dysregulation and impacts in diverse malignancies, and discuss the clinical implications of m⁶ A modification in cancer.

Novel insights into the m6A-RNA methyltransferase METTL3 in cancer

N6-methyladenosine (m⁶A) is a prevalent internal RNA modification in higher eukaryotic cells. As the pivotal m⁶A regulator, RNA methyltransferase-like 3 (METTL3) is responsible for methyl group transfer in the progression of m⁶A modification. This epigenetic regulation contributes to the structure and functional regulation of RNA and further promotes tumorigenesis and tumor progression. Accumulating evidence has illustrated the pivotal roles of METTL3 in a variety of human cancers. Here, we systemically summarize the interaction between METTL3 and RNAs, and illustrate the multiple functions of METTL3 in human cancer. METLL3 is aberrantly expressed in a variety of tumors. Elevation of METTL3 is usually associated with rapid progression and poor prognosis of tumors. On the other hand, METTL3 may also function as a tumor suppressor in several cancers. Based on the tumor-promoting effect of METTL3, the possibility of applying METTL3 inhibitors is further discussed, which is expected to provide novel insights into antitumor therapy.

A novel tp53-associated nomogram to predict the overall survival in patients with pancreatic cancer

BACKGROUND

Gene mutations play critical roles in tumorigenesis and cancer development. Our study aimed to screen survival-related mutations and explore a novel gene signature to predict the overall survival in pancreatic cancer.

METHODS

Somatic mutation data from three cohorts were used to identify the common survival-related gene mutation with Kaplan-Meier curves. RNA-sequencing data were used to explore the signature for survival prediction. First, Weighted Gene Co-expression Network Analysis was conducted to identify candidate genes. Then, the ICGC-PACA-CA cohort was applied as the training set and the TCGA-PAAD cohort was used as the external validation set. A TP53-associated signature calculating the risk score of every patient was developed with univariate Cox, least absolute shrinkage and selection operator, and stepwise regression analysis. Kaplan-Meier and receiver operating characteristic curves were plotted to verify the accuracy. The independence of the signature was confirmed by the multivariate Cox regression analysis. Finally, a prognostic nomogram including 359 patients was constructed based on the combined expression data and the risk scores.

RESULTS

TP53 mutation was screened to be the robust and survival-related mutation type, and was associated with immune cell infiltration. Two thousand, four hundred fifty-five genes included in the six modules generated in the WGCNA were screened as candidate survival related TP53-associated genes. A seven-gene signature was constructed: Risk score = (0.1254 × ERRFI1) - (0.1365 × IL6R) - (0.4400 × PPP1R10) - (0.3397 × PTOV1-AS2) + (0.1544 × SCEL) - (0.4412 × SSX2IP) - (0.2231 × TXNL4A). Area Under Curves of 1-, 3-, and 5-year ROC curves were 0.731, 0.808, and 0.873 in the training set and 0.703, 0.677, and 0.737 in the validation set. A prognostic nomogram including 359 patients was constructed and well-calibrated, with the Area Under Curves of 1-, 3-, and 5-year ROC curves as 0.713, 0.753, and 0.823.

CONCLUSIONS

The TP53-associated signature exhibited good prognostic efficacy in predicting the overall survival of PC patients.

High G2M Pathway Score Pancreatic Cancer is Associated with Worse Survival, Particularly after Margin-Positive (R1 or R2) Resection

Pancreatic cancer is highly mortal due to uncontrolled cell proliferation. The G2M checkpoint pathway is an essential part of the cell cycle. We hypothesized that a high G2M pathway score is associated with cell proliferation and worse survival in pancreatic cancer patients. Gene set variation analysis using the Hallmark G2M checkpoint gene set was used as a score to analyze a total of 390 human pancreatic cancer patients from 3 cohorts (TCGA, GSE62452, GSE57495). High G2M score tumors enriched other cell proliferation genes sets as well as MKI67 expression, pathological grade, and proliferation score. Independent of other prognostic factors, G2M score was predictive of disease-specific survival in pancreatic cancer. High G2M tumor was associated with high mutation rate of KRAS and TP53 and significantly enriched these pathway gene sets, as well as high infiltration of Th2 cells. High G2M score consistently associated with worse overall survival in 3 cohorts, particularly in R1/2 resection, but not in R0. High G2M tumor in R1/2 highly enriched metabolic and cellular components' gene sets compared to R0. To our knowledge, this is the first study to use gene set variation analysis as a score to examine the clinical relevancy of the G2M pathway in pancreatic cancer.

N6-methyladenosine (m6A) RNA modification in cancer stem cells

Cancer stem cells (CSCs), a unique subset of undifferentiated cells with stem cell-like properties, have emerged as driving forces in mediating tumor growth, metastasis, and therapeutic resistance. Recent advances have highlighted that N6-methyladenosine (m6A) RNA modification plays an important role in cancer biology and CSCs. Dynamic m6A decoration has been demonstrated to be involved in CSC generation and maintenance, governing cancer progression and therapeutic resistance. In this review, we provide the first overview of the current knowledge of m6A modification implicated in CSCs and their impact on CSC properties, tumor progression, and responses to treatment. Finally, we also highlight the potential of m6A machinery as novel targets for cancer therapeutics. The involvement of m6A modification in CSCs provides a new direction for exploring cancer pathogenesis and inspires the development of effective strategies to fully eliminate both cancer cells and CSCs.