m6A Methylation Modification Patterns and Tumor Microenvironment Infiltration Characterization in Pancreatic Cancer

Ovarian squamous cell carcinoma: clinicopathological features, prognosis and immunotherapy outcomes

OBJECTIVE

To explore the characteristics and survival outcomes of ovarian squamous cell carcinoma (SCC) and the treatment effectiveness of immune checkpoint inhibitors (ICIs).

METHODS

Patients diagnosed with ovarian SCC at Peking Union Medical College Hospital between January 2000 and September 2023 were included. Overall survival (OS) and progression-free survival (PFS) were analyzed using the Kaplan-Meier method. Univariate and multivariate analysis of OS were performed using the Cox proportional hazards model.

RESULTS

A total of 42 patients were included, with a median age of 51.5 years (range, 23-74). The majority had SCC arising from teratomas (54.8%), followed by endometriosis (14.3%) and Brenner's tumor (2.4%). Patients undergoing molecular testing exhibited a median tumor mutation burden (TMB) of 10.00 mutations/Mb (range, 7.28-46.86), predominantly featuring PIK3CA mutations. Thirty-eight patients (90.5%) received adjuvant chemotherapy. The median OS was 42.0 months, with the 1- and 5-year OS rates were 73.7% and 48.7%, respectively. And the median PFS was 26.9 months, with the 1- and 5-year PFS rates were 57.5% and 43.8%, respectively. Five patients underwent first-line postoperative adjuvant therapy combining ICIs with chemotherapy. During the 9.5 to 25.1 months follow-up, 4 patients showed no evidence of disease, while 1 relapsed and received treatment. Late-stage disease and younger age at diagnosis were associated with worse survival outcomes.

CONCLUSION

The prognosis for ovarian SCC remains unfavorable. The stage and age were prognostic predictors for survival. ICIs may be beneficial for patients with ovarian SCC, particularly those with a high TMB.

The role of m6A modification in the risk prediction and Notch1 pathway of Alzheimer's disease

N6-methyladenosine (m6A) methylation and abnormal immune responses are implicated in neurodegenerative diseases, yet their relationship in Alzheimer's disease (AD) remains unclear. We obtained AD datasets from GEO databases and used AD mouse and cell models, observing abnormal expression of m6A genes in the AD group, alongside disruptions in the immune microenvironment. Key m6A genes (YTHDF2, LRPPRC, and FTO) selected by machine learning were associated with the Notch pathway, with FTO and Notch1 displaying the strongest correlation. Specifically, FTO expression decreased and m6A methylation of Notch1 increased in AD mouse and cell models. We further silenced FTO expression in HT22 cells, resulting in upregulation of the Notch1 signaling pathway. Additionally, increased Notch1 expression in dendritic cells heightened inflammatory cytokine secretion in vitro. These results suggest that reduced FTO expression may contribute to the pathogenesis of AD by activating the Notch1 pathway to interfere with the immune response.

N6-methyladenosine modification of circMARK2 enhances cytoplasmic export and stabilizes LIN28B, contributing to the progression of Wilms tumor

BACKGROUND

The potential involvement of circular RNAs (circRNAs) and N6-methyladenosine (m6A) modification in the progression of Wilms tumor (WT) has not been fully elucidated. This study investigates the regulatory mechanisms and clinical significance of m6A-modified circMARK2 and its role in WT progression.

METHODS

We identified dysregulated circRNAs through deep sequencing and validated their expression by qRT-PCR in WT tissues. The biological functions of circMARK2 were assessed using clone formation, transwell migration, and orthotopic animal models. To dissect the underlying mechanisms, we employed RNA immunoprecipitation, RNA pull-down, dual-luciferase reporter assays, Western blotting, and immunofluorescence and immunohistochemical staining.

RESULTS

CircMARK2, upregulated in WT tissues, was found to be m6A-modified and promoted cytoplasmic export. It facilitated WT progression by stabilizing LIN28B mRNA through the circMARK2/IGF2BP2 interaction. In vitro and in vivo studies demonstrated that circMARK2 enhances the malignant behavior of WT cells. Clinically, higher circMARK2 levels in tumor tissues of WT patients were linked to increased tumor aggressiveness and reduced survival rates.

CONCLUSIONS

Our study provides the first comprehensive evidence that m6A-modified circMARK2 contributes to WT progression by enhancing LIN28B mRNA stability, promoting cellular aggressiveness. CircMARK2 emerges as a potential biomarker for prognosis and a promising target for therapeutic intervention in WT, underscoring the clinical relevance of m6A modification in pediatric renal cancer.

Identification of the expression patterns and potential prognostic role of m6A-RNA methylation regulators in Wilms Tumor

BACKGROUND

To explore the potential role of m6A methylation modification in Wilms Tumor (WT) by m6A-RNA Methylation (m6A) regulators.

METHODOLOGY

The association of m6A modification patterns with immune and prognostic characteristics of tumors was systematically evaluated using 19 m6A regulators extracted from Wilms Tumor's samples in public databases. A comprehensive model of "m6Ascore" was constructed using principal component analysis, and its prognostic value was evaluated.

RESULTS

Almost all m6A regulators were differentially expressed between WT and normal tissues. Unsupervised clustering identified three distinct m6A clusters that differed in both immune cell infiltration and biological pathways. The m6Ascore was constructed to quantify m6A modifications in individual patients. Our analysis suggests that m6Ascore is an independent prognostic factor for WT and can be used as a novel predictor of WT prognosis.

CONCLUSIONS

This study comprehensively explored and systematically characterized m6A modifications in WT. m6A modification patterns play a critical role in the tumor immune microenvironment (TIME) and WT prognosis. m6Ascore provides a more comprehensive understanding of m6A modifications in WT and offers a practical tool for predicting WT prognosis. This study will help clinicians to identify valid indicators of WT to improve the poor prognosis of this disease.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at https://www.aliyundrive.com/drive/folder/64be739cd6956a741fb24670baeea53422be6024 .

METTL3 enhances pancreatic ductal adenocarcinoma progression and gemcitabine resistance through modifying DDX23 mRNA N6 adenosine methylation

The aim of the present study was to clarify the mechanism of how METTL3 regulated pancreatic ductal adenocarcinoma (PDAC) progression by m6A modification of its downstream target mRNA and signaling pathway. Immunoblotting and qRT-PCR assays was employed to determine the expression levels of METTL3. In situ fluorescence hybridization was conducted to localize the cellular distribution of METTL3 and DEAD-box helicase 23 (DDX23). CCK8, colony formation, EDU incorporation, TUNEL, wound healing and Transwell assays were carried out accordingly to study the viability, proliferation, apoptosis, and mobility of cells under different treatments in vitro. Xenograft and animal lung metastasis experiments were also conducted to study the functional role of METTL3 or DDX23 on tumor growth and lung metastasis in vivo. MeRIP-qPCR and bioinformatical analyses were used to obtain the potential direct targets of METTL3. It was shown that m6A methyltransferase METTL3 was upregulated in PDAC tissues with gemcitabine resistance, and its knockdown sensitized pancreatic cancer cells to chemotherapy. Furthermore, silencing METTL3 remarkably reduced pancreatic cancer cell proliferation, migration, and invasion both in vitro and in vivo. Mechanistically, validation experiments confirmed that DDX23 mRNA was a direct target of METTL3 in YTHDF1-dependent manner. Additionally, DDX23 silence resulted in the suppression of pancreatic cancer cell malignancy and PIAK/Akt signaling inactivation. Strikingly, rescuse experiments demonstrated the inhibitive effects of METTL3 silence on cell phenotypes and gemcitabine resistance were partially reversed by forcibly expressed DDX23. In summary, METTL3 promotes PDAC progression and gemcitabine resistance by modifying DDX23 mRNA m6A methylation and enhancing PI3K/Akt signaling activation. Our findings establish a potential tumor promotive and chemo-resistant role for METTL3/DDX23 axis in PDAC.

IMPDH1, a prognostic biomarker and immunotherapy target that correlates with tumor immune microenvironment in pan-cancer and hepatocellular carcinoma

Backgrounds

IMPDH1, a rate-limiting enzyme in de novos synthesis of guanine nucleotides, plays an essential role in the growth and progression of certain tumors. However, there is still a lack of study on IMPDH1 evaluating its role in the tumor immune microenvironment, the potential mechanisms, and its potential as a promising tumor therapeutic target.

Methods

The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Genotype-Tissue Expression (GTEx), TIMER2.0, KM-Plotter, University of Alabama at Birmingham Cancer data analysis Portal (UALCAN), cbioportal, The Human Protein Atlas (HPA), and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) were used to perform the systematic analysis of IMPDH1, including mRNA expression, protein expression, prognostic value, Enrichment analysis, DNA methylation, immune cell infiltration in pan-cancer, Then, we conducted qRT-PCR and immunohistochemistry to analyze the expression level of IMPDH1 in cancer tissues and non-cancer tissues of patients with primary hepatocellular carcinoma (HCC), and performed the same verification at cellular level.

Results

We discovered that IMPDH1 was highly expressed in a variety of tumors and was associated with poor prognosis. IMPDH1 not only had the potential as a tumor prognostic marker and therapeutic target, but also was closely related to immune cells, immune checkpoints and immune-related genes and pathways in the tumor immune microenvironment (TIME). Meanwhile, IMPDH1 expression influenced the efficacy and prognosis of tumor patients treated with immune checkpoint inhibitors.

Conclusions

IMPDH1 may be as a potential combined target of immunotherapy.

Identification of necroptosis-related subtypes, development of a novel signature, and characterization of immune infiltration in colorectal cancer

Introduction

Necroptosis, a type of programmed cell death, has recently been extensively studied as an important pathway regulating tumor development, metastasis, and immunity. However, the expression patterns of necroptosis-related genes (NRGs) in colorectal cancer (CRC) and their potential roles in the tumor microenvironment (TME) have not been elucidated.

Methods

We explored the expression patterns of NRGs in 1247 colorectal cancer samples from genetics and transcriptional perspective. Based on a consensus clustering algorithm, we identified NRG molecular subtypes and gene subtypes, respectively. Furthermore, we constructed a necroptosis-related signature for predicting overall survival time and verified the predictive ability of the model. Using the ESTIMATE, CIBERSORT, and ssGSEA algorithms, we assessed the association between the above subtypes, scores and immune infiltration.

Results

Most NRGs were differentially expressed between CRC tissues and normal tissues. We found that distinct subtypes exhibited different NRGs expression, patients' prognosis, immune checkpoint gene expression, and immune infiltration characteristics. The scores calculated from the necroptosis-related signature can be used to classify patients into high-risk and low-risk groups, with the high-risk group corresponding to reduced immune cell infiltration and immune function, and a greater risk of immune dysfunction and immune escape.

Discussion

Our comprehensive analysis of NRGs in CRC demonstrated their potential role in clinicopathological features, prognosis, and immune infiltration in the TME. These findings help us deepen our understanding of NRGs and the tumor microenvironment landscape, and lay a foundation for effectively assessing patient outcomes and promoting more effective immunotherapy.

Research advances of N6-methyladenosine in diagnosis and therapy of pancreatic cancer

BACKGROUND

N6-methyladenosine (m6A) is the addition of a methyl group on the N6 position of adenosine and is the most prevalent and abundant epigenetic modification in eukaryote mRNA. m6A marks are added to mRNA by the m6A methyltransferase complex ("writers"), removed by m6A demethylases ("erasers"), and recognized by m6A-binding proteins ("readers"). Recent evidence has shown that the m6A modification plays a crucial role in the pathogenic mechanism and malignant progression of pancreatic cancer, with roles in cell survival, proliferation, migration, invasion, tumor metastasis, and drug resistance.

METHODS

Literature was searched in Pubmed and Web of Science for the following keywords: "N6-methyladenosine", "pancreatic cancer", "epigenetic modification", "immunotherapy".

RESULTS

Among classical m6A regulators, while METTL3, METTL14, WTAP, FTO, YTHDF2, IGF2BP1-3, hnRNPC, and NKAP are upregulated in pancreatic cancer, METTL16 and ALKBH5 are downregulated in pancreatic cancer. m6A modification has been investigated in pancreatic cancer therapy.

CONCLUSION

Dysregulated m6A and its related factors in pancreatic cancer cells and patients indicate their potential values as novel biomarkers in pancreatic cancer diagnosis and targeted therapy.

A signature based on m6A pattern and tumor microenvironment infiltration in clear cell renal cell carcinoma

BACKGROUND

RNA N6-methyladenosine (m6A) has been found to have a critical impact on clear cell renal cell carcinoma (ccRCC) by affecting the tumor microenvironment (TME) and immune cell (IC) infiltration and is related to the treatment and survival rate of patients with ccRCC. However, the mechanism of m6A in TME and IC infiltration remained unclear.

METHODS

Nonnegative Matrix Factorization (NMF) clustering was performed on 650 ccRCC cases from the Cancer Genome Atlas (TCGA) and the Gene-Expression Omnibus (GEO) datasets. The immune infiltration was generated by the single-sample gene-set enrichment analysis (ssGSEA) algorithm. Survival analyses were performed using the Kaplan-Meier method, and the significance of the differences was determined using the log-rank test. The m6A score was constructed based on the expression of m6A regulators to quantify m6A modification. The package "survminer R" was employed to layer patients' low and high scores groups and predict the immunotherapy response.

RESULTS

Three different patterns of m6A modification were established, and significant differences in TME and IC infiltration features were found in these three patterns. Survival analysis demonstrated that m6A cluster A and m6A gene cluster A experienced a longer survival time. Evaluation of m6A modification patterns in individual tumors was initiated by the m6A score. The low m6A score subtype was characterized by increased tumor mutation burden (TMB) and immune infiltration, whereas a high m6A score with a lack of immune cell infiltration showed significantly better overall survival. m6A score was also associated with the expression of programmed cell death protein 1 (PD-L1) and cytotoxic T lymphocyte antigen 4 (CTLA-4). Patients in the high m6A score group had high PD-L1 expression and low CTLA-4 expression. Significant differences in prognosis were identified among types of different TMB and m6A scores, where low TMB and high m6A score had longer survival time.

CONCLUSIONS

This research indicated that m6A modification greatly affected TME and IC infiltration. Physicians can develop practical immunotherapy strategies for patients with ccRCC by evaluating m6A-associated genes.

The significance of m6A RNA methylation modification in prognosis and tumor microenvironment immune infiltration of cervical cancer

Recent studies have highlighted that N6-methyladenosine (m6A) plays a significant role in tumorigenicity and progression. However, the mechanism of m6A modifications in the tumor microenvironment (TME) immune cell infiltration in cervical cancer (CC) remains unclear. Clinical and RNA sequencing data of 25 m6A RNA methylation regulators were acquired from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. LASSO Cox regression analysis was used to generate a prognostic risk signature. m6A modification patterns were identified based on the expression of 25 m6A regulators, and their correlation with TME immune cell-infiltrating characterization was analyzed. Principal component analysis was used to construct an m6A-scoring signature (m6A score) to evaluate the m6A modification patterns of individual CC samples and guide the selection of more effective immunotherapeutic strategies. Genetic and expression alterations of 25 m6A regulators were highly heterogeneous between CC and normal tissues. METTL14 and IGF2BP1 were selected to conduct the prognostic risk signature. Three m6A modification patterns were identified in 659 CC samples, which were associated with distinct clinical outcomes and biological pathways. The TME immune cell-infiltrating characterization of the three m6A modification patterns was highly consistent with 3 tumor immune phenotypes, including immune-excluded, immune-inflamed, and immune-desert phenotypes. Due to the heterogeneity of m6A modification patterns, an m6A scoring signature was established to evaluate the m6A modification patterns of individual CC samples. Univariate and multivariate Cox regression analyses revealed that the m6A score is a robust and independent prognostic biomarker for assessing the prognosis of CC patients. A low m6A score, characterized by higher somatic mutation and higher expression of proliferation-related and DNA repair-related genes, indicated poor overall survival. Activation of immune infiltration was exhibited by the high m6A score, which was likely to have a good response and clinical benefits to antiPD-1/L1 immunotherapy. This study highlights the prognostic value of 25 m6A regulators in CC. The m6A modification is related to immune regulation and the formation of TME heterogeneity and complexity. An m6A scoring signature to clarify the individual m6A modification pattern could enhance our understanding of TME immune cell-infiltrating characterization and guide immunotherapy strategies.

m6A Methylation Patterns and Tumor Microenvironment Infiltration Characterization in Clear-Cell Renal Cell Carcinoma

Increasing evidence suggests the essential regulation of RNA N6-methyladenosine (m6A) modification in carcinogenesis and immune response. Nevertheless, the potential impacts of these modifications on the tumor microenvironment (TME) immune cell infiltration characteristics in clear-cell renal cell carcinoma (ccRCC) remain unclear. Utilizing a consensus clustering algorithm, we determined three m6A modification patterns and identified three m6A-related gene clusters among 569 ccRCC samples, which were associated with different biological functions and clinical outcomes. Thereafter, the m6A score was constructed using m6A-associated signature genes to accurately exploit the m6A modification patterns within individual tumors. The m6A score was further demonstrated to be noticeably related to ccRCC prognosis. In addition, the m6A score was found to be strongly correlated with tumor mutational burden (TMB), microsatellite instability, immune infiltration, immune checkpoint expression, and immunotherapy response, which was also validated in the pan-cancer analyses. Our findings thoroughly elucidated that m6A modification contributes to tumor microenvironment immune-infiltrating characteristics and prognosis in ccRCC. Assessing the m6A modification patterns of individual patients with ccRCC will offer novel insights into TME infiltration and help develop more effective treatment strategies.

N6-Methyladenosine-Related LncRNAs Are Potential Remodeling Indicators in the Tumor Microenvironment and Prognostic Markers in Osteosarcoma

N6-Adenosine methylation, yielding N6-methyladenosine (m⁶A), is a reversible epigenetic modification found in messenger RNAs and long non-coding RNAs (lncRNAs), which affects the fate of modified RNA molecules and is essential for the development and differentiation of immune cells in the tumor microenvironment (TME). Osteosarcoma (OS) is the most common primary bone tumor in children and adolescents, and is characterized by high mortality. Currently, the possible role of m⁶A modifications in the prognosis of OS is unclear. In the present study, we investigated the correlation between m⁶A-related lncRNA expression and the clinical outcomes of OS patients via a comprehensive analysis. Clinical and workflow-type data were obtained from the Genotype-Tissue Expression Program and The Cancer Genome Atlas. We examined the relationship between m⁶A modifications and lncRNA expression, conducted Kyoto Encyclopedia of Genes analysis and also gene set enrichment analysis (GSEA), implemented survival analysis to investigate the association of clinical survival data with the expression of m⁶A-related lncRNAs, and utilized Lasso regression to model the prognosis of OS. Furthermore, we performed immune correlation analysis and TME differential analysis to investigate the infiltration levels of immune cells and their relationship with clinical prognosis. LncRNA expression and m⁶A levels were closely associated in co-expression analysis. The expression of m⁶A-related lncRNAs was quite low in tumor tissues; this appeared to be a predicting factor of OS in a prognostic model, independent of other clinical features. The NOD-like receptor signaling pathway was the most significantly enriched pathway in GSEA. In tumor tissues, SPAG4 was overexpressed while ZBTB32 and DEPTOR were downregulated. Tissues in cluster 2 were highly infiltrated by plasma cells. Cluster 2 presented higher ESTIMATE scores and stromal scores, showing a lower tumor cell purity in the TME. In conclusion, m⁶A-related lncRNA expression is strongly associated with the occurrence and development of OS, and can be used to as a prognostic factor of OS. Moreover, m⁶A-related lncRNAs and infiltrating immune cells in the TME could serve as new therapeutic targets and prognostic biomarkers for OS.