Construction of a prognostic model for lung adenocarcinoma based on m6A/m5C/m1A genes.

BACKGROUND: Developing a prognostic model for lung adenocarcinoma (LUAD) that utilizes m6A/m5C/m1A genes holds immense importance in providing precise prognosis predictions for individuals. METHODS: This study mined m6A/m5C/m1A-related differential genes in LUAD based on public databases, identified LUAD tumor subtypes based on these genes, and further built a risk prognostic model grounded in differential genes between subtypes. The immune status between high- and low-risk groups was investigated, and the distribution of feature genes in tumor immune cells was analyzed using single-cell analysis. Based on the expression levels of feature genes, a projection of chemotherapeutic and targeted drugs was made for individuals identified as high-risk. Ultimately, cell experiments were further verified. RESULTS: The 6-gene risk prognosis model based on differential genes between tumor subtypes had good predictive performance. Individuals classified as low-risk exhibited a higher (P < 0.05) abundance of infiltrating immune cells. Feature genes were mainly distributed in tumor immune cells like CD4+T cells, CD8+T cells, and regulatory T cells. Four drugs with relatively low IC50 values were found in the high-risk group: Elesclomol, Pyrimethamine, Saracatinib, and Temsirolimus. In addition, four drugs with significant positive correlation (P < 0.001) between IC50 values and feature gene expression were found, including Alectinib, Estramustine, Brigatinib, and Elesclomol. The low expression of key gene NTSR1 reduced the IC50 value of irinotecan. CONCLUSION: Based on the m6A/m5C/m1A-related genes in LUAD, LUAD patients were divided into 2 subtypes, and a m6A/m5C/m1A-related LUAD prognostic model was constructed to provide a reference for the prognosis prediction of LUAD.

Development of m6A/m5C/m1A regulated lncRNA signature for prognostic prediction, personalized immune intervention and drug selection in LUAD.

Research indicates that there are links between m6A, m5C and m1A modifications and the development of different types of tumours. However, it is not yet clear if these modifications are involved in the prognosis of LUAD. The TCGA-LUAD dataset was used as for signature training, while the validation cohort was created by amalgamating publicly accessible GEO datasets including GSE29013, GSE30219, GSE31210, GSE37745 and GSE50081. The study focused on 33 genes that are regulated by m6A, m5C or m1A (mRG), which were used to form mRGs clusters and clusters of mRG differentially expressed genes clusters (mRG-DEG clusters). Our subsequent LASSO regression analysis trained the signature of m6A/m5C/m1A-related lncRNA (mRLncSig) using lncRNAs that exhibited differential expression among mRG-DEG clusters and had prognostic value. The model's accuracy underwent validation via Kaplan-Meier analysis, Cox regression, ROC analysis, tAUC evaluation, PCA examination and nomogram predictor validation. In evaluating the immunotherapeutic potential of the signature, we employed multiple bioinformatics algorithms and concepts through various analyses. These included seven newly developed immunoinformatic algorithms, as well as evaluations of TMB, TIDE and immune checkpoints. Additionally, we identified and validated promising agents that target the high-risk mRLncSig in LUAD. To validate the real-world expression pattern of mRLncSig, real-time PCR was carried out on human LUAD tissues. The signature's ability to perform in pan-cancer settings was also evaluated. The study created a 10-lncRNA signature, mRLncSig, which was validated to have prognostic power in the validation cohort. Real-time PCR was applied to verify the actual manifestation of each gene in the signature in the real world. Our immunotherapy analysis revealed an association between mRLncSig and immune status. mRLncSig was found to be closely linked to several checkpoints, such as IL10, IL2, CD40LG, SELP, BTLA and CD28, which could be appropriate immunotherapy targets for LUAD. Among the high-risk patients, our study identified 12 candidate drugs and verified gemcitabine as the most significant one that could target our signature and be effective in treating LUAD. Additionally, we discovered that some of the lncRNAs in mRLncSig could play a crucial role in certain cancer types, and thus, may require further attention in future studies. According to the findings of this study, the use of mRLncSig has the potential to aid in forecasting the prognosis of LUAD and could serve as a potential target for immunotherapy. Moreover, our signature may assist in identifying targets and therapeutic agents more effectively.

Targeting Method for rTMS for Treating Depression in Japanese Patients: A Comparison of the Standard, F3, and Neuronavigation Approaches.

INTRODUCTION: The left dorsolateral prefrontal cortex (lDLPFC) is a commonly targeted brain region for repetitive transcranial magnetic stimulation (rTMS) for depression. The lDLPFC has been identified using the "5-cm rule." However, identification of the lDLPFC may deviate from the ideal stimulation site localized by neuronavigation. Therefore, we aimed to compare this method with other methods and examine the relationship between deviation from the ideal stimulation site and treatment effects. While most existing studies have focused on participants of European descent, this study focused on Japanese participants. METHODS: The study participants were 16 patients who underwent rTMS and had the stimulus location identified using the 5-cm method. The lDLPFC was identified by the F3 electrode position and neuronavigation in addition to the 5-cm rule, and these locations were compared. We then performed a correlation analysis of the distance between the sites identified by the 5-cm method and by neuronavigation, as well as changes in scores on the 17-item Hamilton Depression Scale (HAMD-17). RESULTS: The lDLPFC identified by the F3 site and neuronavigation was approximately 3 cm more anterolateral than that identified by the 5-cm method. A significant correlation was found between the distance between the sites identified by the 5-cm method and neuronavigation and the rate of change in HAMD-17 scores. CONCLUSION: The ideal stimulation site may be approximately 3 cm anterior to the site identified by the 5-cm method, and stimulation of the F3 site may be a valid alternative to the 5-cm method.

Breast cancer prognosis and immunological characteristics are predicted using the m6A/m5C/m1A/m7G-related long noncoding RNA signature.

According to statistics, breast cancer (BC) has replaced lung cancer as the most common cancer in the world. Therefore, specific detection markers and therapeutic targets need to be explored as a way to improve the survival rate of BC patients. We first identified m6A/m5C/m1A/m7G-related long noncoding RNAs (MRlncRNAs) and developed a model of 16 MRlncRNAs. Kaplan-Meier survival analysis was applied to assess the prognostic power of the model, while univariate Cox analysis and multivariate Cox analysis were used to assess the prognostic value of the constructed model. Then, we constructed a nomogram to illustrate whether the predicted results were in good agreement with the actual outcomes. We tried to use the model to distinguish the difference in sensitivity to immunotherapy between the two groups and performed some analyses such as immune infiltration analysis, ssGSEA and IC50 prediction. To explore the novel anti-tumor drug response, we reclassified the patients into two clusters. Next, we assessed their response to clinical treatment by the R package pRRophetic, which is determined by the IC50 of each BC patient. We finally identified 11 MRlncRNAs and based on them, a risk model was constructed. In this model, we found good agreement between calibration plots and prognosis prediction. The AUC of ROC curves was 0.751, 0.734, and 0.769 for 1-year, 2-year, and 3-year overall survival (OS), respectively. The results showed that the IC50 was significantly different between the risk groups, suggesting that the risk groups can be used as a guide for systemic treatment. We regrouped patients into two clusters based on 11 MRlncRNAs expression. Next, we conducted immune scores for 2 clusters, which showed that cluster 1 had higher stromal scores, immune scores and higher estimated (microenvironment) scores, demonstrating that TME of cluster 1 was different from cluster 2. The results of this study support that MRlncRNAs can predict tumor prognosis and help differentiate patients with different sensitivities to immunotherapy as a basis for individualized treatment for BC patients.

The m6A/m5C/m1A regulator genes signature reveals the prognosis and is related with immune microenvironment for hepatocellular carcinoma.

BACKGROUND: RNA methylation is a crucial in many biological functions, and its aberrant regulation is associated with cancer progression. N6-Methyladenosine (m6A), 5-Methylcytosine (m5C), N1-methyladenosine (m1A) are common modifications of RNA methylation. However, the effect of methylation of m6A/m5C/m1A in hepatocellular carcinoma (HCC) remains unclear. METHOD: The transcriptome datasets, clinic information, and mutational data of 48 m6A/m5C/m1A regulator genes were acquired from the TCGA database, and the prognostic hazard model was established by univariate and Least absolute shrinkage and selection operator (Lasso) regression. The multivariate regression was performed to determine whether the risk score was an independent prognostic indicator. Kaplan-Meier survival analysis and ROC curve analysis were used to evaluate the predictive ability of the risk model. Decision curve analysis（DCA）analysis was conducted to estimate the clinical utility of the risk model. We further analyzed the association between risk score and functional enrichment, tumor immune microenvironment, and somatic mutation. RESULT: The four-gene (YTHDF1, YBX1, TRMT10C, TRMT61A) risk signature was constructed. The high-risk group had shorter overall survival (OS) than the low-risk group. Univariate and multivariate regression analysis indicated that risk score was an independent prognostic indicator. Risk scores in male group, T3 + T4 group and Stage III + IV group were higher in female group, T1 + T2 group and stage I + II group. The AUC values for 1-, 2-, and 3-year OS in the TCGA dataset were 0.764, 0.693, and 0.689, respectively. DCA analysis showed that the risk score had a higher clinical net benefit in 1- and 2-year OS than other clinical features.The risk score was positively related to some immune cell infiltration and most immune checkpoints. CONCLUSION: We developed a novel m6A/m5C/m1A regulator genes' prognostic model, which could be applied as a latent prognostic tool for HCC and might guide the choice of immunotherapies.

Comparison of safety and short-term outcomes between endoscopic and laparoscopic resections of gastric gastrointestinal stromal tumors with a diameter of 2-5 cm.

BACKGROUND AND AIM: Developments of endoscopic techniques brought the possibility of endoscopic resection for gastrointestinal stromal tumors (GISTs) of larger sizes. We aim to compare safety and short-term outcomes between endoscopic and laparoscopic resections of gastric GISTs with a diameter of 2-5 cm. METHODS: This is a single-center, retrospective cohort study. The clinical data, perioperative conditions, and the adverse events of patients who underwent endoscopic or laparoscopic resection for gastric GIST of 2-5 cm in Zhongshan Hospital, Fudan University, from January 2016 to December 2020 were retrospectively reviewed. RESULTS: A total of 346 patients were reviewed; 12 patients who failed to accomplish the planned procedure were excluded; 182 underwent laparoscopic resection; and 152 underwent endoscopic resection. Significant differences exist in the tumor size between the laparoscopic group (3.43 ± 0.86 cm) and the endoscopic group (2.78 ± 0.73 cm) (P < 0.01). Compared with laparoscopic resection, endoscopic resection was associated with faster recovery (P < 0.01), shorter hospital stays (P < 0.01), and lower cost (P < 0.01). The incidence of Clavien-Dindo grade II-V adverse events in the endoscopic group (3/152) was significantly lower than that in the laparoscopic group (12/182) (P = 0.04). After a propensity score matching analysis, the endoscopic group showed similar incidences of complications with the laparoscopic group, while the advantages over laparoscopic resection in postoperative hospital stay, time to first oral intake, and hospitalization expenses remained significant (P < 0.01). CONCLUSIONS: Endoscopic resection is a safe and cost-effective method for 2-5 cm of gastric GISTs compared with laparoscopic resection.

Combined therapy with conventional trans-arterial chemoembolization (cTACE) and microwave ablation (MWA) for hepatocellular carcinoma >3-<5 cm.

PURPOSE: To compare safety and efficacy of combined therapy with conventional transarterial chemoembolization (cTACE)+microwave ablation (MWA) versus only TACE or MWA for treatment of hepatocellular carcinoma (HCC) >3-<5 cm. METHODS: This randomized controlled trial (NCT04721470) screened 278 patients with HCC >3-<5 cm. Patients were randomized into three groups: 90 underwent TACE (Group 1); 95 underwent MWA (Group 2); and 93 underwent combined therapy (Group 3). Patients were followed-up with contrast-enhanced CT or MRI. Images were evaluated and compared for treatment response and adverse events based on modified response evaluation criteria in solid tumor. Serum alpha-fetoprotein (AFP) concentration was measured at baseline and during every follow-up visit. RESULTS: Final analysis included 265 patients (154 men, 111 women; mean age = 54.5 ± 11.8 years; range = 38-76 years). Complete response was achieved by 86.5% of patients who received combined therapy compared with 54.8% with only TACE and 56.5% with only MWA (p = 0.0002). The recurrence rate after 12 months was significantly lower in Group 3 (22.47%) than Groups 1 (60.7%) and 2 (51.1%) (p = 0.0001). The overall survival rate (three years after therapy) was significantly higher in Group 3 (69.6%) than Groups 1 (54.7%) and 2 (54.3%) (p = 0.02). The mean progression-free survival was significantly higher in Group 3 than groups 1 and 2 (p < 0.001). A decrease in AFP concentration was seen in 75%, 63%, and 48% patients of Group 3, 2, and 1, respectively. CONCLUSIONS: Combined therapy with cTACE + MWA is safe, well-tolerated, and more effective than TACE or MWA alone for treatment of HCC >3-<5 cm.

Laparoscopic liver resection for large HCC: short- and long-term outcomes in relation to tumor size.

OBJECTIVE: In this study, we aim to assess the impact of tumor size on clinical and oncological outcomes in patients undergoing laparoscopic liver resection (LLR) for hepatocellular carcinoma (HCC). BACKGROUND: LLR has been shown to be feasible, safe, and oncologically efficient. However, it has been slow to develop in patients with HCC who often suffer from chronic liver disease which represents an additional challenge for the surgeon. The experience with large HCCs is even more limited. METHODS: Between 2003 and 2016, 172 patients from two high-volume liver surgery centers underwent LLR for HCC. Prospectively collected data were analyzed after stratification in 3 groups according to tumor major diameter (group 1: < 3 cm; group 2: between 3 and 5 cm; group 3: ≥ 5 cm). Perioperative and long-term outcomes were compared between the three groups and sub-analyses were carried out on the extent and location of the resections. RESULTS: Groups 1, 2, and 3 consisted of 82, 52, and 38 patients, respectively. Minor and major resections were performed in 98.8% and 1.2% in group 1, in 90.4% and 9.6% in group 2, and in 68.4% and 31.6% in group 3, respectively. Postero-superior "technically major" resections were performed in 15.8% patients in group 1, in 19.2% in group 2, and in 15.8% in group 3, respectively. Group 3 had higher conversion rates (p < 0.001), more frequent (p = 0.056) and more prolonged (p = 0,075) pedicle clamping and longer operative time (p < 0.001), higher blood losses (p = 0.025), and longer total hospital and intensive care unit stays. These differences ceased after removing the major resections from the study population, except for the postoperative length of stay. There were no differences in morbidity, mortality, completeness of resection rates, and long-term outcomes between the three groups. CONCLUSION: LLR for HCC appears to be safe and oncologically efficient when performed in high-volume HPB and laparoscopic centers. Tumor size does not appear to impact negatively on the outcomes except for postoperative hospital stay.

Staging laparoscopy for advanced gastric cancer: significance of preoperative clinicopathological factors.

PURPOSE: Although the use of staging laparoscopy (SL) for detecting peritoneal metastasis (P) and determining peritoneal lavage cytology (CY) is widespread in advanced gastric cancer, an indication for SL based on preoperative clinicopathological factors is controversial. METHODS: From May 2006 to September 2015, 120 patients with advanced gastric cancer with primary tumors ≥5 cm and/or with bulky regional lymph nodes (bulky N) underwent SL for assessment of P/CY status. Clinicopathological factors were analyzed retrospectively to determine their influence on peritoneal spread (P1 and/or CY1). An additional analysis of 379 consecutive patients with clinically T2 or deeper gastric cancer in the same time period was carried out to confirm the SL results. RESULTS: Peritoneal spread was confirmed by SL in 54 cases (45%). The presence of type-4 tumors (n = 38, p < 0.0001) and diffuse-type tumors (n = 85, p = 0.04) correlated significantly with peritoneal spread. These two factors were also correlated significantly with increased peritoneal spread in a subgroup analysis among patients with tumors with bulky N (n = 44). The additional analysis of 379 patients showed results consistent with the SL results. The frequency of peritoneal spread was 78% among type-4 tumors, 47% among diffuse-type tumors ≥5 cm, and 38% among diffuse-type tumors with bulky N, whereas among intestinal-type tumors, it was 18% in tumors ≥5 cm and 13% among tumors with bulky N. CONCLUSIONS: Among tumors ≥5 cm or with bulky N, type-4 tumors and diffuse-type tumors had a high potential for peritoneal spread and patients with such tumors were considered more suitable candidates for SL.

A novel m6A/m5C/m1A/m7G-related classification and risk signature predicts prognosis and reveals immunotherapy inclination in gastric cancer.

Background: Gastric cancer (GC) is characterized by high morbidity and mortality rates, and the prognosis is not optimistic. Therefore, the search for new biomarkers is crucial. Methylation modifications in RNA modifications play a crucial role in tumors. However, the role of methylation modification of integrated m6A/m5C/m1A/m7G, in GC and its related analysis have not been reported. It still needs to be studied in depth. Our study aims to deepen our understanding of m6A/m5C/m1A/m7G methylation and potentially provide new strategies for GC treatment. Methods: We used TCGA-STAD (The Cancer Genome Atlas-Stomach Adenocarcinoma) as a training set and GSE84433 as a validation set to analyze and determine potential associations between m6A/m5C/m1A/m7G-related genes and clinical risk of GC. In addition, we explored the prognostic value and potential biological mechanisms of m6A/m5C/m1A/m7G-related genes in GC through consistent clustering, differential expression gene identification, enrichment analysis, and immune infiltration analysis. Finally, we constructed m6A/m5C/m1A/m7G-related risk signature (MRRS) to evaluate the correlation between risk grade and survival prognosis, drug sensitivity, and immune infiltration, and validated the validity by immunohistochemical staining. Results: We identified subgroups of C1, C2, and C3 patients by consensus clustering using data from 45 m6A/m5C/m1A/m7G-related genes. The three groups showed significant differences in survival, immune scores, and immune cell infiltration. We then constructed MRRS using least absolute shrinkage and selection operator (LASSO) regression analysis, including SLC5A6, FKBP10, GPC3, and GGH, which could accurately differentiate between high-/low-risk populations. Its accuracy was further validated in the validation set and immunohistochemical staining. These results suggest that m6A/m5C/m1A/m7G are closely related to the GC tumor immune microenvironment, and MRRS has good performance in predicting the survival of GC patients. Conclusions: In this study, we highlighted the association of m6A/m5C/m1A/m7G subtypes with changes in the GC immunotumor microenvironment. We constructed and validated MRRS, which is valuable in predicting survival, immune infiltration and drug sensitivity in GC patients. This helps to deepen our understanding of m6A/m5C/m1A/m7G methylation and potentially provides new strategies for GC treatment.

The m5C/m6A/m7G-related non-apoptotic regulatory cell death genes for the prediction of the prognosis and immune infiltration status in hepatocellular carcinoma.

Background: 5-methylcytosine/N6-methyladenosine/N7-methylguanosine (m5C/m6A/m7G)-related genes play a critical role in tumor occurrence and progression, and non-apoptotic regulatory cell death (NARCD) is closely linked to tumor development and immunity. However, the role of m5C/m6A/m7G-related NARCD genes in hepatocellular carcinoma (HCC) remains unclear. We used m5C/m6A/m7G-related NARCD genes to construct a prognostic model of HCC for prognostic prediction and clinical treatment of patients. Methods: We obtained transcriptome data for HCC from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Using the least absolute shrinkage and selection operator (LASSO) regression, we identified m5C/m6A/m7G-related NARCD genes and constructed a prognostic model through multivariate Cox regression. Model performance was assessed using Kaplan-Meier and receiver operating characteristic (ROC) curves, with external validation using the ICGC. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were used to study differentially expressed genes between high- and low-risk groups. We also examined immune cell infiltration, drug response, and cell communication between tumor cells and immune cells in high-risk groups. Results: We identified 140 m5C/m6A/m7G-related NARCD genes, using five of them to build the prognostic model. Functional enrichment analysis revealed enrichment in tumor and immune-related pathways for risk genes. The high-risk group displayed increased immune cell infiltration and better responses to immune checkpoint inhibitors (ICIs). High-risk patients were more responsive to cisplatin, doxorubicin, and mitomycin C, while low-risk patients were more sensitive to erlotinib. Cell communication analysis indicated that high-risk tumor cells used insulin-like growth factor (IGF) and macrophage migration inhibitory factor (MIF) signaling pathways to send signals to immune cells and received signals through the bone morphogenetic protein (BMP) and lymphotoxin-related inducible ligand (LIGHT) pathways. Conclusions: We have developed a prognostic model with m5C/m6A/m7G-related NARCD genes to predict the prognosis of HCC patients. This model can offer insights into the effectiveness of immunotherapy and chemotherapy for HCC patients.

A novel m6A/m5C/m1A score signature to evaluate prognosis and its immunotherapy value in colon cancer patients.

BACKGROUND: Colon cancer features strong heterogeneity and invasiveness, with high incidence and mortality rates. Recently, RNA modifications involving m6A, m5C, and m1A play a vital part in tumorigenesis and immune cell infiltration. However, integrated analysis among various RNA modifications in colon cancer has not been performed. METHODS: RNA-seq profiling, clinical data and mutation data were obtained from The Cancer Genome Atlas and Gene Expression Omnibus. We first explored the mutation status and expression levels of m6A/m5C/m1A regulators in colon cancer. Then, different m6A/m5C/m1A clusters and gene clusters were identified by consensus clustering analysis. We further constructed and validated a scoring system, which could be utilized to accurately assess the risk of individuals and guide personalized immunotherapy. Finally, m6A/m5C/m1A regulators were validated by immunohistochemical staining and RT-qPCR. RESULTS: In our study, three m6A/m5C/m1A clusters and gene clusters were identified. Most importantly, we constructed a m6A/m5C/m1A scoring system to assess the clinical risk of the individuals. Besides, the prognostic value of the score was validated with three independent cohorts. Moreover, the level of the immunophenoscore of the low m6A/m5C/m1A score group increased significantly with CTLA-4/PD-1 immunotherapy. Finally, we validated that the mRNA and protein expression of VIRMA and DNMT3B increased in colon cancer tissues. CONCLUSIONS: We constructed and validated a stable and powerful m6A/m5C/m1A score signature to assess the survival outcomes and immune infiltration characteristics of colon cancer patients, which further guides optimization of personalized treatment, making it valuable for clinical translation and implementation.

A randomized trial comparing beam F3 and 5.5 cm targeting in rTMS treatment of depression demonstrates similar effectiveness.

BACKGROUND: The Beam F3 and 5.5 cm methods are the two most common targeting strategies for localizing the left dorsolateral prefrontal cortex (DLPFC) treatment site in repetitive transcranial magnetic stimulation (rTMS) protocols. This prospective, randomized, double-blind comparative effectiveness trial assesses the clinical outcomes for these two methods in a naturalistic sample of patients with major depressive disorder (MDD) undergoing clinical rTMS treatment. METHODS: 105 adult patients with MDD (mean age = 43.2; range = 18-73; 66% female) were randomized to receive rTMS to the Beam F3 (n = 58) or 5.5 cm (n = 47) target. Between group differences from pre-to post-treatment were evaluated with the Patient Health Questionnaire-9 (PHQ-9) [primary outcome measure], Generalized Anxiety Disorder-7 (GAD-7), and clinician-administered Montgomery-Åsberg Depression Scale (MADRS). Primary treatment endpoint was completion of daily treatment series. RESULTS: Per-protocol analyses showed no statistically significant differences on any measure between the 5.5 cm and F3 groups (all p ≥ 0.50), including percent improvement (PHQ-9: 39% vs. 39%; GAD-7: 34% vs. 27%; MADRS: 40% vs. 38%), response rate (PHQ-9: 37% vs. 43%; GAD-7: 27% vs. 30%; MADRS: 43% vs. 43%), and remission rate (PHQ-9: 22% vs. 21%; MADRS: 20% vs. 19%). Post hoc analysis of anxiety symptom change while controlling for depression severity suggested more favorable anxiolytic effects with 5.5 cm targeting (p = 0.03). CONCLUSIONS: Similar antidepressant effects were observed with DLFPC rTMS using either the Beam F3 or 5.5 cm targeting method, supporting clinical equipoise in MDD patients with head circumference ≤ 60 cm. Comparison to MRI-based targeting and differential effects on anxiety symptoms require further investigation. TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT03378570.

The abdominal aortic aneurysm-related disease model based on machine learning predicts immunity and m1A/m5C/m6A/m7G epigenetic regulation.

Introduction: Abdominal aortic aneurysms (AAA) are among the most lethal non-cancerous diseases. A comprehensive analysis of the AAA-related disease model has yet to be conducted. Methods: Weighted correlation network analysis (WGCNA) was performed for the AAA-related genes. Machine learning random forest and LASSO regression analysis were performed to develop the AAA-related score. Immune characteristics and epigenetic characteristics of the AAA-related score were explored. Results: Our study developed a reliable AAA-related disease model for predicting immunity and m1A/m5C/m6A/m7G epigenetic regulation. Discussion: The pathogenic roles of four model genes, UBE2K, TMEM230, VAMP7, and PUM2, in AAA, need further validation by in vitro and in vivo experiments.

Establishment of a new molecular subtyping and prognostic signature with m6A/m5C/m1A/m7G regulatory genes for hepatocellular carcinoma.

Background: RNA modification, including m6A, m5C, m1A, and m7G, participated in tumor progress. Therefore, the purpose of the present study was to explore the role of m6A/m5C/m1A/m7G regulatory genes in the prognosis and tumor microenvironment (TME) for hepatocellular carcinoma (HCC). Methods: 71 m6A/m5C/m1A/m7G regulatory genes expression for HCC was detected, differentially expressed genes were screened, and molecular forms were classified by unsupervised consensus clustering. Cox regression and the Least Absolute Shrinkage and Selection Operator (LASSO) analysis were applied to establish a prognostic signature. Time-dependent receiver operating characteristic (ROC) curves were evaluated for clinical effectiveness and accuracy of the prognostic hazard model. In cluster subtypes and risk models, the differences in prognosis, immune cell infiltration, immune checkpoint, immunotherapy, and drug sensitivity between different subtypes were evaluated. Results: HCC patients were classified into two clusters (cluster 1 and cluster 2) according to the expression of 71 m6A/m5C/m1A/m7G regulatory genes. Cluster 1 had a poor prognosis and different immune cell infiltration. Cluster 1 had higher immune checkpoint expression and TIDE score than cluster 2. Subsequently, we construct a five-gene prognostic model of m6A/m5C/m1A/m7G regulatory genes (YTHDF2, YTHDF1,YBX1, TRMT61A, TRMT10C). The Kaplan-Meier and ROC curve analysis showed that the prognostic signature exhibited good predictability. The risk score was considered an independent poor prognostic index. The high-risk group had higher immune checkpoint expression and higher TIDE scores. 5-Fluorouracil, docetaxel, doxorubicin, etoposide, gemcitabine, paclitaxel, sorafenib, and vinblastine were more suitable for high-risk patients. ECM receptor interaction, cell cycle, and Leishmania infection were enriched in the high-risk group. Conclusion: The clustering subgroups and prognostic model of m6A/m5C/m1A/m7G regulatory genes were linked with bad prognosis and TME for HCC, and had the potential to be a novel tool to evaluate the outcomes of HCC patients.

Novel methylation-related long non-coding RNA clinical outcome prediction method: the clinical phenotype and immune infiltration research in low-grade gliomas.

Background: Recent studies have suggested that long non-coding RNAs (lncRNAs) may play crucial role in low-grade glioma; however, the underlying mechanisms linking them to epigenetic methylation remain unclear. Methods: We downloaded expression level data for regulators associated with N1 methyladenosine (m1A), 5-methyladenine (m5C), and N6 methyladenosine (m6A) (M1A/M5C/M6A) methylation from the Cancer Genome Atlas-low-grade glioma (TCGA-LGG) database. We identified the expression patterns of lncRNAs, and selected methylation-related lncRNAs using Pearson correlation coefficient>0.4. Non-negative matrix dimensionality reduction was then used to determine the expression patterns of the methylation-associated lncRNAs. We constructed a weighted gene co-expression network analysis (WGCNA) network to explore the co-expression networks between the two expression patterns. Functional enrichment of the co-expression network was performed to identify biological differences between the expression patterns of different lncRNAs. We also constructed prognostic networks based on the methylation presence in lncRNAs in low-grade gliomas. Results: We identified 44 regulators by literature review. Using a correlation coefficient greater than 0.4, we identified 2330 lncRNAs, among which 108 lncRNAs with independent prognostic values were further screened using univariate Cox regression at P< 0.05. Functional enrichment of the co-expression networks revealed that regulation of trans-synaptic signaling, modulation of chemical synaptic transmission, calmodulin binding, and SNARE binding were mostly enriched in the blue module. The calcium and CA2 signaling pathways were associated with different methylation-related long non-coding chains. Using the Least Absolute Shrinkage Selector Operator (LASSO) regression analysis, we analyzed a prognostic model containing four lncRNAs. The model's risk score was 1.12 *AC012063 + 0.74 * AC022382 + 0.32 * AL049712 + 0.16 * GSEC. Gene set variation analysis (GSVA) revealed significant differences in mismatch repair, cell cycle, WNT signaling pathway, NOTCH signaling pathway, Complement and Cascades, and cancer pathways at different GSEC expression levels. Thus, these results suggest that GSEC may be involved in the proliferation and invasion of low-grade glioma, making it a prognostic risk factor for low-grade glioma. Conclusion: Our analysis identified methylation-related lncRNAs in low-grade gliomas, providing a foundation for further research on lncRNA methylation. We found that GSEC could serve as a candidate methylation marker and a prognostic risk factor for overall survival in low-grade glioma patients. These findings shed light on the underlying mechanisms of low-grade glioma development and may facilitate the development of new treatment strategies.

Patterns of Failure and Optimal Treatment Paradigm for Large, Inoperable, Node-Negative Non-small Cell Lung Cancer.

OBJECTIVES: The ideal non-operative treatment for patients with large, node-negative non-small cell lung cancer (NSCLC) is poorly defined. To inform optimal treatment paradigms for this cohort, we examined patterns of failure and the impact of radiation therapy (RT) and chemotherapy receipt. MATERIALS AND METHODS: Node-negative NSCLC patients with 5+ cm primary tumors receiving definitive RT at our institution were identified. Sites of initial progression were analyzed. Local progression, regional/distant progression, progression-free survival, and overall survival were analyzed via cumulative incidence function and Kaplan-Meier. Associations between local vs. regional/distant progression with treatment and clinicopathologic variables were assessed via univariable and multivariable competing risks regression. RESULTS AND CONCLUSION: We identified 88 patients for analysis. Among patients with recurrent disease (N = 36), initial patterns of failure analysis showed that isolated distant (27.8%) and isolated regional progression (22.2%) were most common. Distant or regional failure as a component of initial failure was seen in 88.9% of patients who progressed, while isolated local failure was uncommon (11.1%). Univariable and multivariable competing risks regression showed that receipt of SBRT was associated with reduced risk of local progression (HR 0.23, P = .012), and receipt of chemotherapy was associated with reduced risk of regional/distant progression (HR 0.12, P = .040). In conclusion, patients with large, node-negative NSCLC treated with definitive RT are at high risk of regional and distant progression. SBRT correlates with a reduced risk of local failure while chemotherapy is associated with reduced regional/distant progression in this patient population. Ideal treatment may include SBRT when feasible with appropriate systemic therapy.

Postmastectomy Radiation Therapy for Node-Negative Breast Cancer of 5 cm or Larger Tumors: A Multicenter Retrospective Analysis (KROG 20-03).

PURPOSE: To evaluate the role of postmastectomy radiation therapy (PMRT) in patients with node-negative breast cancer of 5cm or larger tumors undergoing mastectomy. MATERIALS AND METHODS: Medical records of 274 patients from 18 institutions treated with mastectomy between January 2000 and December 2016 were retrospectively reviewed. Among these, 202 patients underwent PMRT, while 72 did not. Two hundred and forty-one patients (88.0%) received systemic chemotherapy, and 172 (62.8%) received hormonal therapy. Patients receiving PMRT were younger, more likely to have progesterone receptor-positive tumors, and received adjuvant chemotherapy more frequently compared with those without PMRT (p <0.001, 0.018, and <0.001, respectively). Other characteristics were not significantly different between the two groups. RESULTS: With a median follow-up of 95 months (range, 1-249), there were 9 locoregional recurrences, and 20 distant metastases. The 8-year locoregional recurrence-free survival rates were 98.0% with PMRT and 91.3% without PMRT (p=0.133), and the 8-year disease-free survival (DFS) rates were 91.8% with PMRT and 73.9% without PMRT (p=0.008). On multivariate analysis incorporating age, histologic grade, lymphovascular invasion, hormonal therapy, chemotherapy, and PMRT, the absence of lymphovascular invasion and the receipt of PMRT were associated with improved DFS (p=0.025 and 0.009, respectively). CONCLUSION: Locoregional recurrence rate was very low in node-negative breast cancer of 5cm or larger tumors treated with mastectomy regardless of the receipt of PMRT. However, PMRT was significantly associated with improved DFS. Further investigation is needed to confirm these findings.

Management of Soft-tissue Tumors With a Size of 2-5 cm, Including Malignancy.

BACKGROUND/AIM: The management of soft-tissue tumors of 2-5 cm is not specified. We investigated the management of these cases. PATIENTS AND METHODS: Among 105 cases with soft-tissue tumors from 2014 to 2021, 38 with tumors of 2-5 cm were retrospectively reviewed. The clinical characteristics, diagnosis, and management were investigated. RESULTS: The study population included 14 males and 24 females (mean age=57 years). Common histological diagnoses included lipoma, epidermal cyst, and hemangioma as benign tumors, and leiomyosarcoma (n=2) and metastatic soft-tissue carcinoma (n=1) as malignant tumors. Magnetic resonance imaging, needle and excisional biopsy were performed in 35, 19 and 19 cases, respectively. The mean follow-up period was 7 months. No recurrence was observed. CONCLUSION: Malignancy exists, even in soft-tissue tumors of 2-5 cm (3/38; 8%). To avoid unplanned excision, needle biopsy should be considered for cases with magnetic resonance imaging abnormalities.

Stereotactic Body Radiotherapy for Large (> 5 cm) Non-Small-Cell Lung Cancer.

BACKGROUND: Stereotactic body radiotherapy (SBRT) is a well-established treatment option for early stage non-small-cell lung cancer (NSCLC) tumors < 5 cm. There is limited information on tumors > 5 cm. PATIENTS AND METHODS: We performed retrospective data collection of patients enrolled onto a prospective SBRT registry study. Eligible patients for this study had node-negative NSCLC measuring > 5 cm in any dimension. Data from 41 patients were analyzed. Median patient age was 75 years, and median tumor size was 5.6 cm (range, 5.0-12.2 cm). Sixteen patients had squamous disease, 20 patients adenocarcinoma, and 1 mixed tumor; 4 patients had no biopsy. Median radiation dose per fraction was 50 Gy in 5 fractions. Radiation was prescribed to isodose line, median 66% (range, 50%-84%). RESULTS: Before SBRT, 6 patients had previous chemotherapy and 7 patients had previous radiation. Median follow-up for all patients was 15.2 months (range, 0.56-48.1 months). At last follow-up, 16 patients were still alive, with a median follow-up of 16.1 months for surviving patients. The median survival was 17.5 months with 1- and 2-year survivals of 65% and 34%. Two patients (4.8%) had local failure, and 13 patients (31%) had distant failure. Four patients (9.8%) had acute toxicity, and 7 patients (17.1%) had late toxicity, including 2 (4.8%) grade 3 late toxicities. CONCLUSION: SBRT for tumors > 5 cm is effective, with good local control rates and acceptable toxicity. The main pattern of failure is distant, suggesting a possible role for systemic chemotherapy in these patients.