Tumor Mutation Research Articles

The key role of the NUDT3 gene in lung adenocarcinoma progression and its association with the manganese ion metabolism family.

Lung adenocarcinoma is one of the most common malignant tumors worldwide. Its complex molecular mechanisms and high tumor heterogeneity pose significant challenges for clinical treatment. The manganese ion metabolism family plays a crucial role in various biological processes, and the abnormal expression of the NUDT3 gene in multiple cancers has drawn considerable attention. This study aims to systematically analyze the expression characteristics of the NUDT3 gene in lung adenocarcinoma and its association with tumor progression, integrating single-cell transcriptomic analysis and experimental validation using cell lines. This study employed a comprehensive set of analytical approaches. Single-cell transcriptomic analysis of two normal and four lung adenocarcinoma samples from the GSE149655 dataset was performed using the Seurat package to identify and annotate distinct cell populations, focusing on epithelial and macrophage subtypes. Non-negative matrix factorization (NMF) and gene set variation analysis (GSVA) were applied to assess the functional enrichment and expression profiles of the manganese ion metabolism family across 14 cancers. Quantitative PCR (qPCR) was conducted to evaluate the relative mRNA expression of NUDT3 in A549 lung adenocarcinoma cell lines compared to BEAS-2B normal bronchial epithelial cell lines. GAPDH was used as the reference gene for normalization, and the relative expression levels of NUDT3 in these cell lines were analyzed to confirm bioinformatics findings. NUDT3 was found to be significantly upregulated in lung adenocarcinoma and highly correlated with tumor mutation burden (TMB) and mutation enrichment (MEs). Single-cell transcriptomic analyses demonstrated elevated NUDT3 expression in lung adenocarcinoma epithelial cells, with expression levels increasing in cells associated with advanced tumor stages. Furthermore, qPCR analysis confirmed the upregulation of NUDT3 in A549 cells compared to BEAS-2B cells, consistent with transcriptomic data. These results also highlighted significant expression differences of the manganese ion metabolism family across various cancers, including BLCA, BRCA, and COAD, with notable NUDT3 mutations enriched in these cancers. This study underscores the critical role of NUDT3 in lung adenocarcinoma progression and its potential as a therapeutic target. These findings contribute to the understanding of the manganese ion metabolism family in cancer biology and provide a foundation for precision therapies targeting NUDT3 in lung adenocarcinoma.

Subtype-Specific Patterns of Tumor Purity and Mutation Load Suggest Treatment Implications

Subtype-Specific Patterns of Tumor Purity and Mutation Load Suggest Treatment Implications

Improving molecular subtypes and prognosis of pancreatic cancer through multi group analysis and machine learning

BackgroundPancreatic cancer (PAC) has a complex tumor immune microenvironment, and currently, there is a lack of accurate personalized treatment. Establishing a novel consensus machine learning driven signature (CMLS) that offers a unique predictive model and possible treatment targets for this condition was the goal of this study.MethodsThis study integrated multiple omics data of PAC patients, applied ten clustering techniques and ten machine learning approaches to construct molecular subtypes for PAC, and created a new CMLS.ResultsUsing multi-omics clustering, we discovered two cancer subtypes (CSs) associated with prognosis, among which CS1 exhibited poor prognostic outcomes. Subsequently, 13 central genes were identified through screening, constituting CMLS with a significant prognostic ability. The low CMLS group had a better prognosis and was more likely to possess a “hot” tumor phenotype. The prognosis for the high CMLS group was dismal. Still, the tumor mutation burden (TMB) and tumor neoantigen burden (TNB) levels in this group of patients were higher than in the low CMLS group, which were more favorable for immune therapy response.ConclusionThis study emphasizes that CMLS provides a beneficial instrument for early prediction of patient prognosis and screening of probable patients appropriate for immunotherapy and has broad implications for clinical practice.

Multi-Omics Analysis Reveals Immune Infiltration and Clinical Significance of Phosphorylation Modification Enzymes in Lung Adenocarcinoma

Protein phosphorylation is a dynamic and reversible modification involved in almost all cellular processes. Numerous investigations have shown that protein phosphorylation modification enzymes (PPMEs) that regulate protein phosphorylation play an important role in the occurrence and treatment of tumors. However, there is still a lack of effective insights into the value of PPMEs in the classification and treatment of patients with lung adenocarcinoma (LUAD). Here, four topological algorithms identified 15 hub PPMEs from a protein–protein interaction (PPI) network. This PPI network was constructed using 124 PPMEs significantly correlated with 35 cancer hallmark-related pathways. Our study illustrates that these hub PPMEs can affect the survival of patients with LUAD in the form of somatic mutation or expression perturbation. Consistency clustering based on hub PPMEs recognized two phosphorylation modification subtypes (namely cluster1 and cluster2) from LUAD. Compared with patients in cluster1, the survival prognosis of patients in cluster2 is worse. This disparity is probably attributed to the higher tumor mutation burden, the higher male proportion, and the more significant expression disturbance in patients in cluster2. Moreover, phosphorylation modification subtypes also have different characteristics in terms of immune activity, immune infiltration level, immunotherapy response, and drug sensitivity. We constructed a PSig scoring system by using a principal component analysis algorithm to estimate the level of phosphorylation modification in individual LUAD patients. Patients in the high and low PSig score groups demonstrated different characteristics in terms of survival rate, tumor mutation burden, somatic gene mutation rate, immune cell abundance, and sensitivity to immunotherapy and drug treatment. This work reveals that phosphorylation plays a non-negligible role in the tumor microenvironment and immunotherapy of LUAD. Evaluating the phosphorylation status of individual LUAD patients by the PSig score can contribute to enhancing our cognition of the tumor microenvironment and guiding the formulation of more effective personalized treatment strategies.

Pan-cancer and experimental analyses reveal the immunotherapeutic significance of CST2 and its association with stomach adenocarcinoma proliferation and metastasis

PurposeCystatin 2 (CST2) is a cysteine protease inhibitor, and recent research suggests its potential involvement in cancer development. However, its role in the occurrence, progression, and prognosis of pan-cancer has not been systematically investigated.Materials and methodsThis study comprehensively analyzes the differential expression of CST2 in pan-cancer. The expression distribution patterns of CST2 were examined using single-cell datasets. Furthermore, we conducted a comprehensive evaluation of the correlation between CST2 expression and various factors. These factors include prognosis, immune cell infiltration, immune-related genes, mutations, methylation, tumor mutation burden (TMB), and microsatellite instability (MSI). In addition, we analyzed the sensitivity of drugs dependent on CST2 expression. We utilized gene set enrichment analysis (GSEA) analysis to explore the biological functions of CST2 across different cancer types. Finally, in gastric cancer cell lines, we will investigate the impact of CST2 knockout on expression levels, clonal proliferation, cell apoptosis, and cell migration.ResultsCST2 exhibits abnormal overexpression in multiple tumors. Single-cell analysis reveals high expression of CST2 in fibroblasts. CST2 is closely associated with prognosis, immune cell infiltration, immune-related genes, mutations, methylation, TMB, and MSI. Enrichment analysis demonstrated a significant correlation between CST2 and immune-related pathways. In stomach adenocarcinoma (STAD), CST2-related risk models are associated with prognosis and demonstrate strong predictive capabilities, while also being closely linked to the immune microenvironment. Drug sensitivity analysis indicates the correlation between CST2 and 21 chemotherapy drugs. Finally, experimental validation revealed significantly elevated expression of CST2 in STAD, indicating its role as a driver gene in regulating malignant cell proliferation and migration.ConclusionCST2 serves as a potential tumor immune biomarker, playing a critical facilitating role in the proliferation and migration processes of STAD.

Identification of a metabolic-immune signature associated with prognosis in colon cancer and exploration of potential predictive efficacy of immunotherapy response

The role of metabolic reprogramming of the tumor immune microenvironment in cancer development and immune escape has increasingly attracted attention. However, the predictive value of differences in metabolism-immune microenvironment on the prognosis of colon cancer (CC) and the response to immunotherapy have not been elucidated. The aim of this study was to investigate changes in metabolism and immune profile of CC and to identify a reliable signature for predicting prognosis and therapeutic response. The metabolism and immune-related differential genes in CC were screened out by differential gene expression analysis. A metabolism and immune related prognostic signature was established by the least absolute shrinkage and selection operator (LASSO) Cox algorithm. The training cohort with 417 patients from The Cancer Genome Atlas (TCGA) database and the validation cohort of 232 patients from GSE17538 were used to confirm the robustness of the prognostic signature. Immunohistochemical staining scores were used to assess gene expression levels in our clinical samples. Gene ontology (GO) analysis, gene set enrichment analysis (GSEA), single nucleotide variation (SNV) analysis, immune infiltration and immune factors analysis were used to explore the characteristics of patients with different subtypes. Multiple cancer immunotherapy datasets were used to assess the response of patients with different subtypes to immune checkpoint inhibitors. We established the Metabolism and Immune-Related Prognostic Score (MIRPS) based on six genes (CD36, PCOLCE2, SCG2, CALB2, STC2, CLDN23) to predict the prognosis of CC patients. We found a correlation between MIRPS and the malignant phenotype, microsatellite subtype, mutation load, and immune escape in CC. Tumors with high MIRPS presented a higher tumor mutation load and a more prominent immunosuppressive microenvironment. This subset of patients may potentially respond well to immune checkpoint inhibitor therapy. MIRPS may be used as a novel prognostic tool for CC and have potential value for immunotherapy response prediction.

Identification of the clinical and genetic characteristics of gliomas with gene fusions by integrated genomic and transcriptomic analysis

The identification of oncogenic gene fusions in diffuse gliomas may serve as potential therapeutic targets and prognostic indicators, representing a novel strategy for treating gliomas consistent with the principles of personalized medicine. This study identified detectable oncogene fusions in glioma patients through an integrated analysis of genomic and transcriptomic data, which encompassed whole exon sequencing and next-generation RNA sequencing. In addition, this study also conducted a comparison of the genetic characteristics, tumor microenvironment, mutation burden and survival between glioma patients with or without gene fusions. A total of 68 glioma patients were enrolled in this study, including glioblastoma (GBM), low grade glioma (LGG) and diffuse midline glioma (DMG). 14 cases of GBM patients (51.9%, 14/27) were found to harbor the following 70 oncogenic gene fusions: ROS1 (n = 8), NTRK (n = 5), KIF5 (n = 5), RET (n = 3) and other infrequent gene fusions (n = 49). A total of 11 gene fusions were identified in 8 LGG patients (32.0%, 8/25) and seven gene fusions were identified in one DMG patient (16.7%, 1/6). In GBM patient group, five genes including HOXA3, ACTB, CDK5, GNA12 and CARD11 exhibited a statistically significant higher copy number amplification frequency in the GBM group without gene fusions compared to that in the GBM group with gene fusions. In LGG patient group, CDK5 gene was also found to exhibit a statistically significant higher amplification frequency in the LGG group without gene fusions. In addition, KMT2D exhibited a statistically significant higher mutation frequency in the LGG group with gene fusions compared to that in the LGG group without gene fusions. Comparison of the other genetic characteristics including immune cell infiltration score, tumor mutation burden (TMB), and microsatellite instability (MSI). The results showed no statistically significant differences were observed between fusion and non-fusion group of GBM and LGG. The survival analysis revealed that GBM patients without gene fusions exhibited a longer median survival (737 days) compared to GBM patients with gene fusions (642 days), but without a statistical significancy. Our study has identified a set of gene fusions present in gliomas, including a number of novel gene fusions that have not been previously reported. We have also elucidated the underlying genetic characteristics of glioma with gene fusions. Collectively, our findings have the potential to inform future clinical treatment strategies for patients with glioma.

Clinical value of preoperative circulating tumor DNA before surgery in patients with esophageal squamous cell carcinoma.

A precise preoperative tumor monitoring method that reflects tumor burden during neoadjuvant treatment is required to guide individualized perioperative treatment strategies for esophageal squamous cell carcinoma (ESCC). This study examined the clinical significance of preoperative circulating tumor DNA (ctDNA) in the plasma of patients undergoing neoadjuvant chemotherapy (NAC) followed by esophagectomy. Plasma samples were collected longitudinally for ctDNA analysis as well as genomic DNA from primary lesions from patients with histologically confirmed ESCC who received neoadjuvant chemotherapy (NAC) followed by subtotal esophagectomy. Next-generation sequencing was used to identify mutations in both the plasma and primary tumors. We evaluated the relationship between ctDNA alterations and recurrence in patients with locally advanced ESCC. Pretreatment samples from 25 patients (100%) showed the same mutations in both ctDNA and primary tumors; therefore, they were classified as ctDNA-positive before treatment. In the cohort of 25 patients analyzed, those who tested positive for ctDNA after NAC had a significantly higher risk of recurrence; the 36-month recurrence-free survival rates were 92% for ctDNA-negative patients and 8% for ctDNA-positive patients (p<0.001). Preoperative ctDNA status may be a promising prognostic biomarker that can be assessed before surgery in patients with ESCC who received NAC. Expanded cohort validation will allow for more personalized multidisciplinary treatment approaches for ESCC tailored to ctDNA analysis.

N6-Methylandenosine-related lncRNAs as potential biomarkers for predicting prognosis and the immunotherapy response in pancreatic cancer

Emerging evidence has shown that the N6-methyladenosine (m6A) modification of RNA plays key roles in tumorigenesis and the progression of various cancers. However, the potential roles of the m6A modification of long noncoding RNAs (lncRNAs) in pancreatic cancer (PaCa) are still unknown. To analyze the prognostic value of m6A-related lncRNAs in PaCa, an m6A-related lncRNA signature was constructed as a risk model via Pearson’s correlation and univariate Cox regression analyses in The Cancer Genome Atlas (TCGA) database. The tumor microenvironment (TME), tumor mutation burden, and drug sensitivity of PaCa were investigated by m6A-related lncRNA risk score analyses. We established an m6A-related risk prognostic model consisting of five lncRNAs, namely, LINC01091, AC096733.2, AC092171.5, AC015660.1, and AC005332.6, which not only revealed significant differences in immune cell infiltration associated with the TME between the high-risk and low-risk groups but also predicted the potential benefit of immunotherapy for patients with PaCa. Drugs such as WZ8040, selumetinib, and bortezomib were also identified as more effective for high-risk patients. Our results indicate that the m6A-related lncRNA risk model could be an independent prognostic indicator, which may provide valuable insights for identifying therapeutic approaches for PaCa.

A novel ubiquitination-related gene signature for overall survival prediction in patients with liver hepatocellular carcinoma

Liver hepatocellular carcinoma (LIHC) is a highly heterogeneous disease, necessitating the discovery of novel biomarkers to enhance individualized treatment approaches. Recent research has shown the significant involvement of ubiquitin-related genes (UbRGs) in the progression of LIHC. However, the prognostic value of UbRGs in LIHC has not been investigated. In this study, the mRNA expression profiles and clinical data were obtained from public databases of LIHC patients. The least absolute shrinkage and selection operator Cox regression model was employed to construct a multigene signature in the TCGA cohort. Our results showed that a twelve UbRGs signature was developed to categorize patients into two risk groups, with significant differences in expression between LIHC and normal tissues. Patients in the high-risk group exhibited significantly reduced overall survival (OS) and progression-free survival compared to those in the low-risk group. The risk score was identified as an independent predictor for OS in multivariate Cox regression analyses. Receiver operating characteristic curve analysis confirmed the predictive capacity of the signature. Functional analysis revealed enrichment of immune-related pathways and differences in immune status between the two risk groups. The risk score was correlated with 35 transcription factors and 26 eRNA enhancers, and positively associated with tumor mutation burden. Patients in the high-risk group demonstrated decreased sensitivity to targeted and chemotherapeutic drugs than those in the low-risk group. In conclusion, our study identified a twelve UbRGs signature that may serve as a prognostic predictor for LIHC patients and and provide valuable insights for cancer treatment.

Not all uterine carcinosarcomas are created equal: Survival outcomes according to molecular characterization of uterine carcinosarcoma.

To assess if ProMisE classifier molecular subtypes are associated with differing survival outcomes in uterine carcinosarcoma (UCS) and compare these outcomes to endometrioid endometrial cancer (EEC) tumors. There were 2235 UCS and 6469 EEC tumors using next-generation sequencing of DNA, whole exome sequencing, and RNA. Microsatellite instability (MSI) was tested by IHC and NGS. Real-world overall survival (OS) was obtained from Caris Life Sciences database and paired with insurance claims data. Hazard ratios (HR) were calculated using the Cox proportional hazards model, and p-values were calculated using the log-rank test. Of the 2235 UCS samples, 2.7% (n=48) were POLE mutant (MT), 7.4% (n=132) MSI-H, 78.2% (n=1402), TP53 MT, and 11.7% (n=210), TP53 wild type (WT). In UCS POLE MT tumors, median OS (74.8 mos; 95% CI: 30.5-not reached [NR]; p<0.01) was significantly longer than all other subtypes. There was no difference in median post-chemo OS between POLE MT UCS and POLE MT EEC (p=0.75) or MSI-H UCS and MSI-H EEC (p=0.14). TP53 MT UCS and TP53 WT UCS tumors had worse median OS compared their respective ECC subtypes (27.9 vs 35.3 mos; HR: 1.3 95% CI (1.1-1.5); p=0.01, 29.4 vs 70.7 mos; HR: 2.0 95% CI (1.5-2.7); p<0.01). HER2 negative UCS had worse post-chemo OS compared to HER2 negative EEC (32.9 vs 77 mos; HR 1.60 95% CI (1.092-2.348); p=0.02). TP53 MT is the most common molecular UCS sub-type. Overall, UCS has tiered survival according to molecular classification, which mirrors EEC survival patterns. Despite UCS being considered a more aggressive histology, POLE MT and MSI-H outcomes when comparing UCS and EEC were not statistically different.

Dual role of Cathepsin S in cutaneous melanoma: insights from mendelian randomization and bioinformatics analysis

BackgroundCutaneous melanoma (CM) is strongly associated with ultraviolet (UV) radiation, which contributes to the transformation of melanocytes into melanoma by inducing specific DNA damage. Here, we investigated the causal relationship between CM and genes related to sun-damaged skin, exploring specific target genes through various bioinformatics analyses.MethodsThe Gene Expression Omnibus (GEO) database was used to obtain differential genes for CM and normal skin, and the Genome-Wide Association Studies (GWAS) analysis offered summary-level melanoma data for CM. Mendelian randomization (MR) analyses were used to examine the correlated linkage between CM and sun-exposed skin genes. The MR studies were conducted mainly using Inverse Variance Weighting (IVW), MR-Egger, Weighted Median, simple and weighted patterns to predict the correlation between sun-exposed skin and CM. Finally, the role of target genes in CM was revealed by pan-cancer analysis, expression and immune-infiltration evaluations, immuno-checking targeting analysis, immunotherapy response analysis, survival analysis, and protein-protein interactions (PPI) network and enrichment analyses.ResultUsing matrix data from the GSE15605, GSE46517, and GSE111452 datasets, bioinformatics analysis revealed 232 differentially expressed genes (DEGs) between CM and typical tissues. MR analysis indicated that only CTSS has a deleterious effect linking skin exposure to sunlight and CM. Analysis of CTSS expression in tumors and tissues, along with the construction of a prognostic model, revealed that CTSS expression was higher in both primary CM and metastatic CM compared to normal skin tissue. However, patients with higher CTSS expression had a higher prognosis. In addition, high CTSS expression was significantly and positively correlated with tumor mutation rate, tumor microenvironment, immune cell infiltration, immune checkpoints and immunotherapy efficacy.ConclusionUsing MR analysis, we found a positive causal relationship between the CTSS gene in sun-exposed skin and CM. Additionally, increased CTSS may provide a basis for biomarker prediction of CM prognosis, immune status and immunotherapy.

Systems-level immunomonitoring in children with solid tumors to enable precision medicine.

Cancer is the leading cause of death from disease in children. Survival depends not only on surgery, cytostatic drugs, and radiation but also on systemic immune responses. Factors influencing these immune responses in children of different ages and tumor types are unknown. Novel immunotherapies can enhance anti-tumor immune responses, but few children have benefited, and markers of effective responses are lacking. Here, we present a systems-level analysis of immune responses in 191 children within a population-based cohort with diverse tumors and reveal that age and tumor type shape immune responses differently. Systemic inflammation and cytotoxic Tcell responses correlate with tumor mutation rates and immune cell infiltration. Clonally expanded Tcell responses are rarely detected in blood or tumors at diagnosis but are sometimes elicited during treatment. Expanded Tcells are similarly regulated in children and adults with more immunogenic cancers. This research aims to facilitate the development of precision immunotherapies for children with cancer.

Lenvatinib in advanced radioiodine-refractory differentiated thyroid cancer: what’s new?

The article provides the latest data of our foreign colleagues on the potential use and dosing regimen of lenvatinib in real clinical practice. Since adverse events during lenvatinib treatment often lead to dose reduction or its discontinuation and, as a consequence, to a decrease in progression-free survival and overall survival benefit, optimization of lenvatinib dosing regimen is of great interest to experts from different countries. Today, so-called drug holidays are being actively studied as a possible option to reduce lenvatinib toxicity, without loss of efficacy in patients with advanced radioiodine-refractory differentiated thyroid cancer. In addition, given the small number of therapeutic options for this patient group, their low efficacy and poor availability of tumor mutation profiling and effect on target genes, a question arises: “Is it possible to benefit in progression-free survival and overall survival with lenvatinib rechallenge after disease progression in the 2nd or 3rd treatment lines?”

Characterization of the genomic landscape in liver oligometastatic NSCLC

ObjectivesEmerging data have shown that local treatment could provide clinical benefit for non-small cell lung cancer (NSCLC) patients with oligometastasis. Liver metastases have the worst prognosis in advanced NSCLC, but the genomic characteristics of liver oligometastasis remain unclear. The aim of our study was to elucidate the molecular features of liver oligometastatic NSCLC.MethodsPaired liver metastatic tissue samples and peripheral blood from 32 liver oligometastatic NSCLC patients were concurrently collected for comprehensive genomic analysis using next-generation sequencing.ResultsA total of 206 mutated genes in 32 patients were detected, with a median of 4 mutations per sample. The most frequent alterations (> 10%) in liver oligometastasis were TP53 (72%), EGFR (50%), RB1 (19%) and SMARCA4 (12%). The co-occurrence rate of TP53 and RB1 in our cohort was significantly higher than that in the TCGA-LUAD cohort. Age, APOBEC, homologous recombination deficiency (HRD) and deficient mismatch repair (dMMR) established the mutational signature of liver oligometastatic NSCLC. The median tumor mutation burden (TMB) was 4.8 mutations/Mb. A total of 78.12% patients harbored at least one potentially actionable molecular alteration that may guide further targeted therapy according to the OncoKB evidence.ConclusionsOur study comprehensively delineated the genomic characteristics of liver oligometastatic NSCLC - such findings were helpful to better understand the distinct clinic-biological features of oligometastasis and optimize personalized treatment of this population.

Mutation Analysis of TMB-High Colorectal Cancer: Insights Into Molecular Pathways and Clinical Implications.

Colorectal cancer (CRC) is well characterized in terms of genetic mutations and the mechanisms by which they contribute to carcinogenesis. Mutations in APC, TP53, and KRAS are common in CRC, indicating key roles for these genes in tumor development and progression. However, for certain tumors with low frequencies of these mutations that are defined by tumor location and molecular phenotypes, a carcinogenic mechanism dependent on BRAF mutations has been proposed. We here analyzed targeted sequence data linked to clinical information for CRC, focusing on tumors with a high tumor mutation burden (TMB) in order to identify the characteristics of associated mutations, their relations to clinical features, and the mechanisms of carcinogenesis in tumors lacking the major driver oncogenes. Analysis of overall mutation frequencies confirmed that APC, TP53, and KRAS mutations were the most prevalent in our cohort. Compared with other tumors, TMB-high tumors were more frequent on the right side of the colon, had lower KRAS and higher BRAF mutation frequencies as well as a higher microsatellite instability (MSI) score, and showed a greater contribution of a mutational signature associated with MSI. Ranking of variant allele frequencies to identify genes that play a role early in carcinogenesis suggested that mutations in genes related to the DNA damage response (such as ATM and POLE) and to MSI (such as MSH2 and MSH6) may precede BRAF mutations associated with activation of the serrated pathway in TMB-high tumors. Our results thus indicate that TMB-high tumors suggest that mutations of genes related to mismatch repair and the DNA damage response may contribute to activation of the serrated pathway in CRC.

Identification of IGF2BP2 and long non-coding RNA TUG1 for the prognosis and tumour microenvironment in head and neck squamous cell carcinoma.

This study aimed to investigate the role of m6A-related long non-coding RNAs (lncRNAs) in the prognosis and tumour microenvironment of head and neck squamous cell carcinoma (HNSCC). 497 samples from The Cancer Genome Atlas were analysed to identify m6A-related lncRNAs via correlation models. Tripartite regression models, Kaplan-Meier analysis and nomograms were then utilised to assess the prognostic significance of these lncRNAs. Tumour mutation burden and immune cell infiltration analyses were also performed. Moreover, m6A-related lncRNAs expression and relation with IGF2BP2 were confirmed by RT-qPCR. The risk model revealed that high-risk scores predicted poorer survival outcomes. The area under ROC curves for predicting 1-, 3-, 5-year survival in the training set were 0.70, 0.68, and 0.64, respectively. Seven key m6A-related lncRNAs showed associations with immune checkpoint molecules, especially CTLA4 and PD-1. Finally, we found that knockdown of TUG1 repressed the expression of IGF2BP2. Our results suggest that the m6A-related lncRNA risk model has potential clinical utility in predicting prognosis and immunotherapeutic responses in patients with HNSCC. Identification of candidate compounds for immunotherapy further emphasises the model's relevance in guiding treatment decisions for HNSCC.

Construction of a prognostic model for gastric cancer based on immune infiltration and microenvironment, and exploration of MEF2C gene function

BackgroundAdvanced gastric cancer (GC) exhibits a high recurrence rate and a dismal prognosis. Myocyte enhancer factor 2c (MEF2C) was found to contribute to the development of various types of cancer. Therefore, our aim is to develop a prognostic model that predicts the prognosis of GC patients and initially explore the role of MEF2C in immunotherapy for GC.MethodsTranscriptome sequence data of GC was obtained from The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO) and PRJEB25780 cohort for subsequent immune infiltration analysis, immune microenvironment analysis, consensus clustering analysis and feature selection for definition and classification of gene M and N. Principal component analysis (PCA) modeling was performed based on gene M and N for the calculation of immune checkpoint inhibitor (ICI) Score. Then, a Nomogram was constructed and evaluated for predicting the prognosis of GC patients, based on univariate and multivariate Cox regression. Functional enrichment analysis was performed to initially investigate the potential biological mechanisms. Through Genomics of Drug Sensitivity in Cancer (GDSC) dataset, the estimated IC50 values of several chemotherapeutic drugs were calculated. Tumor-related transcription factors (TFs) were retrieved from the Cistrome Cancer database and utilized our model to screen these TFs, and weighted correlation network analysis (WGCNA) was performed to identify transcription factors strongly associated with immunotherapy in GC. Finally, 10 patients with advanced GC were enrolled from Sun Yat-sen University Cancer Center, including paired tumor tissues, paracancerous tissues and peritoneal metastases, for preparing sequencing library, in order to perform external validation.ResultsLower ICI Score was correlated with improved prognosis in both the training and validation cohorts. First, lower mutant-allele tumor heterogeneity (MATH) was associated with lower ICI Score, and those GC patients with lower MATH and lower ICI Score had the best prognosis. Second, regardless of the T or N staging, the low ICI Score group had significantly higher overall survival (OS) compared to the high ICI Score group. For its mechanisms, consistently, for Camptothecin, Doxorubicin, Mitomycin, Docetaxel, Cisplatin, Vinblastine, Sorafenib and Paclitaxel, all of the IC50 values were significantly lower in the low ICI Score group compared to the high ICI Score group. As a result, based on univariate and multivariate Cox regression, ICI Score was considered to be an independent prognostic factor for GC. And our Nomogram showed good agreement between predicted and actual probabilities. Based on CIBERSORT deconvolution analysis, there was difference of immune cell composition found between high and low ICI Score groups, probably affecting the efficacy of immunotherapy. Then, MEF2C, a tumor-related transcription factor, was screened out by WGCNA analysis. Higher MEF2C expression is significantly correlated with a worse OS. Moreover, its higher expression is also negatively correlated with tumor mutation burden (TMB) and microsatellite instability (MSI), but positively correlated with several immunosuppressive molecules, indicating MEF2C may exert its influence on tumor development by upregulating immunosuppressive molecules. Finally, based on transcriptome sequencing data on 10 paired tumor tissues from Sun Yat-sen University Cancer Center, MEF2C expression was significantly lower in paracancerous tissues compared to tumor tissues and peritoneal metastases, and it was also lower in tumor tissues compared to peritoneal metastases, indicating a potential positive association between MEF2C expression and tumor invasiveness.ConclusionsOur prognostic model can effectively predict outcomes and facilitate stratification GC patients, offering valuable insights for clinical decision-making. The identified transcription factor MEF2C can serve as a biomarker for assessing the efficacy of immunotherapy for GC.

The Morphologic and Molecular Heterogeneity of Fumarate Hydratase-deficient Leiomyomas: Integrative Molecular Profiling of Uterine Smooth Muscle Tumors With Histologic Feature Correlation.

The morphologic features of uterine smooth muscle tumors (USMTs) are subject to interobserver variability and are complicated by consideration of features of fumarate hydratase deficiency (FHd) and other morphologic subtypes, with difficult cases occasionally diagnosed as smooth muscle tumor of uncertain malignant potential (STUMP). We compare immunohistochemical findings and detailed morphologic analysis of 45 USMTs by 4 fellowship-trained gynecologic pathologists with comprehensive molecular analysis, focusing on FHd leiomyomas (n=15), compared to a variety of other USMTs with overlapping morphologic features, including 9 STUMPs, 8 usual-type leiomyomas (ULM), 11 apoplectic leiomyomas, and 2 leiomyomas with bizarre nuclei (LMBN). FHd leiomyomas, defined by immunohistochemical (IHC) loss of FH and/or 2SC accumulation, showed FH mutations and/or FH copy loss in all cases, with concurrent TP53 mutations in 2 tumors. Severe and/or symplastic-type cytologic atypia was seen more often in FHd leiomyomas with only FH copy loss (6/8, and 2/2 with concurrent TP53 mutations) compared to those with FH mutations (2/7) and typically showed increased genomic instability. This subset of FHd tumors often showed morphologic overlap with STUMPs and LMBN, but all cases of FHd tumors showed 2SC accumulation and/or FH loss by IHC. In conclusion, we highlight the importance of investigating USMTs with severe and/or symplastic-type cytologic atypia with FH and 2SC IHC, as many of these tumors are FH-deficient via focal deep deletion (2-copy loss) of the FH locus. In addition, we report the presence of concurrent TP53 mutations in FHd tumors with more severe cytologic atypia; further data about clinical outcomes for these tumors are needed.

Bioinformatics Analysis Reveals Microrchidia Family Genes as the Prognostic and Therapeutic Markers for Colorectal Cancer.

The aim of this study is to examine the role of the microrchidia (MORC) family, a group of chromatin remodeling proteins, as the therapeutic and prognostic markers for colorectal cancer (CRC). MORC protein family genes are a highly conserved nucleoprotein superfamily whose members share a common domain but have distinct biological functions. Previous studies have analyzed the roles of MORCs as epigenetic regulators and chromatin remodulators; however, the involvement of MORCs in the development and pathogenesis of CRC was less examined. The current work examined the role of the MORCs as the therapeutic and prognostic markers for CRC. The expressions and prognostic significance of MORC family genes in CRC were explored. The role of these genes in tumor immunity was comprehensively analyzed in terms of their functions in immune cell infiltration, tumor microenvironment (TME), and their interaction with immune regulatory genes such as immunosuppressive genes, immune checkpoints and immunostimulatory genes. The relations between MORC family genes, tumor mutation burden (TMB), DNA, mismatch repair (MMR), RNA methylation, microsatellite instability (MSI), and drug sensitivity were investigated using the R statistical software. The expressions of MORC4 in 150 CRC tissues and 60 paracancer tissues were detected by immunohistochemical method. CRC cell proliferation, migration, and invasion were measured by cell counting kit-8 (CCK-8), scratch assay, and transwell cell invasion assay. The expressions of MORC2 and MORC4 were significantly upregulated, whereas those of MORC1 and MORC3 were noticeably downregulated in CRC in comparison to their expressions in normal colorectal mucosal tissues. Patients with high-expressed MORC2 showed a more unfavorable prognosis than those with a low MORC2 level. Functional annotation analysis identified 100 MORC family genes with the most significant negative or positive correlations to diabetic cardiomyopathy, amyotrophic lateral sclerosis, oxidative phosphorylation, Huntington's disease, thermogenesis, Parkinson's disease, olfactory transduction, Alzheimer's disease, prion disease. MORC3 expression was positively correlated with Stromal score, Immune score and ESTIMATE score, while MORC2 expression was negatively related to the three scores in CRC, these correlations were not statistically significant. Additionally, the MORC family genes were significantly positively correlated with tumor-infiltrating immune cells such as T helper cells and exhibited close relations to some immunosuppressive genes such as CXCR4 and PVR, immunostimulatory genes such as TGFBR1, KDR, and CD160 as well as some immune checkpoint genes. It was found that the expressions of some members of MORC family genes were positively correlated with DNA methylation, MSI, TMB, MMRs, and drug sensitivity in CRC and that the mRNA and protein levels of MORC4 were remarkably upregulated in CRC tissues than in adjacent normal tissues (P<0.05). In the MORC4 knockdown group, DLD-1 cell proliferation was more inhibited than in the negative control (NC) and siRNA groups (P<0.05). Furthermore, the migratory capacity of DLD-1 cells and the number of cells crossing the basement membrane in the MORC4 knockdown group were reduced compared to the NC and siRNA groups (all P<0.05). The expressions of MORC family genes were significantly different in CRC samples, which was related to the immune cell infiltration and prognosis of CRC. Thus, the MORC family genes were considered as markers for indicating the clinical immunotherapy and prognostic outcome of CRC.