Adam Put, Katerina Smesny Trtkova, Marcel Mittak, Petra Herentinova, Jana Vaculova, Radoslava Cernekova, Jozef Skarda
Introduction: Large cell neuroendocrine carcinoma (LCNEC) is a subtype of non-small-cell lung carcinoma with poorly understood methylation characteristics, including the activity of DNA methyltransferases. Despite the pivotal role of DNA methyltransferases in epigenetic regulation, their expression profile in LCNEC remains unexplored. This study represents the first effort to evaluate the expression of DNMT1, DNMT3A, and DNMT3B genes in patients with LCNEC.
Materials and methods: We performed quantitative expression analyses of DNMT1, DNMT3A, and DNMT3B on formalin-fixed, paraffin-embedded tissue samples obtained from LCNEC patients. Normal lung tissues (n = 4) from healthy patients served as controls to determine differential expression levels.
Results: The analysis revealed upregulation of both DNMT1 and DNMT3A compared to control normal lung tissue. In addition, normalized expression values of DNMT3B were reduced compared to the analyzed DNMT1 and DNMT3A.
Conclusion: In this exploratory pilot of 18 LCNEC cases, DNMT1 and DNMT3A transcripts were frequently higher relative to a normal-lung calibrator, while DNMT3B results were inconclusive due to technical limitations and small sample size. These descriptive findings warrant validation in larger, isoform-resolved cohorts before clinical inference. Future research should prioritize investigating these DNA methyltransferases to explore their therapeutic implications. Moreover, future research should also aim to detect and characterize individual DNMT3B isoforms in LCNEC patients to further elucidate their specific contributions to the pathology of the disease.
{"title":"Altered DNA Methyltransferase Expression in Pulmonary Large-Cell Neuroendocrine Carcinoma: Pilot Experimental Data Targeted DNMT1, DNMT3A, and DNMT3B.","authors":"Adam Put, Katerina Smesny Trtkova, Marcel Mittak, Petra Herentinova, Jana Vaculova, Radoslava Cernekova, Jozef Skarda","doi":"10.1002/cnr2.70513","DOIUrl":"https://doi.org/10.1002/cnr2.70513","url":null,"abstract":"<p><strong>Introduction: </strong>Large cell neuroendocrine carcinoma (LCNEC) is a subtype of non-small-cell lung carcinoma with poorly understood methylation characteristics, including the activity of DNA methyltransferases. Despite the pivotal role of DNA methyltransferases in epigenetic regulation, their expression profile in LCNEC remains unexplored. This study represents the first effort to evaluate the expression of DNMT1, DNMT3A, and DNMT3B genes in patients with LCNEC.</p><p><strong>Materials and methods: </strong>We performed quantitative expression analyses of DNMT1, DNMT3A, and DNMT3B on formalin-fixed, paraffin-embedded tissue samples obtained from LCNEC patients. Normal lung tissues (n = 4) from healthy patients served as controls to determine differential expression levels.</p><p><strong>Results: </strong>The analysis revealed upregulation of both DNMT1 and DNMT3A compared to control normal lung tissue. In addition, normalized expression values of DNMT3B were reduced compared to the analyzed DNMT1 and DNMT3A.</p><p><strong>Conclusion: </strong>In this exploratory pilot of 18 LCNEC cases, DNMT1 and DNMT3A transcripts were frequently higher relative to a normal-lung calibrator, while DNMT3B results were inconclusive due to technical limitations and small sample size. These descriptive findings warrant validation in larger, isoform-resolved cohorts before clinical inference. Future research should prioritize investigating these DNA methyltransferases to explore their therapeutic implications. Moreover, future research should also aim to detect and characterize individual DNMT3B isoforms in LCNEC patients to further elucidate their specific contributions to the pathology of the disease.</p>","PeriodicalId":9440,"journal":{"name":"Cancer reports","volume":"9 3","pages":"e70513"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147484790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Male patients were twice as likely to develop gastric cancer (GC) compared to females, partly due to the protective effect of estrogen. However, the proportion of females increased in the young GC patients.
Aims: The study was designed to explore comprehensive molecular profiles of younger female GC patients, as well as develop a prognostic gene model for female GC patients.
Materials&methods: Gene expression and clinical data of GC and nontumor patients were downloaded from the Gene Expression Omnibus (GEO) database. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were used to find molecular characteristics and potential mechanisms of younger female GC patients. The prognostic gene model containing six differential expressed genes (DEGs), which were between younger and older female patients, was established using Lasso-Cox regression. Its performance was validated by external validation. Then, receiver operating characteristic (ROC) curve was applied to determine the prognostic value of the prognostic gene model.
Results: Six GEO cohorts with 305 female GC patients (69 younger patients and 236 older patients) and 38 female nontumor patients were included. A total of 4557 DEGs between female GC patients and nontumor patients were identified, including 2212 upregulated genes and 2345 downregulated genes. Estrogen response early (p < 0.001) and estrogen response late (p < 0.001) were enriched in female GC patients. In KEGG analysis, aldosterone (p = 0.023) and relaxin pathways (p = 0.043) were concentrated in the younger group. Moreover, we further used the GSE84437 cohort to construct a prognostic gene model containing six genes, namely NREP, GAD1, SLCO4A1, KRT17, DEFB1, and P3H2, to predict the overall survival (OS) of female GC patients (AUC = 0.810). In the overall analysis of female GC patients, high-risk patients showed worse OS than low-risk patients (HR = 5.7688, 95% CI: 3.0108-11.0530, p < 0.001). Compared with older female patients, younger female patients had a higher tendency to be in the high-risk group (31.1% vs. 18.3%, p = 0.018).
Conclusions: In conclusion, we provided the comprehensive molecular profiles of younger female GC patients and found that there was a significant difference in enriched hormone-related pathways between the younger group and the older group. Compared with older female patients, younger female patients were more likely to be in the high-risk group, which showed worse OS than low-risk patients.
背景:男性患者发生胃癌(GC)的可能性是女性的两倍,部分原因是雌激素的保护作用。然而,女性在年轻胃癌患者中所占比例增加。目的:本研究旨在探索年轻女性GC患者的综合分子图谱,并建立女性GC患者预后的基因模型。材料与方法:从Gene expression Omnibus (GEO)数据库下载胃癌和非肿瘤患者的基因表达和临床数据。采用基因本体(GO)、京都基因与基因组百科全书(KEGG)和基因集富集分析(GSEA)等方法寻找年轻女性GC患者的分子特征和潜在机制。采用Lasso-Cox回归建立了包含6个差异表达基因(DEGs)的年轻和老年女性患者预后基因模型。通过外部验证对其性能进行了验证。然后应用受试者工作特征(ROC)曲线确定预后基因模型的预后价值。结果:6个GEO队列共纳入305例女性胃癌患者(年轻69例,老年236例)和38例女性非肿瘤患者。女性胃癌患者与非肿瘤患者共鉴定出4557个基因,其中上调基因2212个,下调基因2345个。结论:综上所述,我们提供了年轻女性GC患者的全面分子图谱,发现年轻组与老年组在丰富的激素相关通路上存在显著差异。与老年女性患者相比,年轻女性患者更有可能属于高危组,其OS表现较低危患者差。
{"title":"Molecular Characteristics, Potential Mechanisms, and Prognostic Gene Model of Younger Female Patients With Gastric Cancer.","authors":"Xiaoyi Luan, Lulu Zhao, Wanqing Wang, Penghui Niu, Xue Han, Zerong Wang, Xiaojie Zhang, Dongbing Zhao, Yingtai Chen","doi":"10.1002/cnr2.70469","DOIUrl":"10.1002/cnr2.70469","url":null,"abstract":"<p><strong>Background: </strong>Male patients were twice as likely to develop gastric cancer (GC) compared to females, partly due to the protective effect of estrogen. However, the proportion of females increased in the young GC patients.</p><p><strong>Aims: </strong>The study was designed to explore comprehensive molecular profiles of younger female GC patients, as well as develop a prognostic gene model for female GC patients.</p><p><strong>Materials&methods: </strong>Gene expression and clinical data of GC and nontumor patients were downloaded from the Gene Expression Omnibus (GEO) database. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were used to find molecular characteristics and potential mechanisms of younger female GC patients. The prognostic gene model containing six differential expressed genes (DEGs), which were between younger and older female patients, was established using Lasso-Cox regression. Its performance was validated by external validation. Then, receiver operating characteristic (ROC) curve was applied to determine the prognostic value of the prognostic gene model.</p><p><strong>Results: </strong>Six GEO cohorts with 305 female GC patients (69 younger patients and 236 older patients) and 38 female nontumor patients were included. A total of 4557 DEGs between female GC patients and nontumor patients were identified, including 2212 upregulated genes and 2345 downregulated genes. Estrogen response early (p < 0.001) and estrogen response late (p < 0.001) were enriched in female GC patients. In KEGG analysis, aldosterone (p = 0.023) and relaxin pathways (p = 0.043) were concentrated in the younger group. Moreover, we further used the GSE84437 cohort to construct a prognostic gene model containing six genes, namely NREP, GAD1, SLCO4A1, KRT17, DEFB1, and P3H2, to predict the overall survival (OS) of female GC patients (AUC = 0.810). In the overall analysis of female GC patients, high-risk patients showed worse OS than low-risk patients (HR = 5.7688, 95% CI: 3.0108-11.0530, p < 0.001). Compared with older female patients, younger female patients had a higher tendency to be in the high-risk group (31.1% vs. 18.3%, p = 0.018).</p><p><strong>Conclusions: </strong>In conclusion, we provided the comprehensive molecular profiles of younger female GC patients and found that there was a significant difference in enriched hormone-related pathways between the younger group and the older group. Compared with older female patients, younger female patients were more likely to be in the high-risk group, which showed worse OS than low-risk patients.</p>","PeriodicalId":9440,"journal":{"name":"Cancer reports","volume":"9 3","pages":"e70469"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12954549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147343691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Randy S D'Amico, Patricia Avancena, Alon Kashanian, Rosivel Galvez, Deborah Gruber, Sami Saba, Avraham Zlochower, Manju Harshan, Morana Vojnic
Background: Pleomorphic xanthoastrocytomas (PXAs) are rare primary central nervous system (CNS) tumors that appear heterogeneous on imaging and histology and typically cause headaches or seizures on initial presentation. Alongside high rates of favorable prognosis after surgical excision exist similarly high rates of recurrence. Leptomeningeal spread on recurrence is even rarer and more challenging to diagnose.
Case: We describe a case of a 40-year-old man with a history of surgically resected PXA presenting 12 years later with persistent headaches and lower back pain. Imaging studies revealed arachnoiditis, and a subsequent brain biopsy was nondiagnostic. Serial CSF studies only revealed the presence of atypical cells too few to further characterize via standard histology studies, with rare small lymphocytes and monocytoid cells. Submitting these cells for next-generation sequencing ultimately revealed a BRAF V600E mutation typically found in PXAs, thereby confirming the diagnosis of leptomeningeal recurrence and revealing a therapeutic target.
Conclusion: This case highlights the utility of next-generation sequencing as a means of non-invasively diagnosing leptomeningeal disease in recurrent PXA and potentially in other cancer types as well.
{"title":"Identification of BRAF V600E Mutation in Cerebrospinal Fluid Aids in Diagnosing Leptomeningeal Carcinomatosis Arising From Pleomorphic Xanthoastrocytoma: A Case Report.","authors":"Randy S D'Amico, Patricia Avancena, Alon Kashanian, Rosivel Galvez, Deborah Gruber, Sami Saba, Avraham Zlochower, Manju Harshan, Morana Vojnic","doi":"10.1002/cnr2.70487","DOIUrl":"https://doi.org/10.1002/cnr2.70487","url":null,"abstract":"<p><strong>Background: </strong>Pleomorphic xanthoastrocytomas (PXAs) are rare primary central nervous system (CNS) tumors that appear heterogeneous on imaging and histology and typically cause headaches or seizures on initial presentation. Alongside high rates of favorable prognosis after surgical excision exist similarly high rates of recurrence. Leptomeningeal spread on recurrence is even rarer and more challenging to diagnose.</p><p><strong>Case: </strong>We describe a case of a 40-year-old man with a history of surgically resected PXA presenting 12 years later with persistent headaches and lower back pain. Imaging studies revealed arachnoiditis, and a subsequent brain biopsy was nondiagnostic. Serial CSF studies only revealed the presence of atypical cells too few to further characterize via standard histology studies, with rare small lymphocytes and monocytoid cells. Submitting these cells for next-generation sequencing ultimately revealed a BRAF V600E mutation typically found in PXAs, thereby confirming the diagnosis of leptomeningeal recurrence and revealing a therapeutic target.</p><p><strong>Conclusion: </strong>This case highlights the utility of next-generation sequencing as a means of non-invasively diagnosing leptomeningeal disease in recurrent PXA and potentially in other cancer types as well.</p>","PeriodicalId":9440,"journal":{"name":"Cancer reports","volume":"9 3","pages":"e70487"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147472743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}