Article
Respiratory System
Anne-Sophie Lamort, Jan Christian Kaiser, Mario A. A. Pepe, Ioannis Lilis, Giannoula Ntaliarda, Kalman Somogyi, Magda Spella, Sabine J. Behrend, Georgia A. Giotopoulou, Willem Kujawa, Michael Lindner, Ina Koch, Rudolf A. Hatz, Juergen Behr, Rocio Sotillo, Andrea C. Schamberger, Georgios T. Stathopoulos
Summary: Two molecular subtypes of LUAD have been identified, and their identification provides important prognostic information.
EUROPEAN RESPIRATORY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Heng Wang, Chuangye Wei, Peng Pan, Fengfeng Yuan, Jiancheng Cheng
Summary: The aim of this study was to identify DNA methylation-based biomarkers for predicting overall survival of stage I-II lung adenocarcinoma patients. An 11-DNA methylation signature was found to be significantly associated with patient survival and showed high prognostic effectiveness. A diagnostic nomogram based on methylation risk score and clinical factors demonstrated robustness in predicting patient survival.
SCIENTIFIC REPORTS
(2021)
Article
Medicine, General & Internal
Hui Zeng, Ying Wang, Ying Wang, Yongjun Zhang
Summary: The methylation level of XXYLT1 gene is significantly higher in lung adenocarcinoma tissues compared to para-carcinoma and normal lung tissues, while the mRNA expression of XXYLT1 is significantly lower. This difference is particularly significant in male patients.
Article
Biochemical Research Methods
K. Athira, P. V. Sunil Kumar, M. Manju, G. Gopakumar
Summary: This study used multiplex network modeling to investigate biomarker genes and signaling pathways in lung adenocarcinoma. The results provide potential targets for novel diagnostic biomarkers and can aid in treatment decision-making by identifying patients based on cancer stage.
CURRENT BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Jin Ren, Yun Yang, Chuanyin Li, Lu Xie, Ronggui Hu, Xiong Qin, Menghuan Zhang
Summary: Lung adenocarcinoma (LUAD) is influenced by multiple biological factors, and studying the prognosis from the perspective of omics integration is more meaningful. By combining aberrant methylation and tumor infiltration CD8 T cell-related genes, a prognostic model was successfully established to explore key biomarkers of early-stage LUAD.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Kai Yang, Ying Wu
Summary: In this study, six prognosis-related molecular subtypes were identified for early-stage non-small cell lung carcinoma (NSCLC), including 4 subtypes for lung squamous cell carcinoma (LUSC) and 2 subtypes for lung adenocarcinoma (LUAD). The molecular subtypes were determined by both mRNA and DNA methylation information, with selected biomarkers for prediction using random forest (RF) and support vector machine (SVM) models. This research provides important insights for personalized therapy of patients with early-stage NSCLC.
Article
Cell Biology
Bo Peng, Huawei Li, Ruisi Na, Tong Lu, Yongchao Li, Jiaying Zhao, Han Zhang, Linyou Zhang
Summary: This study identified lncRNAs associated with genomic instability and constructed a predictive signature for early stage lung adenocarcinoma patients. The developed six-lncRNA signature showed good predictive performance and was confirmed to be an independent prognostic factor. Validation with external datasets further supported the utility of this prognostic lncRNA signature.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rong Qiao, Feifei Di, Jun Wang, Yujie Wei, Tian Xu, Liping Dai, Wanjian Gu, Baohui Han, Rongxi Yang
Summary: This study aims to identify blood-based biomarkers for the early detection of lung cancer (LC). By conducting a discovery study and two independent case-control studies, LC-associated hypomethylation in the FUT7 gene is identified. Blood-based FUT7 hypomethylation is found in early-stage LC patients, as well as in patients with small malignant nodules and adenocarcinoma in situ. Gender, tumor stage, lymph node involvement, and tumor size all influence FUT7 hypomethylation.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Multidisciplinary Sciences
Kaja Kostyrko, Marta Roman, Alex G. Lee, David R. Simpson, Phuong T. Dinh, Stanley G. Leung, Kieren D. Marini, Marcus R. Kelly, Joshua Broyde, Andrea Califano, Peter K. Jackson, E. Alejandro Sweet-Cordero
Summary: In this study, researchers used RNAi screens to identify UHRF1 as an epigenetic regulator that is specifically vulnerable in KRAS mutant lung cancer cells. Knocking out UHRF1 selectively impaired the growth and induced apoptosis in KRAS mutant cells by causing global DNA hypomethylation and upregulation of tumor suppressor genes. In vivo experiments showed that UHRF1 knock-out inhibits tumor growth in KRAS-driven mouse lung cancer models. High UHRF1 expression in lung cancer patients is associated with low TSG expression and predicts worse outcomes in KRAS mutant tumors. These findings suggest that UHRF1 could be a potential target for therapeutic intervention in KRAS-driven cancer.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Quanyou Wu, Lin Feng, Yaru Wang, Yousheng Mao, Xuebing Di, Kaitai Zhang, Shujun Cheng, Ting Xiao
Summary: Alternative RNA splicing is a crucial mechanism in posttranscriptional gene regulation that contributes to protein diversity. In this study, we investigated the aberrant alternative splicing events in lung adenocarcinoma (LUAD) and their biological and clinical implications using multi-omics data. We identified 3688 aberrant alternative splicing events in LUAD, mainly involving alternative promoter and exon skip. Our findings demonstrated the regulatory roles of RNA binding proteins, somatic mutations, and DNA methylations on alternative splicing. We also identified a subtype of LUAD with a specific alternative splicing pattern that was associated with better prognosis and response to immunotherapy. These findings provide insights into tumorigenesis and tumor immune microenvironment, and have implications for the development of splice-switching therapies for LUAD.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Cell Biology
Guo Li, Zhijie Xu, Jinwu Peng, Yuanliang Yan, Yong Liu, Xin Zhang, Yuanzheng Qiu, Chencheng Fu
Summary: The RIPK5 family plays an important role in lung adenocarcinoma, with its expression being associated with pathological stage and patient survival. The functions of the RIPK5 family are involved in cellular senescence, kinase activity, apoptosis, and immune cell infiltration.
Article
Oncology
Batkhishig Munkhjargal, Kazuya Kondo, Shiho Soejima, Bilguun Tegshee, Chikako Takai, Naoya Kawakita, Hiroaki Toba, Hiromitsu Takizawa
Summary: DPP6 is the most significantly hypermethylated CpG island in LADC and it regulates A-type potassium channels in neurons. Previous studies have shown that DPP6 is downregulated in certain cancers and upregulated in others, depending on methylation levels. This study examines the methylation and expression of DPP6 in LADC tissues and finds higher levels of methylation are associated with worse prognosis.
Article
Oncology
Xinyan Li, Yixiao Yuan, Mintu Pal, Xiulin Jiang
Summary: This study reveals the correlation between high expression of inflammation-related genes and tumor progression and poor prognosis in non-small-cell lung cancer. Furthermore, the study identifies the correlation between IRRGs and tumor mutational burden, immune cell infiltration, and drug sensitivity. Lastly, a regulatory axis model is constructed to investigate the regulatory mechanism of IRRGs.
FRONTIERS IN ONCOLOGY
(2022)
Article
Respiratory System
Duoduo Xu, Cheng Li, Youjing Zhang, Jizhou Zhang
Summary: This study constructed a prognostic model for predicting the prognosis of LUAD patients, by analyzing DNA methylation differences to identify potential biomarkers. The results showed that specific methylation sites were associated with patient prognosis.
BMC PULMONARY MEDICINE
(2022)
Article
Biophysics
Dechan Lu, Yanping Chen, Longfeng Ke, Weilin Wu, Liwen Yuan, Shangyuan Feng, Zufang Huang, Yudong Lu, Jing Wang
Summary: DNA methylation plays a critical role in human tumor development, but current methods for characterizing DNA methylation are time-consuming and labor-intensive. In this study, we developed a sensitive and simple surface-enhanced Raman spectroscopy (SERS) approach to identify DNA methylation patterns in early-stage lung cancer (LC) patients. By comparing SERS spectra of methylated DNA bases or sequences with unmethylated counterparts, a reliable spectral marker of cytosine methylation was identified. Our results showed distinct methylation patterns in genomic DNA (gDNA) between early-stage LC and benign lung disease (BLD) patients, suggesting cancer-induced DNA methylation alterations. Furthermore, combining SERS profiling with machine learning allowed for the differentiation of early-stage LC and BLD patients with high accuracy.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Oncology
Jiajin Chen, Yunjie Song, Yi Li, Yongyue Wei, Sipeng Shen, Yang Zhao, Dongfang You, Li Su, Maria Moksnes Bjaanaes, Anna Karlsson, Maria Planck, Johan Staaf, Aslaug Helland, Manel Esteller, Hongbing Shen, David C. C. Christiani, Ruyang Zhang, Feng Chen
Summary: This study identified significant gene-gene interactions associated with non-small-cell lung cancer survival through a three-step analytic strategy. Two interactions were found at both the epigenetic and transcriptional levels, providing potential clues for precision treatment of NSCLC.
MOLECULAR ONCOLOGY
(2023)
Article
Oncology
Bo Jiang, Junyuan Qi, Mingyuan Sun, Weiwei Zheng, Yongyue Wei, Jianxiang Wang, Fengkui Zhang
Summary: This study evaluated the pharmacokinetic profiles of flumatinib mesylate tablets at doses of 400 mg and 600 mg in patients with CML-CP. The results showed that flumatinib exposure increased in an approximately dose-proportional manner, with slow elimination and manageable adverse events. Further research is needed in a larger sample size study.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jiajin Chen, Jiaqi Tang, Mengli Nie, Yi Li, Mark M. Wurfel, Nuala J. Meyer, Yongyue Wei, Yang Zhao, Angela J. Frank, B. Taylor Thompson, David C. Christiani, Feng Chen, Ruyang Zhang
Summary: The WNT gene family is associated with late-onset ARDS and 28-day survival, and the WNT9A gene plays a crucial role in the pathogenesis and prognosis of late-onset ARDS. This study provides insights into ARDS treatment by elucidating the roles of WNT9A in immunity and fibrosis.
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
(2023)
Letter
Oncology
Ruyang Zhang, Yi Li, Feng Chen, David C. Christiani
JOURNAL OF THORACIC ONCOLOGY
(2023)
Article
Cell Biology
Sipeng Shen, Jiajin Chen, Hongru Li, Yongyue Wei, Yunke Jiang, Ruyang Zhang, Yang Zhao, Feng Chen
Summary: In this study, the influences of DNA methylation (DNAm) on non-coding RNAs (ncRNAs) were characterized, and significant associations between DNAm sites and various ncRNAs across multiple cancer types were identified. A subtype called ncmcluster was developed based on cancer-specific ncRNAs, which showed associations with tumor microenvironment, clinical outcome, and biological pathways. To comprehensively describe the ncQTM patterns, a database named Pancan-ncQTM was developed.
Article
Oncology
Ziang Xu, Xinlei Chen, Xiaomeng Song, Xinxin Kong, Jiajin Chen, Yunjie Song, Maojie Xue, Lin Qiu, Mingzhu Geng, Changyue Xue, Wei Zhang, Ruyang Zhang
Summary: By leveraging autophagy-related epigenetic biomarkers, we have developed a better prognostic prediction model for head and neck squamous cell carcinoma (HNSCC) that incorporates CpG probes with main effects or gene-gene interactions. Compared to models that only use demographic and clinical information, ATHENA has significantly improved discriminative ability, prediction accuracy, and clinical net benefits. Furthermore, ATHENA is robust in different subpopulations and external populations, and its epigenetic score is associated with tumor immune microenvironment, immune cell abundances, immune checkpoints, somatic mutation, and immunity-related drugs.
CLINICAL EPIGENETICS
(2023)
Article
Oncology
Zheng Wu, Fengwei Tan, Yaozeng Xie, Wei Tang, Fei Wang, Yongjie Xu, Wei Cao, Chao Qin, Xuesi Dong, Yadi Zheng, Zilin Luo, Chenran Wang, Liang Zhao, Changfa Xia, Jiang Li, Renda Li, Feiyue Feng, Jibin Li, Jiansong Ren, Jufang Shi, Hong Cui, Sipeng Shen, Ning Wu, Wanqing Chen, Ni Li, Jie He
Summary: In order to reduce the high false-positive rate of LDCT in lung cancer screening in China, this study constructed lung cancer risk prediction models and validated them externally. The results showed that these models can effectively reduce the false-positive rate of LDCT screening.
Editorial Material
Oncology
Maxime Janin, Manel Esteller
Summary: Mutations in splicing factors are commonly found in CLL, but other mechanisms such as METTL3 overexpression can also lead to abnormal splicing. METTL3 deposits epitranscriptomic marks in spliceosome transcripts, causing aberrant splicing, but also vulnerability to METTL3 inhibitors.
BLOOD CANCER DISCOVERY
(2023)
Review
Oncology
Maxime Janin, Veronica Davalos, Manel Esteller
Summary: Most cancer-related deaths and illnesses can be attributed to metastasis. The role of epigenetic and epitranscriptomic changes in the origin and progression of cancer has been extensively demonstrated. These two-layer regulatory mechanisms, driven by DNA or RNA modifiers, are finely controlled in normal tissue but dysregulated in cancer. Understanding these mechanisms could have important clinical implications for prevention and management of advanced malignancies. Reversing these epi-alterations with small molecules or inhibitors against epi-modifiers could offer novel therapeutic alternatives.
CANCER AND METASTASIS REVIEWS
(2023)
Article
Virology
Xiao Ning, Jinxing Guan, Xi-An Li, Yongyue Wei, Feng Chen
Summary: This study proposes an advanced artificial intelligence approach based on physics-informed neural networks (PINNs) to estimate time-varying parameters from given data for the compartmental model. The experimental findings on real-world reported data have demonstrated that our method robustly and accurately learns the dynamics and forecasts future states.
Review
Public, Environmental & Occupational Health
Zilin Luo, Xuesi Dong, Chenran Wang, Wei Cao, Yadi Zheng, Zheng Wu, Yongjie Xu, Liang Zhao, Fei Wang, Jibin Li, Jiansong Ren, Jufang Shi, Wanqing Chen, Ni Li
Summary: This study systematically reviewed observational studies on the association between socioeconomic status (SES) and adherence to colorectal cancer (CRC) screening. The findings showed that individuals with high SES had higher adherence to screening compared to those with low SES. Neighborhood SES or small-area SES was more effective in assessing the association between SES and adherence than individual SES.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2023)
Article
Medicine, General & Internal
Zoucheng Pan, Ruyang Zhang, Sipeng Shen, Yunzhi Lin, Longyao Zhang, Xiang Wang, Qian Ye, Xuan Wang, Jiajin Chen, Yang Zhao, David C. Christiani, Yi Li, Feng Chen, Yongyue Wei
Summary: This study developed a reliable lung cancer risk prediction model called OWL using machine learning techniques and validated its performance on multiple datasets, demonstrating its superior performance in identifying individuals at high risk of lung cancer.
Article
Biochemistry & Molecular Biology
Edilene Siqueira, Bo-Hyun Kim, Larry Reser, Robert Chow, Kerry Delaney, Manel Esteller, Mark M. Ross, Jeffrey Shabanowitz, Donald F. Hunt, Sonia Guil, Juan Ausio
Summary: This study used a neural cell line derived from the human ventral mesencephalon, called ReNCell, and its MeCP2 knock out to investigate the changes in linker histones during neural cell differentiation. The results showed that MeCP2 played a crucial role in dendrite and axon development and exhibited extensive co-localization with linker histones. Additionally, the size of the nucleus decreased during differentiation, but the MeCP2 knock out cells showed a significant increase in nucleus size after differentiation.