Article
Biochemistry & Molecular Biology
Liwei Cao, Chen Huang, Daniel Cui Zhou, Yingwei Hu, T. Mamie Lih, Sara R. Savage, Karsten Krug, David J. Clark, Michael Schnaubelt, Lijun Chen, Felipe da Veiga Leprevost, Rodrigo Vargas Eguez, Weiming Yang, Jianbo Pan, Bo Wen, Yongchao Dou, Wen Jiang, Yuxing Liao, Zhiao Shi, Nadezhda Terekhanova, Song Cao, Rita Jui-Hsien Lu, Yize Li, Ruiyang Liu, Houxiang Zhu, Peter Ronning, Yige Wu, Matthew A. Wyczalkowski, Hariharan Easwaran, Ludmila Danilova, Arvind Singh Mer, Seungyeul Yoo, Joshua M. Wang, Wenke Liu, Benjamin Haibe-Kains, Mathangi Thiagarajan, Scott D. Jewell, Galen Hostetter, Chelsea J. Newton, Qing Kay Li, Michael H. Roehr, David Fenyo, Pei Wang, Alexey Nesvizhskii, D. R. Mani, Gilbert S. Omenn, Emily S. Boja, Mehdi Mesri, Ana Robles, Henry Rodriguez, Oliver F. Bathe, Daniel W. Chan, Ralph H. Hruban, Li Ding, Bing Zhang, Hui Zhang
Summary: This study conducted comprehensive proteogenomic analysis of PDAC to understand the molecular alterations that drive oncogenesis. Multiple analyses were performed on tissues from patients, providing valuable resources for early detection and identification of therapeutic targets.
Review
Biochemistry & Molecular Biology
Jorge Melendez-Zajgla, Vilma Maldonado
Summary: This review summarizes the current knowledge about the positive and negative effects of lncRNAs in the stemness phenotype of pancreatic ductal adenocarcinoma cancer (PDAC).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Steve E. Kalloger, Joanna M. Karasinska, Martin S. Keung, Danielle L. Thompson, Julie Ho, Christine Chow, Dongxia Gao, James T. Topham, Cassia Warren, Hui-Li Wong, Michael Kuan-Ching Lee, Daniel J. Renouf, David F. Schaeffer
Summary: The study examined the epithelial and stromal components in pancreatic ductal adenocarcinoma (PDAC) using laser capture microdissected (LCM) samples, revealing that the stromal component had independent prognostic differences. Specific gene expression differences in the epithelium and stroma may help improve prognostication for PDAC.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Oncology
Lixing Li, Lu Shen, Hao Wu, Mo Li, Luan Chen, Qiang Zhou, Jingsong Ma, Cong Huai, Wei Zhou, Muyun Wei, Mingzhe Zhao, Xianglong Zhao, Huihui Du, Bixuan Jiang, Yidan Sun, Na Zhang, Shengying Qin, Tonghai Xing
Summary: Pancreatic cancer can be stratified into six molecular subtypes, including squamous basal-like, immune mesenchymal-like, normal mesenchymal-like, exocrine-like, pure classical-like, and quiescent-like subtypes.
Article
Biochemical Research Methods
Narges Rezaie, Farilie Reese, Ali Mortazavi
Summary: PyWGCNA is a Python package designed to identify co-expression modules from large RNA-seq datasets. It has a faster implementation than the R version and provides additional functionalities such as functional enrichment analysis, protein-protein interaction analysis, and comparison of multiple co-expression modules.
Article
Parasitology
Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Summary: The study constructed a gene co-expression network of insect-stage trypanosomes using RNA-Seq data and identified enriched modules for genes that play key roles in the parasite's development in the tsetse fly. Additionally, potential 3' UTR regulatory elements for genes in the same module were predicted using the FIRE tool. This network provides a valuable resource for identifying candidate genes for functional studies and understanding the molecular mechanisms underlying important biological processes during the parasite's development in the tsetse fly, which could lead to the identification of potential molecular targets for disease control.
PARASITES & VECTORS
(2021)
Article
Immunology
Hao Yuan, Jinhui Liu, Li Zhao, Pengfei Wu, Guosheng Chen, Qun Chen, Peng Shen, Taoyue Yang, Shaoqing Fan, Bin Xiao, Kuirong Jiang
Summary: Through analysis of clinical information and genetic transcriptome data of PDAC patients, a m5C-related lncRNA prognostic risk model was established and its relationship with PDAC immune microenvironment was studied. The risk model showed predictive ability and could potentially serve as a therapeutic target for PDAC patients.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Genetics & Heredity
Zhengze Shen, Shengwei Liu, Jie Liu, Jingdong Liu, Caoyuan Yao
Summary: This study aimed to predict hub genes affecting LUAD recurrence using weighted gene co-expression network analysis. Through analysis of microarray samples, a protein-protein interaction network was established, and eight hub genes closely related to LUAD recurrence were identified. Transcription factors regulating these hub genes were predicted, and drugs for treating these genes were explored.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Qiong Wu, Lei Chen, Dongliu Miao, Yiqi Jin, Zhigang Zhu
Summary: This study identified m6A-related lncRNAs that are associated with the prognosis and tumor immune environment in PDAC. A prognostic signature based on 9 m6A-related lncRNAs was established, which predicted the prognosis of PDAC patients, with high-risk patients having worse outcomes. The signature was also correlated with somatic mutations, immunocyte infiltration, immune function, immune checkpoints, tumor microenvironment score, and sensitivity to chemotherapeutic drugs.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Nausika Betriu, Juan Bertran-Mas, Anna Andreeva, Carlos E. Semino
Summary: Syndecans, a subfamily of proteoglycans, play critical roles in various physiological processes and have implications in disease progression. Their interactions with other macromolecules contribute to normal cellular functions and disease pathogenesis.
Article
Genetics & Heredity
Qihang Yuan, Jie Ren, Zhizhou Wang, Li Ji, Dawei Deng, Dong Shang
Summary: Through WGCNA and LASSO algorithms, real hub genes for PAAD were identified and a prognostic panel was constructed for predicting PAAD prognosis. The study confirmed SAFB as the real hub gene of PAAD, and the multigene prognostic signature showed superior predictive accuracy for PAAD prognosis. Additionally, an accurate prognostic nomogram was developed to aid in precise tumor treatment and early intervention.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Giulio Innamorati, Thomas M. Wilkie, Giorgio Malpeli, Salvatore Paiella, Silvia Grasso, Borislav Rusev, Biagio Eugenio Leone, Maria Teresa Valenti, Luca dalle Carbonare, Samuele Cheri, Alice Giacomazzi, Marco Zanotto, Vanessa Guardini, Michela Deiana, Donato Zipeto, Michela Serena, Marco Parenti, Francesca Guzzi, Rita Teresa Lawlor, Giovanni Malerba, Antonio Mori, Giuseppe Malleo, Luca Giacomello, Roberto Salvia, Claudio Bassi
Summary: The GNA15 gene is ectopically expressed in human pancreatic ductal adenocarcinoma cancer cells and is associated with poor prognosis. Elevated GNA15 expression in pancreatic cancer can affect signaling and cell motility during progression.
SCIENTIFIC REPORTS
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Jing Chen, Shuxue Liu, Yude Tang, Xiongbiao Zhang, Mingming Cao, Zheng Xiao, Mingda Ren, Xianteng Chen
Summary: The study assessed the diagnostic performance of IVIM and DWI for PDAC, demonstrating comparable diagnostic power and good performance. Factors such as study design, ROI delineation, field strength, and slice thickness contributed to the heterogeneity of ADC.
EUROPEAN JOURNAL OF RADIOLOGY
(2021)
Review
Oncology
Eleonora Lai, Pina Ziranu, Dario Spanu, Marco Dubois, Andrea Pretta, Simona Tolu, Silvia Camera, Nicole Liscia, Stefano Mariani, Mara Persano, Marco Migliari, Clelia Donisi, Laura Demurtas, Valeria Pusceddu, Marco Puzzoni, Mario Scartozzi
Summary: Despite ongoing research, there is still insufficient data on BRCA1/2-mutant PDAC, and more understanding is needed on the specific landscape of PDAC with BRCA mutations.
BRITISH JOURNAL OF CANCER
(2021)
Article
Genetics & Heredity
Cangang Zhang, Zhe Zhao, Haibo Liu, Shukun Yao, Dongyan Zhao
Summary: This study established a 13-gene signature to predict prognosis in colon adenocarcinoma (COAD) patients, with NAT1 and NAT2 identified as biomarkers for prognosis and immune response in COAD. The signature showed enhanced predictive power and the two genes were associated with poorer overall survival in COAD patients. Further research is warranted to explore the anti-tumor immune roles of NAT1 and NAT2 in COAD.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Ming Wu, Yadong Wang, Hang Liu, Jukun Song, Jie Ding
BIOSCIENCE REPORTS
(2020)
Article
Virology
Jukun Song, Yamei Li, Xiaolin Huang, Zhihong Chen, Yongdi Li, Chong Liu, Zhu Chen, Xiaofeng Duan
JOURNAL OF MEDICAL VIROLOGY
(2020)
Article
Biochemistry & Molecular Biology
Juan Liu, Zongjian Tan, Jun He, Tingting Jin, Yuanyuan Han, Li Hu, Jukun Song, Shengwen Huang
BIOSCIENCE REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Ming Wu, Yu Xia, Yadong Wang, Fei Fan, Xian Li, Jukun Song, Jie Ding
BIOSCIENCE REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Jukun Song, Wei Wang, Yiwen Yuan, Yong Ban, Jiaming Su, Dongbo Yuan, Weihong Chen, Jianguo Zhu
Summary: This study examined immune cell profiling in prostate cancer, identifying multiple molecular subtypes and investigating their specific clinical characteristics and functional enrichment. Algorithms were used to predict clinical responses and potential chemotherapeutic targets. Results showed an association between a specific subtype and advanced PCa, which was more likely to respond to immunotherapy.
BIOSCIENCE REPORTS
(2021)
Article
Oncology
Guohua Zhu, Jukun Song, Weimin Chen, Dongbo Yuan, Wei Wang, Xiaoyue Chen, Hen Liu, Hao Su, Jianguo Zhu
Summary: Dkk1 plays a complex and diverse role in tumors, with its high expression potentially promoting or inhibiting tumor metastasis and invasion, offering significant research and therapeutic potential.
CANCER MANAGEMENT AND RESEARCH
(2021)
Article
Otorhinolaryngology
Xiaofeng Duan, Xianlin Cheng, Xinhai Yin, Zhao Ke, Jukun Song
Summary: The study identified 249 aberrantly expressed RBPs in head and neck cancer, including 101 downregulated RBPs and 148 upregulated RBPs. By analyzing 15 hub genes among these RBPs, a prognostic prediction model was constructed that showed high-risk patients had better survival outcomes. The predictive value of the RPB gene signature was validated in another HNSC dataset, suggesting potential application in clinical decision-making and personalized treatment.
EUROPEAN ARCHIVES OF OTO-RHINO-LARYNGOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jukun Song, Ganhua You, Xinhai Yin, Guohua Zhu, Wei Wang, Yongwei Yu, Jianguo Zhu
Summary: YTHDC2 gene is overexpressed in prostate cancer patients and associated with poor prognosis. Overexpression of YTHDC2 promotes proliferation, migration, and invasion of prostate cancer cells. These findings suggest that YTHDC2 may serve as a potential biomarker for the prognosis of prostate cancer.
JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY
(2023)
Article
Virology
Jukun Song, Yadong Wu, Xinhai Yin, Hong Ma, Junmei Zhang
Summary: A Mendelian randomization study found that 42 bacterial genera were associated with COVID-19 susceptibility, hospitalization, and severity. Five gut microbiota were significantly associated with COVID-19 hospitalization and severity. Three gut microbiota were significantly associated with COVID-19 hospitalization and susceptibility, while two microbiota were significantly associated with COVID-19 hospitalization, severity, and susceptibility.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Dentistry, Oral Surgery & Medicine
Ruofeng Jiao, Wei Li, Jukun Song, Zhu Chen
Summary: Through two-sample Mendelian randomization analysis, it was found that asthma may be a protective factor for periodontitis, and there was no evidence indicating a causal effect of periodontitis on the risk of asthma in the reverse analysis.
Article
Endocrinology & Metabolism
Ya-Shi Zhou, Ju-Kun Song, Zhi-Jun Zheng, Si-Yu Li, Jian-Guo Liu, Ju-Xiang Peng
Summary: This study used Mendelian randomization analysis to explore the association between heel bone mineral density and various oral diseases. The results showed a negative relationship between heel bone density and periodontitis, suggesting that a decrease in heel bone density could promote the occurrence of periodontitis. No significant relationship was found between heel bone density and other oral diseases.
JOURNAL OF BONE AND MINERAL METABOLISM
(2023)
Article
Public, Environmental & Occupational Health
Jukun Song, Yadong Wu, Xinhai Yin, Junmei Zhang
Summary: Using bidirectional Mendelian randomization (MR), researchers found that there is no causal relationship between COVID-19 and periodontitis. There is also no causal relationship between periodontitis and COVID-19 hospitalization, susceptibility, or severity. Further study is needed to identify the substance in COVID-19 responsible for this effect.
HEALTH SCIENCE REPORTS
(2023)
Article
Public, Environmental & Occupational Health
Xianlin Cheng, Xinhai Yin, Jukun Song
Summary: The expression of CCDC25 is not linked to prognosis in most cancers, but it plays an important role in metastasis and immune infiltration.
HEALTH SCIENCE REPORTS
(2023)
Article
Public, Environmental & Occupational Health
Yan Long, Yadong Wu, Juxiang Peng, Jukun Song, Na Li
Summary: Recent studies have shown the biological significance of pyroptosis in cancer development, but its role in immune modulation and the tumor microenvironment (TME) is still uncertain. This study comprehensively assessed pyroptosis regulatory genes (PRGs) in head and neck cancer samples and correlated them with TME cell infiltration characteristics. A pyrolysis potential index (PPI) was developed to quantify the pyrolysis regulation patterns in head and neck squamous cell carcinoma (HNSC).
HEALTH SCIENCE REPORTS
(2023)
Article
Multidisciplinary Sciences
Li Yuan, Qiang An, Ting Liu, Jukun Song
Summary: This study identified three immunogenomic subgroups of OC based on transcriptome data, namely hyperimmunogenic, moderately immunogenic, and hypoimmunogenic. Each subgroup was associated with specific immune cell infiltration levels and survival prognosis, with the hyperimmunogenic subgroup showing better response to immunotherapy. Additionally, potential chemotherapeutic targets for OC were identified, including Parthenolide and the AKT inhibitor VIII, Paclitaxel.
