Article
Clinical Neurology
Yannick Braun, Katharina Filipski, Simon Bernatz, Peter Baumgarten, Bastian Roller, Jenny Zinke, Pia S. Zeiner, Elena Ilina, Christian Senft, Michael W. Ronellenfitsch, Karl H. Plate, Oliver Baehr, Elke Hattingen, Joachim P. Steinbach, Michel Mittelbronn, Patrick N. Harter
Summary: This study aims to characterize metabolic features in different molecular subgroups of gliomas, focusing on the impact of metabolic alterations on patient outcomes. Results showed that DNA methylation patterns of metabolic genes can distinguish between IDHmut and IDHwt gliomas, and mitochondrial DNA copy number and immune cell content analysis can predict patient survival under anti-angiogenic therapy. Genomic signatures related to metabolism could indicate specific tumor subgroups with metabolic vulnerabilities.
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2021)
Article
Genetics & Heredity
Xinyu Wang, Lijun Dai, Yang Liu, Chenghao Li, Dandan Fan, Yue Zhou, Pengcheng Li, Qingran Kong, Jianzhong Su
Summary: We developed a computational framework based on Hidden Markov Model to identify altered methylation states of under-methylated regions (UMRs) in IDH mutant gliomas. We identified two distinct types of hypermethylated UMRs in IDH mutant gliomas, named partially hypermethylated UMRs (phUMRs) and fully hypermethylated UMRs (fhUMRs). Genes related to phUMRs were up-regulated, while genes related to fhUMRs were more likely to be repressed in IDH mutant gliomas.
EPIGENETICS & CHROMATIN
(2023)
Article
Pathology
Amos Muench, Daniel Teichmann, Dorothee Spille, Peter Kuzman, Eilis Perez, Sven-Axel May, Wolf C. Mueller, Theodoros Kombos, Shokufe Nazari-Dehkordi, Julia Onken, Peter Vajkoczy, Georgios Ntoulias, Conceicao Bettencourt, Andreas von Deimling, Werner Paulus, Frank L. Heppner, Arend Koch, David Capper, David Kaul, Christian Thomas, Leonille Schweizer
Summary: This study identified a novel subtype of adult-type diffuse glioma with distinct molecular and clinical features. The study found that TERT promoter mutations may not be suitable as a standalone marker for glioblastoma without further morphologic or molecular signs of high-grade glioma.
AMERICAN JOURNAL OF SURGICAL PATHOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Dorothee Hoelzl, Georg Hutarew, Barbara Zellinger, Beate Alinger-Scharinger, Hans U. Schlicker, Christoph Schwartz, Karl Sotlar, Theo F. J. Kraus
Summary: In this study, the researchers compared the detection of EGFR amplification in glioma samples using the EPIC Bead Chip and FISH methods. They found that the EPIC analysis was equally effective in detecting EGFR amplification compared to FISH. EGFR amplification was mainly found in high-grade IDH wildtype and TERT mutated gliomas.
Article
Neurosciences
Yan Liu, Adwait Amod Sathe, Kalil G. Abdullah, Samuel K. McBrayer, Steven H. Adams, Andrew J. Brenner, Kimmo J. Hatanpaa, Mariano S. Viapiano, Chao Xing, Jamie M. Walker, Timothy E. Richardson
Summary: This study used global methylation profiling to identify the presence/absence of chromosomal instability (CIN) in IDH-mutant astrocytomas. It was found that IDH-mutant astrocytomas with evidence of CIN have distinct characteristics and worse clinical outcomes compared to chromosomally stable counterparts.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2022)
Article
Oncology
Muhammad Asad Iqbal, Mingyang Li, Jiang Lin, Guoliang Zhang, Miao Chen, Nida Fatima Moazzam, Wei Qian
Summary: This study investigates DNA methylation patterns and gene expression profiles in thyroid cancer tissue samples, shedding new light on the tumorigenesis of thyroid cancer. The study identifies differentially methylated CpG locations and regions, as well as genes associated with these regions. Additionally, the study reveals significant changes in methylation levels of specific genes in thyroid cancer patients. These findings are important for understanding the onset and development of thyroid cancer.
Article
Oncology
Richard Drexler, Ulrich Schueller, Alicia Eckhardt, Katharina Filipski, Tabea Hartung, Patrick N. Harter, Iris Dive, Marie-Therese Forster, Marcus Czabanka, Claudius Jelgersma, Julia Onken, Peter Vajkoczy, David Capper, Christin Siewert, Thomas Sauvigny, Katrin Lamszus, Manfred Westphal, Lasse Duehrsen, Franz L. Ricklefs
Summary: DNA methylation-based tumor classification allows for a more accurate distinction between subgroups of glioblastoma, but its clinical benefit remains inconclusive.
Article
Plant Sciences
Kexin Zhang, Xia Feng, Ying Liu, Yajun Yang, Xinyuan Hao, Dongliang Li, Xinchao Wang, Lu Wang
Summary: The study found that the young shoots of the temperature-sensitive cultivar 'Zhonghuang 2' (ZH2) were yellow at low temperature and green at high temperature due to changes in DNA methylation levels. DNA methylation affected gene expression levels, which in turn influenced the structure and function of chloroplasts and had a phenotypic impact on shoot and leaf color.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Neurosciences
James F. Lyon, Varshini Vasudevaraja, Kanish Mirchia, Jamie M. Walker, Robert J. Corona, Lawrence S. Chin, Ivy Tran, Matija Snuderl, Timothy E. Richardson, Mariano S. Viapiano
Summary: Glioblastoma (GBM) is the most common malignant primary central nervous system neoplasm in adults, with a universally poor prognosis. DNA methylation profiling has emerged as an important technique for classification of CNS tumors. This case highlights molecular diversity in GBM and demonstrates a novel use for methylation profiling in tracking tumor progression.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2021)
Article
Plant Sciences
Dong-ru Kang, Yi Zhu, Shuai-lei Li, Peng-hui Ai, Muhammad Ayoub Khan, Hong-xu Ding, Ying Wang, Zi-cheng Wang
Summary: This study investigates the effect of MET1 gene silencing on gene expression profile in Chrysanthemum x morifolium 'Zijingling', revealing significant changes in differentially expressed genes related to essential plant biological processes. While a sufficient number of candidate genes associated with flowering were identified, the overall number of genes with significant differences between transgenic and control lines was relatively low. This study sheds light on the transcriptional level interference of CmMET1 on chrysanthemum growth and development, providing a basis for further research on epigenetic regulation mechanisms in flower induction and development.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Spectroscopy
Zhiyan Sun, Xianhao Wu, Rui Tao, Tianyao Zhang, Xing Liu, Jiangfei Wang, Haibin Wan, Shaowen Zheng, Xiaoyan Zhao, Zhaohui Zhang, Pei Yang
Summary: This study established a predictive model for IDH mutation status in gliomas based on terahertz spectroscopy data. The results showed that gliomas with different IDH mutation status have distinct terahertz spectral features, indicating the potential of terahertz spectroscopy as a new approach for predicting IDH mutation status in gliomas.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Article
Plant Sciences
Zeyu Zhang, Huihui Wang, Yongsheng Wang, Feihu Xi, Huiyuan Wang, Markus Kohnen, Pengfei Gao, Wentao Wei, Kai Chen, Xuqing Liu, Yubang Gao, Ximei Han, Kaiqiang Hu, Hangxiao Zhang, Qiang Zhu, Yushan Zheng, Bo Liu, Ayaz Ahmad, Yau-Heiu Hsu, Steven E. Jacobsen, Lianfeng Gu
Summary: The study found that CHH methylation gradually accumulates during the transition from vegetative to reproductive growth in moso bamboo, with differentially methylated regions mainly occurring at transcription start and termination sites. Genes with CG methylation changes are enriched in 'vegetative to reproductive phase transition of meristem' GO categories, while circRNA flanking introns are hypermethylated and enriched in LTR retrotransposons.
Article
Biochemistry & Molecular Biology
Jinfeng Chen, Jingfei Cheng, Xiufei Chen, Masato Inoue, Yibin Liu, Chun-Xiao Song
Summary: Long-read sequencing provides valuable information on difficult-to-map genomic regions and can improve genome assembly when combined with short-read sequencing. This study presents a method called whole-genome long-read TAPS (wglrTAPS), which combines TET-assisted pyridine borane sequencing with PacBio single-molecule real-time sequencing. Application of wglrTAPS to mouse embryonic stem cells showed the ability to detect previously uncovered CpG sites in problematic genomic regions. This method enhances the use of third-generation sequencing technologies for DNA epigenetics.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Yongjian Sha, Qianqian Yan, Yan Tan, Xiaochun Wang, Hui Zhang, Guoqiang Yang
Summary: The aim of this study was to establish a radiomics model to predict the molecular subtype of IDH mut combined with MGMT meth in gliomas. The model can effectively provide important auxiliary value for the accurate diagnosis of tumour molecular typing, decision-making of the chemotherapy drug temozolomide, and prognosis assessment in clinical management.
Article
Oncology
Junsheng Li, Jia Wang, Yaowei Ding, Jizong Zhao, Wen Wang
Summary: The study indicated that SGSM1 was significantly down-regulated in lower-grade gliomas (LGGs), and functional enrichment analysis showed its correlation with immune response. Most immune cells and immune checkpoints were negatively correlated with SGSM1 expression. Kaplan-Meier analysis demonstrated that low SGSM1 expression was associated with poor outcomes in LGG and its subtypes. Cox regression analysis identified SGSM1 as an independent prognostic factor for patients with LGG.
Article
Pathology
Jia Chai, Tianqi Xu, Yanru Yang, Yuan Yuan, Junpeng Xu, Jin Liu, Kaijing Wang, Yao Lv, Jialin Chai, Yulin Kang, Ligang Chen, Junhui Qin, Qingge Jia, Mingyang Li
Summary: Esophageal squamous cell carcinoma (ESCC) is a common cancer with poor prognosis. This study found that overexpression of OTX1 is associated with the prognosis and tumorigenesis of ESCC.
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Article
Pathology
Shuai He, Qingge Jia, Lei Zhou, Zhe Wang, Mingyang Li
Summary: SIRT5 expression is associated with prognosis in breast cancer, and it promotes cell proliferation and metastasis through high glucose-dependent aerobic glycolysis.
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Article
Oncology
Kaijing Wang, Jie Wei, Jing Ma, Qingge Jia, Yixiong Liu, Jia Chai, Junpeng Xu, Tianqi Xu, Danhui Zhao, Yingmei Wang, Qingguo Yan, Shuangping Guo, Xinjian Guo, Feng Zhu, Linni Fan, Mingyang Li, Zhe Wang
Summary: TOPK and p-JAK2 are highly expressed in BL tissues. TOPK binds to and is phosphorylated by JAK2, playing a vital role in BL cell proliferation and tumorigenesis. The JAK2/TOPK/histone H3 axis is key in BL progression.
Article
Pathology
Yanru Yang, Yun Zhao, Guorui Sun, Saijie Zuo, Jia Chai, Tianqi Xu, Jin Liu, Lingfei Li, Junyang Song, Shoubin Qian, Yulin Kang, Fang Sui, Mingyang Li, Qingge Jia
Summary: The study found that FBXO39 is highly expressed in cervical squamous cell carcinoma and is closely related to patient prognosis. Further experiments confirmed that overexpression of FBXO39 promotes the proliferation, migration, and invasion of cancer cells. Experimental results on C-33A cells showed that downregulation of FBXO39 can inhibit tumor growth. These findings suggest that FBXO39 may serve as a therapeutic target for cervical squamous cell carcinoma (CESC).
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Review
Pathology
Guorui Sun, Yanru Yang, Jin Liu, Zizhao Gao, Tianqi Xu, Jia Chai, Junpeng Xu, Zhenge Fan, Tian Xiao, Qingge Jia, Mingyang Li
Summary: This review discusses the importance of cancer stem cells (CSCs) in the diagnosis and treatment of esophageal squamous cell carcinoma (ESCC). It outlines the known methods for isolation and verification of CSCs, as well as the significance of CSCs' biomarkers and signaling pathways.
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Article
Immunology
Junsheng Li, Jia Wang, Dongjing Liu, Chuming Tao, Jizong Zhao, Wen Wang
Summary: This study establishes a senescence-related signature to predict the prognosis of lower-grade glioma (LGG) and investigates its prognostic role. The results show that this signature is associated with the prognosis of LGG patients and may be related to immune infiltration level and immune checkpoint expression.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Pathology
Qingge Jia, Junyang Song, Tianqi Xu, Jin Liu, Jia Chai, Yanru Yang, Lingfei Li, Mingyang Li, Xinyuan Yang
Summary: ZIC5 expression is associated with clinical manifestations in cervical squamous cell carcinoma (CESC), and overexpression of ZIC5 promotes the proliferation and migration of CESC cells. ZIC5 may serve as a potential biomarker and therapeutic target for CESC patients.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Article
Pathology
Jian Liu, Yixi Xu, Tianqi Xu, Yixiong Liu, Jin Liu, Jia Chai, Yanru Yang, Peizhen Hu, Mingyang Li, Qingge Jia, Chen Zhang
Summary: Osteosarcoma is a common primary bone malignancy that can be effectively treated with a combination of chemotherapy and surgery. Osteosarcoma stem cells are more malignant than other cancer cells and play a crucial role in the response to therapy. In this study, researchers found that elevated levels of MUC1 promote cancer stemness and tumor metastasis in osteosarcoma. This suggests that targeting MUC1 could be a potential therapeutic strategy for osteosarcoma patients.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Review
Pathology
Tianqi Xu, Yixiong Liu, Zhiwei Zhao, Jin Liu, Jia Chai, Yanru Yang, Saijie Zuo, Mingyang Li, Qingge Jia
Summary: Ferroptosis is an iron-dependent form of cell death that is associated with the accumulation of lipid peroxidation markers. Numerous studies have focused on uncovering the oncogenic pathways and regulators of ferroptosis. The connection between iron metabolism and abnormal iron metabolism in CSCs synergistically positions ferroptosis as a promising target in combating CSCs and reversing resistance. Ferroptosis inducers have the potential to specifically kill CSCs in tumors, making ferroptosis a target for overcoming cancer resistances. By inducing ferroptosis and other cell death pathways in CSCs, the therapeutic outcome of cancer can be improved.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Article
Pathology
Jing Ma, Shaofei He, Mingyang Li, Yang Peng, Xinyu Yang, Ligang Chen, Qingge Jia, Yixiong Liu
Summary: This study found that RUNX1 is overexpressed in renal cell carcinoma and is associated with poor prognosis and shorter survival period. Experimental results showed that RUNX1 can promote the proliferation, migration, and invasion of tumor cells, and knocking down RUNX1 can inhibit these processes.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Article
Pathology
Lingfei Li, Yuxin Yin, Jinping Zhang, Xiaoxu Wu, Jin Liu, Jia Chai, Yanru Yang, Mingyang Li, Qingge Jia, Yixiong Liu
Summary: In this study, it was found that USP18 was up-regulated in glioblastoma, promoting the growth and proliferation of glioblastoma stem cells (GSCs), affecting the epithelial-mesenchymal transition (EMT), and being associated with poor clinical prognosis of patients.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Article
Pathology
Yanru Yang, Saijie Zuo, Wenqing Li, Man Di, Jin Liu, Jia Chai, Jingjing Wang, Yuan Yuan, Mingyang Li, Qingge Jia
Summary: TRIM21 is highly expressed in cervical squamous cell carcinoma (CESC) tissues compared with paracancerous tissues. The overexpression of TRIM21 promotes cell proliferation, migration, invasion, and stemness, while knockdown of TRIM21 inhibits tumor cell activities in CESC. Furthermore, TRIM21 expression levels are associated with individual prognostic factors and may serve as a poor predictor of prognosis for CESC.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Article
Pathology
Qingge Jia, Hongjie Wang, Xin Xiao, Yameng Sun, Xiao Tan, Jia Chai, Yanru Yang, Zhiyong Yin, Mingyang Li, Ke Wang, Jin Liu
Summary: The study revealed that UCHL1 expression in cervical squamous cell carcinoma (CESC) is correlated with prognosis, cancer stemness, proliferation, migration, and invasion. These findings suggest a potential novel therapeutic strategy for CESC treatment.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Article
Pathology
Na Hao, Mingyang Li, Jiachen Wang, Yichen Song, Yuelei Zhao, Ling Zhang, Xinyu Yang, Ligang Chen, Junchi Ma, Qingge Jia, Fang Sui
Summary: PGAP3 is overexpressed in breast cancer and correlates with key susceptibility genes, lymph node metastasis, and CD8 + T cell infiltration.
PATHOLOGY RESEARCH AND PRACTICE
(2023)