Cellular interactions and Ion channel signatures in atrial fibrillation remodeling: insights from single-cell analysis and machine learning by Bin He, Yan Cheng, Juan Wang, Ya Zhan, YanQun Liu

“…Ion channel-related genes were extracted from microarray datasets and analyzed for differential expression and functional relevance to AF pathology. …”
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Interferon-stimulated circHOMER1 attenuates antiviral innate immunity by Ao Zhang, Ranran Yao, Shijin Geng, Haiying Wang, Rong-Chun Tang, Hengxiang Yu, Rui Xu, Hong-Yan Chen, Yunxuan Zhou, Lan Zhang, Jun Zhang

“…These findings identify circHOMER1 as a novel interferon-stimulated circRNA that serves as a negative modulator of the antiviral innate immune response and is essential for immune homeostasis.IMPORTANCEA growing body of evidence suggests that circRNAs are involved in various physiological or pathological processes. Through circRNA microarray screening of virus-induced differentially expressed circRNAs, we identified an upregulated circRNA, circHOMER1. circHOMER1 is abundantly expressed in the brain. …”
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Integrated single-cell sequencing for the development of a GJA4-based precision immuno-prognostic model in melanoma by Yantao Ding, Si Xie, Wenyang Nie, Yun Bai, Tianyu Yao, Yixiao Wang, Jiajie Chen, Bo Liang, Yi Zhou, Hui Cheng, Zaixing Wang, Shengxiu Liu

“…Methods: We conducted an analysis of RNA-seq and microarray data obtained from the TCGA and GEO databases, alongside single-cell RNA sequencing (scRNA-seq) data from glioma patients within the GEO repository. …”
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Delineation of the Genetic Architecture and Clinical Polymorphism of 3q29 Duplication Syndrome: A Review of the Literature and a Report of Two Novel Patients With Single‐Gene BDH1... by A. A. Kashevarova, M. E. Lopatkina, O. Yu. Vasilyeva, D. A. Fedotov, A. D. Lobanov, E. A. Fonova, I. Z. Zhalsanova, A. A. Zarubin, O. A. Salyukova, E. O. Belyaeva, V. V. Petrova, E. G. Ravzhaeva, A. A. Agafonova, A. D. Cheremnykh, N. B. Torkhova, S. L. Vovk, I. N. Lebedev

“…Methods Patients were investigated by performing a cytogenetic analysis of GTG‐banded metaphases, aCGH with the SurePrint G3 Human CGH Microarray 8×60K, qPCR, FISH, and WES. Results Here, we report five new patients with atypical duplications overlapping with the 3q29 duplication syndrome region and no other genetic findings. …”
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Identification of Pivotal ceRNA Networks Associated with Stanford-A Aortic Dissection via Integrated Bioinformatics Analysis by Hu Y, Liu Z, Qin Y, Wu N, Yang T, Cheng X, Wang C, Wang X

“…This study attempts to elucidate the underlying molecular mechanisms of TAAD through lncRNA-associated competitive endogenous RNA (ceRNA) networks.Methods: In this study, aortic vascular of 5 TAAD and 5 control (ischemic heart disease) were subjected to lncRNA and mRNA microarray analysis, and differentially expressed mRNAs (DEGs) and differentially expressed lncRNAs (DELs) were identified. …”
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SFB flagellin mediates cell adhesion, endocytosis and immune regulation in germ-free mice by Huahai Chen, Huahai Chen, Huahai Chen, Huahai Chen, Huahai Chen, Liu Wu, Liu Wu, Xiongyu Cao, Xiongyu Cao, Zongyan Li, Zongyan Li, Renjun Zhu, Renjun Zhu, Xiaojing Wang, Jun Li, Jun Li, Jun Li, Zuzhang Wei, Zuzhang Wei, Dengfeng Yang, Dengfeng Yang, Dengfeng Yang, Yeshi Yin, Yeshi Yin

“…Bacterial counts, immunohistochemical analysis, the AAM-ISO-G1 and QAM-TH17–1 microarray systems, RNA sequencing and molecular docking were employed to assess the outcomes in this study.Results and discussionThe results of in vitro co-culture experiments demonstrated significantly improved bacterial adhesion capabilities mediated by SFB flagellin. …”
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Evaluation of Organoid‐Derived Exosomal microRNA as Liquid Biopsy for Colorectal Cancer: A Multicenter Cross‐Sectional Study by Atsuhiro Sasaki, Masatake Kuroha, Masaki Tosa, Seiichi Takahashi, Shinya Oomori, Eiki Nomura, Tatsuya Kikuchi, Motoyuki Onodera, Yuichiro Sato, Teruko Miyazawa, Hirofumi Chiba, Naonobu Yokoyama, Jun Kusaka, Daisuke Okamoto, Tomoyuki Handa, Mikako Sugimura, Masahiro Iwabuchi, Keiichiro Hiramoto, Hidekazu Shirota, Hideya Iwaki, Hiroshi Nagai, Yusuke Shimoyama, Takeo Naito, Rintaro Moroi, Hisashi Shiga, Yoichi Kakuta, Yoshitaka Kinouchi, Atsushi Masamune

“…Exosomes were isolated from conditioned media. miRNAs were extracted from exosomes and compared using microarray analysis. Exosomal miRNAs expression levels in the sera of healthy patients and patients with colorectal cancer were compared at a single institution. …”
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E2F2(E2F transcription factor 2) as a potential therapeutic target in meibomian gland carcinoma: evidence from functional and epigenetic studies by Wei Wang, Hetong Wang, Xun Liu, Fei Xu, Qin Tang, Chuanli Zhang, Jiaqi Lin, Limin Zhu, Tingting Lin

“…Tissue samples from 3 normal meibomian glands (MG) and 36 MGC patients were used to construct a tissue microarray. Functional assays were performed by modifying E2F2 expression, including CCK8, wound healing, Transwell, and analysis of epithelial-mesenchymal transition (EMT)-related markers. …”
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Eurycomalactone switched hepatocellular carcinoma cells into quiescence through 5’tRFAla/DVL/β-catenin pathway inhibition by Zhipeng Zhang, Yanmei Wu, Wenqiang Liang, Zhifang Liao, Hongbo Liao, Xingxing Xing, Wenxin Yi, Zixuan Liu, Yicheng Li, Mengya Shi, Dongling Lin, Ting Gu, Biao Wu, Mingzhi Zou, Huilai Miao, Xin Wu

“…Subsequently, two new tsRNAs, namely 5’tRFAla and 5’tiRNAAla, which match well with the mRNAs of two pivotal upstream regulators (DVL2 and DVL3) of β-catenin based on bioinformatics analyses, were detected to be significantly decreased in ELT-treated PLC/PRF/5 cells using Arraystar small RNA microarray analyses. Consistently, the concentrations of the DVL2 and DVL3 proteins were also found to be reduced by ELT. …”
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Identification and external validation of tumor DNA methylation panel for the recurrence risk stratification of stage II colon cancer by Tanwei Yuan, Dominic Edelmann, Víctor Moreno, Elisabeth Georgii, Lisa Barros de Andrade e Sousa, Helena Pelin, Xiaofeng Jiang, Jakob Nikolas Kather, Katrin E. Tagscherer, Wilfried Roth, Melanie Bewerunge-Hudler, Alexander Brobeil, Matthias Kloor, Hendrik Bläker, Hermann Brenner, Michael Hoffmeister

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Long Noncoding RNA Expression Profiles of Periodontal Ligament Stem Cells from the Periodontitis Microenvironment in Response to Static Mechanical Strain by Jia Liu, Yan Zhao, Qiannan Niu, Ni Qiu, Shuangyun Liu, Chunrong Li, Cuixia Li, Pei Miao, Libo Yan, Qiang Li, Zuolin Jin

“…First, we subjected PDLSCs obtained from healthy periodontal tissues (HPDLSCs) and PPDLSCs to static mechanical strain (SMS) with 12% elongation at 0.1 Hz frequency using an FX-4000T system and screened overall lncRNA profiles in both cell types by microarray. Among lncRNAs with a fold change FC>20.0, 27 lncRNAs were upregulated in strained HPDLSCs, and 16 lncRNAs (9 upregulated and 7 downregulated) were detected in strained PPDLSCs. …”
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The role of collagen type VI alpha 6 chain as a potential tumor suppressor in breast cancer: an immune regulation perspective by Jian-Di Li, Li-Li Deng, Jia-Yuan Luo, Chao-Hua Mo, Bang-Teng Chi, Wan-Ying Huang, Rong-Quan He, Di-Yuan Qin, Chang Song, Wen Zou, Gang Chen

“…Methods Immunohistochemical staining of COL6A6 was conducted on 136 breast cancer tissues and 50 non-breast-cancer controls in-house. Global microarray and high-throughput sequencing datasets were analyzed to confirm mRNA expression trends, supported by single-cell RNA sequencing for expression intensity and distribution. …”
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Chronic sleep deprivation induces plasma exosome-derived miR-150-5p downregulation as a novel mechanism involved in Parkinson’s disease progression by targeting DCLK1 by Li Liu, Xiangting Liu, Runze Zhang, Xiao Sun, Keping Zhang, Beibei Zheng, Ruoxi Yang, Kaiyue Yang, Guohua Song, Zhaoqiang Zhang

“…Levels of miRNA in exos were analyzed by gene expression profile microarray. Levels of miR-150-5p in exos and substantia nigra pars compacta (SNpc) were further confirmed by reverse transcription quantitative polymerase chain reaction (RT-qPCR). …”
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Inhibitory Effect of PRMT5/MTA Inhibitor on MTAP‐Deficient Glioma May Be Influenced by Surrounding Normal Cells by Yunjie Wang, Xiaohui Sun, Runchen Ma, Xiaofan Zhang, Shengmin Ji, Zhaofeng Liu, Gangqiang Yang, Hongbo Wang, Peng Zhang, Jianzhao Zhang, Jingwei Tian

“…Methods We first analyzed whether there were MTAP‐expressing normal intracerebral cells around MTAP‐deficient glioma tissues by paraffin‐embedded tissue microarray of human glioma specimens. Then, in vivo and in vitro models of MTAP‐deficient gliomas coexisting with neurons or glial cells were constructed for evaluating the effectiveness of the anti‐tumor effects of MRTX1719 in this setting. …”
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Metabolic‐Immune Suppression Mediated by the SIRT1‐CX3CL1 Axis Induces Functional Enhancement of Regulatory T Cells in Colorectal Carcinoma by Ruiyang Zi, Xiang Zhao, Limei Liu, Yijie Wang, Rui Zhang, Zhiheng Bian, Haoran Jiang, Taorui Liu, Yixin Sun, Han Peng, Xuesong Wang, Fanghao Lu, Chao Zhang, Fan Zhang, Qing Qin, Houjie Liang, Jianjun Li, Zhihao Wei, Yan Dong

“…Multiplex immunofluorescence (mIHC) analysis of a CRC tissue microarray confirmed the promoting effect of CX3CL1 on Treg infiltration. …”
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Improvement of bone regeneration by a synergistic combination of octacalcium phosphate and water glass by Won-Pyo Lee, Euisin Yang, Woong Kim, Riessa Nanda Mertamani, Hana Lee, Se Eun Kim, Kyung Mi Shim, Seong Soo Kang, Sukyoung Kim, Seok-Jun Kim, Jooseong Kim

“…After treating MG-63 cells with a W-OCP elution medium, changes in gene expression levels that promoted bone formation were verified via microarray analysis. From the results, W-OCP can be inferred that sodium and silicate ions in water glass play an important role in the recruitment of osteoblasts, significantly increasing the bone growth rate at the early implantation stages. …”
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Urinary TYROBP and HCK as genetic biomarkers for non-invasive diagnosis and therapeutic targeting in IgA nephropathy by Boji Xie, Shuting Pang, Yuli Xie, Yuli Xie, Qiuyan Tan, Shanshan Li, Mujia Jili, Mujia Jili, Yian Huang, Yian Huang, Binran Zhao, Hao Yuan, Hao Yuan, Junhao Mi, Junhao Mi, Junhao Mi, Xuesong Chen, Liangping Ruan, Hong Chen, Xiaolai Li, Boning Hu, Jing Huang, Rirong Yang, Rirong Yang, Wei Li

“…Bulk RNA sequencing (RNA-seq) of urine offers a promising approach for identifying molecular changes relevant to IgAN.MethodsWe performed bulk RNA-seq on 53 urine samples from 11 untreated IgAN patients and 11 healthy controls, integrating these data with public renal RNA-seq, microarray, and scRNA-seq datasets. Machine learning was used to identify key differentially expressed genes, with protein expression validated by immunohistochemistry (IHC) and drug-target interactions explored via molecular docking.ResultsUrine RNA-seq analysis revealed differential expression profiles, from which TYROBP and HCK were identified as key biomarkers using machine learning. …”
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MiR-145-5p arrests the cell cycle by modulating SMAD5/cyclin D1 to inhibit gastric cancer progression by Li Wang, Li Wang, Jianghong Guo, Caixia Lv, Luke Kong, Luke Kong, Jing Cui, Zhongshuai Wang, Yuanyuan Guo, Ruirui Jia, Tao Guan, Tao Guan, Baofeng Yu, Feng Li

“…PurposeThis study aimed to explore the dysregulation of miR-145-5p in gastric cancer (GC) and its effects on the proliferation and cell cycle of GC cells, exploring the potential regulatory mechanism of miR-145-5p in GC.MethodsIn this study, the TCGA database combined with Microarray was used to detect differentially expressed microRNA (miRNA) in GC tissues and cells. …”
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Cold exposure-induced plasma exosomes impair bone mass by inhibiting autophagy by Li-Min Lei, Fu-Xing-Zi Li, Xiao Lin, Feng Xu, Su-Kang Shan, Bei Guo, Ming-Hui Zheng, Ke-Xin Tang, Yi Wang, Qiu-Shuang Xu, Wen-Lu Ouyang, Jia-Yue Duan, Yun-Yun Wu, Ye-Chi Cao, Zhi-Ang Zhou, Si-Yang He, Yan-Lin Wu, Xi Chen, Zheng-Jun Lin, Yi Pan, Ling-Qing Yuan, Zhi-Hong Li

“…Rapamycin, a potent inducer of autophagy, can reverse cold exposure or CT-EXO-induced bone loss. Microarray sequencing revealed that cold exposure increases the miR-25-3p level in CT-EXO. …”
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Deciphering cholangiocarcinoma heterogeneity and specific progenitor cell niche of extrahepatic cholangiocarcinoma at single-cell resolution by Chunliang Liu, Xiang Wang, Erdong Liu, Yali Zong, Wenlong Yu, Youhai Jiang, Jianan Chen, Mingye Gu, Zhengyuan Meng, Jingfeng Li, Yang Liu, Yongjie Zhang, Jing Tang, Hongyang Wang, Jing Fu

“…Findings were validated using external multi-omics datasets, tissue microarray cohort, spatial RNA in situ sequencing, CCA patient-derived organoids (PDOs), and mouse models. …”
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