The analysis of gene co-expression network and immune infiltration revealed biomarkers between triple-negative and non-triple negative breast cancer by Yao Yi, Yao Yi, Yu Zhong, Yu Zhong, Lianhua Xie, Lianhua Xie, Shuxian Lu, Shuxian Lu, Yifeng Zhang, Yifeng Zhang

“…Lastly, we identified key transcription factors involved in macrophage infiltration and polarization in breast cancer using transcription factor enrichment analysis integrated with orthogonal omics.ResultsThe gene co-expression network and gene ontology analyses revealed 19 modules identified using the dataset GSE76275. …”
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iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control by Huanhuan Gao, Yi Zhu, Dongxue Wang, Zongxiang Nie, He Wang, Guibin Wang, Shuang Liang, Yuting Xie, Yingying Sun, Wenhao Jiang, Zhen Dong, Liqin Qian, Xufei Wang, Mengdi Liang, Min Chen, Houqi Fang, Qiufang Zeng, Jiao Tian, Zeyu Sun, Juan Xue, Shan Li, Chen Chen, Xiang Liu, Xiaolei Lyu, Zhenchang Guo, Yingzi Qi, Ruoyu Wu, Xiaoxian Du, Tingde Tong, Fengchun Kong, Liming Han, Minghui Wang, Yang Zhao, Xinhua Dai, Fuchu He, Tiannan Guo

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Deep application of controlled-release urea increases the yield and saponin content of Panax notoginseng by regulating soil nitrate distribution by Yun-xia Su, Yun-xia Su, Yun-xia Su, Ping Zhao, Li-jie Jia, Li-jie Jia, Li-jie Jia, Yuan-feng Cao, Guan-ze Liu, Guan-ze Liu, Jun-wen Chen, Jun-wen Chen, Sheng-chao Yang, Sheng-chao Yang, Yan-li Zhou, Guang-qiang Long, Guang-qiang Long, Guang-qiang Long

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Dietary Tannic Acid Promotes Growth Performance and Resistance Against <i>Aeromonas hydrophila</i> Infection by Improving the Antioxidative Capacity and Intestinal Health in the Ch... by Liqin Ji, Yisen Shangguan, Chen Chen, Chengqing Wei, Junxian Zhu, Xiaoyou Hong, Xiaoli Liu, Xinping Zhu, Wei Li

“…Integrative analyses of two omics revealed that 2 g/kg of TA mitigated inflammation by activating the PPAR signaling pathway and regulating the lipid metabolism via multiple pathways, such as steroid biosynthesis and α-linolenic acid metabolism. …”
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APOE Christchurch enhances a disease-associated microglial response to plaque but suppresses response to tau pathology by Kristine M. Tran, Nellie E. Kwang, Claire A. Butler, Angela Gomez-Arboledas, Shimako Kawauchi, Cassandra Mar, Donna Chao, Rocio A. Barahona, Celia Da Cunha, Kate I. Tsourmas, Zechuan Shi, Shuling Wang, Sherilyn Collins, Amber Walker, Kai-Xuan Shi, Joshua A. Alcantara, Jonathan Neumann, Duc M. Duong, Nicholas T. Seyfried, Andrea J. Tenner, Frank M. LaFerla, Lindsay A. Hohsfield, Vivek Swarup, Grant R. MacGregor, Kim N. Green

“…We used immunohistochemical and biochemical analysis along with single-cell spatial omics and bulk proteomics to explore the impact of the ApoeCh variant on AD pathological development and the brain’s response to plaques and tau. …”
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Downregulation of MerTK in circulating T cells of patients with non-proliferative diabetic retinopathy by Shimiao Bu, Shimiao Bu, Jiang-Yue Ling, Jiang-Yue Ling, Xiaojun Wu, Xiaojun Wu, Liting Zhang, Liting Zhang, Xiangyu Shi, Lang Huang, Zheng Zhao, Ying Yang, Zongqin Xiang, Yong U. Liu, Yong U. Liu, Yufeng Liu, Yuehong Zhang, Yuehong Zhang

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Chemogenomic Screening in a Patient‐Derived 3D Fatty Liver Disease Model Reveals the CHRM1‐TRPM8 Axis as a Novel Module for Targeted Intervention by Sonia Youhanna, Aurino M. Kemas, Shane C. Wright, Yi Zhong, Britta Klumpp, Kathrin Klein, Aikaterini Motso, Maurice Michel, Nicole Ziegler, Mingmei Shang, Pierre Sabatier, Aimo Kannt, Hongda Sheng, Nuria Oliva‐Vilarnau, Florian A. Büttner, Brinton Seashore‐Ludlow, Jonas Schreiner, Maike Windbergs, Martin Cornillet, Niklas K. Björkström, Andreas J. Hülsmeier, Thorsten Hornemann, Jesper V. Olsen, Yi Wang, Roberto Gramignoli, Michael Sundström, Volker M. Lauschke

“…The model closely mirrors disease‐relevant endpoints, such as steatosis, inflammation and fibrosis, and multi‐omics analyses show excellent alignment with biopsy data from 306 MASH patients and 77 controls. …”
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Gene Therapy for Inflammatory Cascade in Intrauterine Injury with Engineered Extracellular Vesicles Hybrid Snail Mucus‐enhanced Adhesive Hydrogels by Xiaotong Peng, Tao Wang, Bo Dai, Yiping Zhu, Mei Ji, Pusheng Yang, Jiaxin Zhang, Wenwen Liu, Yaxin Miao, Yonghang Liu, Shuo Wang, Jing Sun

“…STAT1‐mediated M1 macrophages are confirmed to secrete pro‐inflammatory cytokines to accelerate inflammatory cascade and IUA formation by multi‐omics analysis and experimental verification. However, clinically used hyaluronic acid (HA) hydrogels are prone to slip out of injury sites due to poor bio‐adhesion properties. …”
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Polymorphisms in immunosuppression-related genes are associated with AML by Mingying Li, Mingying Li, Jingjing Ye, Jingjing Ye, Mengyuan Chang, Mengyuan Chang, Lei Feng, Lei Feng, Tingting Liu, Tingting Liu, Di Zhang, Di Zhang, Yuyan Wu, Yuyan Wu, Yuechan Ma, Yuechan Ma, Guangqiang Meng, Guangqiang Meng, Chunyan Ji, Chunyan Ji, Tao Sun, Tao Sun

“…Despite new immunotherapeutic strategies entering standard clinical care for various tumors, progress in AML remains poor. Multi-omics analyses, such as single-cell transcriptomics, have revealed many potential new targets to improve AML prognosis from an immunological perspective.MethodsDNA from 307 AML patients and 316 healthy individuals were extracted. …”
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Targeted ErbB4 receptor activation prevents D-galactose-induced neuronal senescence via inhibiting ferroptosis pathway by Ji-Ji Dao, Ji-Ji Dao, Wei Zhang, Wei Zhang, Chong Liu, Chong Liu, Qian Li, Qian Li, Chen-Meng Qiao, Chen-Meng Qiao, Chun Cui, Chun Cui, Yan-Qin Shen, Yan-Qin Shen, Shuang-Xi Chen, Shuang-Xi Chen, Wei-Jiang Zhao, Wei-Jiang Zhao

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Gut mycobiome and neuropsychiatric disorders: insights and therapeutic potential by Ines Hadrich, Mariem Turki, Mariem Turki, Imen Chaari, Imen Chaari, Balkiss Abdelmoula, Rahma Gargouri, Nahed Khemakhem, Dhawia Elatoui, Fatma Abid, Sonda Kammoun, Sonda Kammoun, Mona Rekik, Mona Rekik, Samir Aloulou, Samir Aloulou, Mariem Sehli, Mariem Sehli, Aymen Ben Mrad, Aymen Ben Mrad, Sourour Neji, Fabian M. Feiguin, Jihene Aloulou, Jihene Aloulou, Nouha Bouayed Abdelmoula, Hayet Sellami, Hayet Sellami

“…Future research should integrate multi-omics approaches to unravel the complex interkingdom interactions within the gut ecosystem, paving the way for personalized medicine in mental health care.…”
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Comparison of differences in transcriptional and genetic profiles between intra-central nervous system and extra-central nervous system large B-cell lymphoma by Shu Wang, Hong Chen, Bo Dai, Kang Zheng, Jiajun Zheng, Yuqi Zhu, Yan Yuan, Tianling Ding, Qian Wang, Liqian Xie, Rui Feng, Fengping Zhu, Jianbin Xiang, Weiqun Ding, Hong Ding, Yuan Li, Xiaodong Gu, Kunpeng Wu, Yifan Yuan, Jianping Song, Dongxiao Zhuang, Haoshu Zhong, Hanfeng Wu, Ying Mao, Tong Chen

“…To explore its specific pathogenesis and therapeutic targets, we performed multi-omics sequencing on tumor samples from patients diagnosed with PCNS-DLBCL, secondary CNS-DLBCL or extracranial (ec) DLBCL.By single-cell RNA sequencing, highly proliferated and dark zone (DZ)-related B cell subclusters, MKI67_B1, PTTG1_B2 and BTG1_B3, were predominant significantly in PCNS-DLBCL. …”
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Brown Adipose Tissue undergoes pathological perturbations and shapes C2C12 myoblast homeostasis in the SOD1-G93A mouse model of Amyotrophic Lateral Sclerosis by Marco Rosina, Silvia Scaricamazza, Flaminia Riggio, Gianmarco Fenili, Flavia Giannessi, Alessandro Matteocci, Valentina Nesci, Illari Salvatori, Daniela F. Angelini, Katia Aquilano, Valerio Chiurchiù, Daniele Lettieri Barbato, Nicola Biagio Mercuri, Cristiana Valle, Alberto Ferri

“…In this study, we employed a multi-omics approach, including RNA sequencing (GEO identifier GSE273052) and proteomics (ProteomeXchange identifier PXD054147), to investigate the alterations in BAT and its EVs in the SOD1-G93A mouse model of ALS. …”
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Podophyllotoxin mediates hepatic toxicity via the C5a/C5aR/ROS/NLRP3 and cGMP/PKG/mTOR axis in rats based on toxicological evidence chain (TEC) concept by phosphoproteomic analysis by Chuanxin Liu, Xiaobin Huang, Jiao Kong, Xuejiao Li, Yuming Wang, Fangfang Zhang, Jiajia Duan

“…Histopathological examination revealed liver sinusoidal congestion in the liver tissue (AOE). Omics analysis revealed that hepatotoxicity primarily affected the complement-pyroptosis and cGMP-PKG-autophagy pathways. …”
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Slow Metabolism–Driven Amplification of Hepatic PPARγ Agonism Mediates Benzbromarone‐Induced Obesity‐Specific Liver Injury by Guanting Li, Yourong Hu, Han Zhao, Ziyu Peng, Xin Shang, Jia Zhang, Kunxin Xie, Meiwei Li, Xiaohang Zhou, Qinyao Zhou, Kai Li, Fang Zhou, Heyao Wang, Zhijian Xu, Jiali Liu, Peng Sun

“…In this study, through a combined multi‐omics, pharmacological, and pharmacokinetic approaches, it is found that BBR‐induced obesity‐specific DILI is primarily through the potentiation of peroxisome proliferator‐activated receptor gamma (PPARγ) signaling pathways. …”
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A noncanonical role of roX RNAs in autosomal epigenetic repression by Jianjian Li, Shuyang Xu, Zicong Liu, Liuyi Yang, Zhe Ming, Rui Zhang, Wenjuan Zhao, Huipai Peng, Jeffrey J. Quinn, Manyin Wu, Yushan Geng, Yuying Zhang, Jiazhi He, Minghai Chen, Nan Li, Ning-Yi Shao, Qing Ma

“…Here, using an integrative multi-omics approach, we show that roX RNAs not only govern the X chromosome but also target genes on autosomes that lack male-specific lethal (MSL) complex occupancy, together with Polycomb repressive complexes (PRCs). …”
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2-Hydroxyisobutyric acid targeted binding to MT-ND3 boosts mitochondrial respiratory chain homeostasis in hippocampus to rescue diabetic cognitive impairment by Minzhen Xie, Siqi Gu, Yan Liu, Haolin Yang, Yuqi Wang, Wei Yin, Yang Hong, Wanying Lu, Chengbing He, Lin Li, Limin Zhao, Jianjia Zhang, Heng Liu, Tian Lan, Shuijie Li, Qi Wang

“…Methods: Metabolic substances and differentially active metabolic pathways in the serum of diseased mice were identified based on multi-omics analysis. The nanoLC-Obitrap-MS technology was utilized to detect the content of selected small molecules with differential metabolic activity in the hippocampus and mitochondria of mice to evaluate their permeability through the blood-brain barrier (BBB) and outer mitochondrial membrane. …”
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DCAF13-mediated K63-linked ubiquitination of RNA polymerase I promotes uncontrolled proliferation in Breast Cancer by Zhi-Zhi Yang, Bing Yang, Haiyan Yan, Xingyu Ma, Bin Tian, Bingqi Zheng, Yong-Xian Chen, Yi-Ming Dong, Jinsi Deng, Ziling Zhan, Yanmei Shi, Jing Yuan Zhang, Daning Lu, Jie-Hua He, Yin Zhang, KaiShun Hu, Shuang Zhu, Keda Zhou, Yu-Chan Zhang, Yiqing Zheng, Dong Yin, Jian-You Liao

“…In this study, we perform a comprehensive multi-omics analysis and reveal that assembly and maturation factors (AMFs), a subclass of RiBPs, are upregulated at both RNA and protein levels in BC, correlating with poor patient outcomes. …”
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The study of interactome in Russian patients with Usher syndrome to select priority approaches in pathogenetically oriented treatment by M.E. Ivanova, D.S. Atarshchikov, A.M. Demchinsky, V.V. Strelnikov, D. Barh, G.V. Poryadin, L.M. Balashova, J.M. Salmasi

“…Salmasi⁶</b><br> </p> <p> <b>¹LLC “Oftalmic”, Moscow, Russian Federation</b> </p> <p> <b>²Central Clinical Hospital under Presidential Affairs, Moscow, Russian Federation</b> </p> <p> <b>³Autonomous nonprofit organization “Scientific and industrial laboratory “Sensor technology <br> </b><b>&nbsp; </b><b>for deafblind”, Moscow, Russian Federation</b> </p> <p> <b>⁴Research Centre for Medical Genetics, Moscow, Russian Federation</b> </p> <p> <b>⁵Institute of Integrative Omics and Applied Biotechnology (IIOAB), Bangalore, India</b> </p> <p> <b>⁶Pirogov Russian National Research Medical University, Moscow, Russian Federation</b> </p> <p> <b>⁷Non-profit partnership International Scientific and Practical Center for the Proliferation of </b><b>Tissues of Russia, Moscow, Russian Federation</b> </p> <p> <br> </p> <p> <i><b>Background</b>: Usher syndrome (USH) is a heterogeneous syndrome characterized by hearing loss and vision loss. …”
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Case of phenotype of optic nerve atrophy due to mutation in С19orf12 gene (neurodegeneration with the brain iron accumulation (nbia)) by M.E. Ivanova, V.V. Kadyshev, D.S. Atarshchikov, I.V. Zolnikova, N.P. Akchurina, N.K. Serova, F.A. Konovalov, E.R. Lozier, E.A. Pomerantseva, N.V. Vetrova, D. Barh, L.M. Balashova, J.M. Salmasi

“…Burdenko National Medical Research Center of Neurosurgery, Moscow, Russian <br> Federation</b> </p> <p> <b>⁶Independent Clinical Bioinformatics Laboratory, Moscow, Russian Federation</b> </p> <p> <b>⁷Center for Genetics and Reproductive Medicine “Genetiko”, Moscow, Russian <br> Federation</b> </p> <p> <b>⁸Institute of Integrative Omics and Applied Biotechnology (IIOAB), Bangalore, India</b> </p> <p> <b>⁹ Non-profit partnership International Scientific and Practical Center for the Proliferation <br> of Tissues of Russia, Moscow, Russian Federation</b> </p> <p> <b>¹⁰Pirogov Russian National Research Medical University, Moscow, Russian Federation</b> </p> <p> <i>The article describes the clinical case of optic atrophy due to a homozygous mutation in exon 3 of the C19orf12 gene (chr19: 30193863AACAGCCCCCCG&gt; A, rs515726204), the frequency of which in the ExAC control sample is 0.0074. …”
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