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Exosome proteomes reveal glycolysis-related enzyme enrichment in primary canine mammary gland tumor compared to metastases Proteome Sci. (IF 2.0) Pub Date : 2024-02-28 Hui-Su Kim, Je-Yoel Cho
Numerous evidence has highlighted the differences between primary tumors and metastases. Nonetheless, the differences in exosomal proteins derived from primary tumor and metastases remain elusive. Here, we aimed to identify differentially expressed exosomal proteins from primary canine mammary gland tumor and metastases to understand how they shape their own tumor microenvironment. We clearly distinguished
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Comparative proteomics reveals different protein expression in platelets in patients with alcoholic liver cirrhosis Proteome Sci. (IF 2.0) Pub Date : 2024-01-26 Nima Haji Begli, Cora Freund, Karl-Heinz Weiss, Daniel Gotthardt, Andreas Wannhoff
The role of platelets in disease progression as well as the function of platelets as part of the haemostatic and immunological system in patients with liver cirrhosis is only incompletely understood. This is partly due to difficulties in assessing platelet function. Proteome analyses of platelets have been used to further investigate the role of platelets in other diseases. To assess possible changes
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Methionine enkephalin (MENK) protected macrophages from ferroptosis by downregulating HMOX1 and ferritin Proteome Sci. (IF 2.0) Pub Date : 2024-01-20 Jing Tian, Wenrui Fu, Zifeng Xie, Yuanlong Zhao, Haochen Yang, Jiafan Zhao
The aim of this work was to investigate the immunological effect of MENK by analyzing the protein spectrum and bioinformatics of macrophage RAW264.7, and to explore the relationship between macrophage and ferroptosis. We employed proteomic analysis to identify differentially expressed proteins (DEPs) between macrophages and macrophages intervened by MENK. A total of 208 DEPs were identified. Among
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Proteomic profile of tepary bean seed storage proteins in germination with low water potential Proteome Sci. (IF 2.0) Pub Date : 2024-01-09 Daniel Padilla-Chacón, Laura Campos-Patiño, Cecilia B. Peña-Valdivia, Antonio García-Esteva, José Cruz Jiménez-Galindo, Jorge Luis Pizeno-García
Tepary bean (Phaseolus acutifolius A. Gray) is one of the five species domesticated from the genus Phaseolus with genetic resistance to biotic and abiotic stress. To understand the mechanisms underlying drought responses in seed storage proteins germinated on water and polyethylene glycol (PEG-6000) at -0.49 MPa, we used a proteomics approach to identify potential molecular target proteins associated
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Upregulation of S100A8 in peripheral blood mononuclear cells from patients with depression treated with SSRIs: a pilot study Proteome Sci. (IF 2.0) Pub Date : 2023-12-04 Concepción Gamboa-Sánchez, Enrique Becerril-Villanueva, Samantha Alvarez-Herrera, Gabriela Leyva-Mascareño, Sandra L. González-López, Enrique Estudillo, Alberto E. Fernández-Molina, José Miguel Elizalde-Contreras, Eliel Ruiz-May, Aldo Segura-Cabrera, Janeth Jiménez-Genchi, Lenin Pavón, Sergio Roberto Zamudio, Gilberto Pérez-Sánchez
Major depressive disorder (MDD) affects more than 350 million people worldwide, and there is currently no laboratory test to diagnose it. This pilot study aimed to identify potential biomarkers in peripheral blood mononuclear cells (PBMCs) from MDD patients. We used tandem mass tagging coupled to synchronous precursor selection (mass spectrometry) to obtain the differential proteomic profile from a
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Systematic proteomics profiling of lysine crotonylation of the lung at Pseudoglandular and Canalicular phases in human fetus Proteome Sci. (IF 2.0) Pub Date : 2023-12-01 Wei Wang, Wei Shi, Yinglan Wang, Yane Yang, Ping Li, Zhipeng Zeng, Wenlong Hu, Yumei Chen, Donge Tang, Yong Dai
Lung tissue is an important organ of the fetus, and genomic research on its development has improved our understanding of the biology of this tissue. However, the proteomic research of developing fetal lung tissue is still very scarce. We conducted comprehensive analysis of two developmental stages of fetal lung tissue of proteomics. It showed the developmental characteristics of lung tissue, such
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TMT quantitative proteomics reveals key proteins relevant to microRNA-1-mediated regulation in osteoarthritis Proteome Sci. (IF 2.0) Pub Date : 2023-11-22 Pinpin Jiang, Dan Liang, Hang Wang, Raorao Zhou, Xianda Che, Linlin Cong, Penghua Li, Chunfang Wang, Wenjin Li, Xiaochun Wei, Pengcui Li
Osteoarthritis (OA) is the second-commonest arthritis, but pathogenic and regulatory mechanisms underlying OA remain incompletely understood. Here, we aimed to identify the mechanisms associated with microRNA-1 (miR-1) treatment of OA in rodent OA models using a proteomic approach. First, N = 18 Sprague Dawley (SD) rats underwent sham surgery (n = 6) or ACL transection (n = 12), followed at an interval
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Quantitative proteomics analysis reveals the key proteins related to semen quality in Niangya yaks Proteome Sci. (IF 2.0) Pub Date : 2023-10-24 Yaomei Wang, Yuchao Liu, Tingting Cao, Chunyuan Shi, Zili Ren, Yanling Zhao
Proteins related to sperm motility and sperm morphology have an important impact on sperm function such as metabolism, motility and fertilisation etc. An understanding of the key proteins related to semen quality in Niangya yaks would help to provide support for breeding. However, the key proteins that affect semen quality in Niangya yaks remain unclear. Herein, we applied tandem mass tag (TMT) labeling
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Label-free quantitative proteomic analysis of serum exosomes in mice with thoracic aortic aneurysm Proteome Sci. (IF 2.0) Pub Date : 2023-10-24 Jia Xu, Jiacheng Liu, Yibai Qu, Linhui Jiang, Rongxin Liang, Bohai Li, Lei Li, Yong Jiang
Thoracic aortic aneurysm (TAA) is a cardiovascular disease with high morbidity and mortality. However, the causes and mechanisms of TAA are not fully understood. Serum exosomes from mice with TAA were used to explore the markers associated with this disease. C57BL/6 mice were divided into three groups and given ordinary drinking water, ordinary drinking water plus a saline osmotic pump, or drinking
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Integrated proteome and malonylome analyses reveal the potential meaning of TLN1 and ACTB in end-stage renal disease Proteome Sci. (IF 2.0) Pub Date : 2023-10-13 Ruqi Tan, Dandan Li, Nan Hu, Jing Qiu, Zhipeng Zeng, Wanxia Cai, Yafang Zhong, Xinzhou Zhang, Pearl Pai, Kang Wang, Donge Tang, Yong Dai
End-stage renal disease (ESRD) is a condition that is characterized by the loss of kidney function. ESRD patients suffer from various endothelial dysfunctions, inflammation, and immune system defects. Lysine malonylation (Kmal) is a recently discovered post-translational modification (PTM). Although Kmal has the ability to regulate a wide range of biological processes in various organisms, its specific
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Effects of µ-Conotoxin GIIIB on the cellular activity of mouse skeletal musculoblast: combined transcriptome and proteome analysis Proteome Sci. (IF 2.0) Pub Date : 2023-10-12 Han-xi Wu, Pei-min He, Rui Jia
µ-Conotoxin GIIIB (µ-CTX GIIIB) is a polypeptide containing three disulfide bridges, produced by the sea snail Conus geographus. This study was aimed to explored the cytotoxic effects of µ-CTX GIIIB on mouse skeletal musculoblast (Sol8). Sol8 cells were exposed to ouabain and veratridine to establish the cell injury model, and then treated with µ-CTX GIIIB. CCK-8 was adopted to evaluate the cytotoxicity
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Proteomic analysis of neonatal mouse hearts shows PKA functions as a cardiomyocyte replication regulator Proteome Sci. (IF 2.0) Pub Date : 2023-10-11 Lizhi Hu, Minglu Liang, Qin Jiang, Youming Jie, Long Chen, Fengxiao Zhang
The ability of the adult mammalian heart to regenerate can save the cardiac muscle from a loss of function caused by injury. Cardiomyocyte regeneration is a key aspect of research for the treatment of cardiovascular diseases. The mouse heart shows temporary regeneration in the first week after birth; thus, the newborn mouse heart is an ideal model to study heart muscle regeneration. In this study,
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Proteomic analysis of ceftazidime and meropenem-exposed Pseudomonas aeruginosa ATCC 9027 Proteome Sci. (IF 2.0) Pub Date : 2023-09-28 Hong Loan Ngo, Thuc Quyen Huynh, Nguyen Bao Vy Tran, Ngoc Hoa Binh Nguyen, Thi Hang Tong, Thi Truc Ly Trinh, Van Dung Nguyen, Prem Prakash Das, Teck Kwang Lim, Qingsong Lin, Thi Thu Hoai Nguyen
Pseudomonas aeruginosa is well known for its intrinsic ability to resist a wide range of antibiotics, thus complicates treatment. Thus, understanding the response of the pathogen to antibiotics is important for developing new therapies. In this study, proteomic response of P. aeruginosa to the commonly used anti-pseudomonas antibiotics, ceftazidime (Caz) and meropenem (Mem) was investigated. P. aeruginosa
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Analysis of differential membrane proteins related to matrix stiffness-mediated metformin resistance in hepatocellular carcinoma cells Proteome Sci. (IF 2.0) Pub Date : 2023-09-22 Xiangyu Gao, Jiali Qian, Yang Zhang, Heming Wang, Jiefeng Cui, Yehong Yang
Our previous work shows that increased matrix stiffness not only alters malignant characteristics of hepatocellular carcinoma (HCC) cells, but also attenuates metformin efficacy in treating HCC cells. Here, we identified differential membrane proteins related to matrix stiffness-mediated metformin resistance for better understand therapeutic resistance of metformin in HCC. Differential membrane proteins
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Insight into the underlying molecular mechanism of dilated cardiomyopathy through integrative analysis of data mining, iTRAQ-PRM proteomics and bioinformatics Proteome Sci. (IF 2.0) Pub Date : 2023-09-22 Hongli Xiong, Zhe Zheng, Congcong Zhao, Minzhu Zhao, Qi Wang, Peng Zhang, Yongguo Li, Ying Zhu, Shisheng Zhu, Jianbo Li
DCM is a common cardiomyopathy worldwide, which is characterized by ventricular dilatation and systolic dysfunction. DCM is one of the most widespread diseases contributing to sudden death and heart failure. However, our understanding of its molecular mechanisms is limited because of its etiology and underlying mechanisms. Hence, this study explored the underlying molecular mechanism of dilated cardiomyopathy
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PRM-based quantitative proteomics analysis of altered HSP abundance in villi and decidua of patients with early missed abortion Proteome Sci. (IF 2.0) Pub Date : 2023-08-16 Xiao-Fang Chen, Xiao-Qing Chen, Hai-Lian Luo, Li-Na Xia, Shu-Hui Huang, Qi Chen
In this study, we aimed to identify differentially expressed heat shock protein (HSP) profiles in the villi and decidua from patients with early missed abortion (EMA). By using high-throughput and high-precision parallel reaction monitoring (PRM)-based targeted proteomics techniques, this study examined the abundance of HSPs in the villi and decidua of 10 patients with EMA and 10 controls. Moreover
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Serum proteomic identification and validation of two novel atherosclerotic aortic aneurysm biomarkers, profilin 1 and complement factor D Proteome Sci. (IF 2.0) Pub Date : 2023-08-05 Yusuke Murakami, Mitsuhiro Nishigori, Hiroaki Yagi, Tsukasa Osaki, Masaki Wakabayashi, Manabu Shirai, Cheol Son, Yutaka Iba, Kenji Minatoya, Kengo Kusano, Tsutomu Tomita, Hatsue Ishibashi-Ueda, Hitoshi Matsuda, Naoto Minamino
Effective diagnostic biomarkers for aortic aneurysm (AA) that are detectable in blood tests are required because early detection and rupture risk assessment of AA can provide insights into medical therapy and preventive treatments. However, known biomarkers for AA lack specificity and reliability for clinical diagnosis. We performed proteome analysis of serum samples from patients with atherosclerotic
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Altered levels of transthyretin in human cerebral microdialysate after subarachnoid haemorrhage using proteomics; a descriptive pilot study Proteome Sci. (IF 2.0) Pub Date : 2023-07-07 Fredrik Ginstman, Bijar Ghafouri, Peter Zsigmond
Subarachnoid haemorrhage (SAH) is one of the most severe forms of stroke in which delayed cerebral ischemia is one of the major complications. Neurointensive care aims at preventing and treating such complications and identification of biomarkers of early signs of ischemia might therefore be helpful. We aimed at describing proteome profile in cerebral microdialysate in four patients with aneurysmal
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Data-independent acquisition-based mass spectrometry(DIA-MS) for quantitative analysis of patients with chronic hepatitis B Proteome Sci. (IF 2.0) Pub Date : 2023-06-06 Bo Wang, Qian Zhang, Lili Wu, Cunliang Deng, Meiyan Luo, Yu Xie, Gang Wu, Wen Chen, Yunjian Sheng, Peng Zhu, Gang Qin
Chronic hepatitis B is a significant public health problem and complex pathologic process, and unraveling the underlying mechanisms and pathophysiology is of great significance. Data independent acquisition mass spectrometry (DIA-MS) is a label-free quantitative proteomics method that has been successfully applied to the study of a wide range of diseases. The aim of this study was to apply DIA-MS for
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Purification and proteomic analysis of potent fibrinolytic enzymes extracted from Lumbricus rubellus Proteome Sci. (IF 2.0) Pub Date : 2023-05-08 Laurentia Stephani, Puji Rahayu, Debbie Retnoningrum, Maggy Thenawidjaja Suhartono, Heni Rachmawati, Raymond R. Tjandrawinata
Lumbrokinase derived from earthworms, Lumbricus rubellus is known to have fibrinolytic enzymes that have potential as therapeutic drugs due to its ability to dissolve fibrin. The current study is aimed to purify the Lumbrokinase from L. rubellus and identify its protein component. Water extract of local earthworm Lumbricus rubellus revealed several proteins. Therefore, to identify its protein component
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Proteomics identifies differentially expressed proteins in glioblastoma U87 cells treated with hederagenin Proteome Sci. (IF 2.0) Pub Date : 2023-04-29 Yesen Zhang, Yi Han, Yuchun Shang, Xiangyu Wang, Jiwei Sun
We investigated differentially expressed proteins (DEPs) in human glioblastoma U87 cells after treatment with hederagenin as a therapeutic screening mechanism and provided a theoretical basis for hederagenin in treating glioblastoma. The Cell Counting Kit 8 assay was used to analyze the inhibitory effect of hederagenin on the proliferation of U87 cells. Protein was identified by tandem mass tags and
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Proteomics profiling for the global and acetylated proteins of papillary thyroid cancers Proteome Sci. (IF 2.0) Pub Date : 2023-04-26 Wei Wei, Yuezhang Wu, Dong-Dong Chen, Yuntao Song, Guohui Xu, Qi Shi, Xiao-Ping Dong
Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy cancer among the malignancies of thyroid. Despite of wide usages of proteomics in PTC, the profile of acetylated proteins in PTC remains unsettled, which is helpful for understanding the carcinogenesis mechanism and identifying useful biomarkers for PTC. The surgically removed specimens of cancer tissues (Ca-T) and adjacent normal
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Effects of Atractylodes lancea extracts on intestinal flora and serum metabolites in mice with intestinal dysbacteriosis Proteome Sci. (IF 2.0) Pub Date : 2023-04-15 BaiNian Zhang, Lan Bu, Hui Tian, ZhangQiang You, MingHai Zhao, Jie Tian, YuanYuan Zhang, Qian Wang, ChengJia Tan, Yu Cao, DaRen Feng, ZhenPeng Xi
This study aims to explore the effect of an extract of Atractylodes lancea (A. lancea) on antibiotics-induced intestinal tract disorder and the probable therapeutic mechanisms employed by this extract to ameliorate these disorders. Three days after acclimatization, nine male and nine female specific-pathogen-free (SPF) mice were randomly assigned into three groups: Group C (normal saline), Group M
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Proteomics analysis of methionine enkephalin upregulated macrophages against infection by the influenza-A virus Proteome Sci. (IF 2.0) Pub Date : 2023-04-11 Wenrui Fu, Zifeng Xie, Mei Bai, Zhen Zhang, Yuanlong Zhao, Jing Tian
Macrophages have a vital role in phagocytosis and antiviral effect against invading influenza viruses. Previously, we found that methionine enkephalin (MENK) inhibited influenza virus infection by upregulating the “antiviral state” of macrophages. To investigate the immunoregulatory mechanism of action of MENK on macrophages, we employed proteomic analysis to identify differentially expressed proteins
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Isolation and proteomic profiling of urinary exosomes from patients with colorectal cancer Proteome Sci. (IF 2.0) Pub Date : 2023-02-09 Ling Ma, Haijiao Yu, Yubing Zhu, Kaiyu Xu, Aimin Zhao, Lei Ding, Hong Gao, Man Zhang
Exosomes in the body fluid are effective cell-derived membranous structures transferring various molecules to mediate intercellular communication. The expression of protein in the urinary exosomes from the colorectal cancer (CRC) patients could reflect the characteristics of tumorigenesis. The urinary exosomes with globular membrane structure, the size of 30 ~ 100 nm and positive expression of CD9
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Quantitative proteomics analysis revealed the potential role of lncRNA Ftx in cardiomyocytes Proteome Sci. (IF 2.0) Pub Date : 2023-01-05 Sun, Xiangfei, Jiang, Ying, Li, Qingbao, Tan, Qi, Dong, Mingliang, Cai, Bi’e, Zhang, Di, Zhao, Qi
This study aims to decode the proteomic signature of cardiomyocytes in response to lncRNA Ftx knockdown and overexpression via proteomic analysis, and to study the biological role of lncRNA Ftx in cardiomyocytes. The expression level of the lncRNA Ftx in cardiomyocytes cultured in vitro was intervened, and the changes in protein levels in cardiomyocytes were quantitatively detected by liquid chromatography-mass
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Proteomic Analysis of Protective Effects of Dl-3-n-Butylphthalide against mpp + -Induced Toxicity via downregulating P53 pathway in N2A Cells Proteome Sci. (IF 2.0) Pub Date : 2023-01-03 Zhao, Yuan, Zhang, Jian, Zhang, Yidan, Li, Shuyue, Gao, Ya, Chang, Cui, Liu, Xiang, Xu, Lei, Yang, Guofeng
Dl-3-n-butylphthalide (NBP) is an important medial therapy for acute ischemic stroke in China. Recent studied have revealed that NBP not only rescued the loss of dopaminergic neurons in cellular and animal models of Parkinson's disease (PD), but also could improve motor symptoms in PD patients. However, the protective mechanism is not fully understood. P53 is a multifunctional protein implicated in
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Responses of the tree peony (Paeonia suffruticosa, Paeoniaceae) cultivar ‘Yu Hong’ to heat stress revealed by iTRAQ-based quantitative proteomics Proteome Sci. (IF 2.0) Pub Date : 2022-12-29 Ma, Jin, Wang, Qun, Wei, Ling-Ling, Zhao, Yu, Zhang, Guo-Zhe, Wang, Jie, Gu, Cui-Hua
Horticulture productivity has been increasingly restricted by heat stress from growing global warming, making it far below the optimum production capacity. As a popular ornamental cultivar of tree peony, Paeonia suffruticosa ‘Yu Hong’ has also been suffering from heat stress not suitable for its optimal growth. To better understand the response mechanisms against heat stress of tree peony, investigations
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TMT-based quantitative proteomics analysis of the effects of Jiawei Danshen decoction myocardial ischemia-reperfusion injury Proteome Sci. (IF 2.0) Pub Date : 2022-12-14 Zhu, Xiang-Mei, Tan, Yang, Shi, Yu-He, Li, Qing, Zhu, Jue, Liu, Xiang-Dan, Tong, Qiao-Zhen
Every year, approximately 17 million people worldwide die due to coronary heart disease, with China ranking second in terms of the death toll. Myocardial ischemia-reperfusion injury (MIRI) significantly influences cardiac function and prognosis in cardiac surgery patients. Jiawei Danshen Decoction (JWDSD) is a traditional Chinese herbal prescription that has been used clinically for many years in China
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Profiles of transcriptome and metabolic pathways after hypobaric hypoxia exposure Proteome Sci. (IF 2.0) Pub Date : 2022-09-24 Xu, Jin, Chen, Wen-jie, Wang, Zhan, Xin, Ming-yuan, Gao, Shen-han, Liu, Wen-jing, Wang, Kai-kun, Ma, Jing-wei, Yan, Xin-zong, Ren, Yan-ming
Hypoxia is a risk factor for non-alcoholic fatty liver diseases, leading to permanent imbalance of liver lipid homeostasis and steatohepatitis. However, a detailed understanding of the metabolic genes and pathways involved remains elusive. In vivo experiments were designed to analyze body weight and lipid metabolism changes of rats under hypoxia. After this, we combined microarray analysis and gene
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A combined protein toxin screening based on the transcriptome and proteome of Solenopsis invicta Proteome Sci. (IF 2.0) Pub Date : 2022-09-21 Cai, Liuyang, Yang, Fengling, Wang, Yongfang, Yang, Jishun, Zhu, Yina, Ma, Xueqi, Höfer, Juan, Wang, Yichao, Ma, Yajun, Xiao, Liang
Multi-omics technology provides a good tool to analyze the protein toxin composition and search for the potential pathogenic factors of Solenopsis invicta, under the great harm of the accelerated invasion in southern China. Species collection, functional annotation, toxin screening, and 3D modeling construction of three interested toxins were performed based on the successfully constructed transcriptome
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Effect of downregulated citrate synthase on oxidative phosphorylation signaling pathway in HEI-OC1 cells Proteome Sci. (IF 2.0) Pub Date : 2022-09-07 Xu, Xiaowen, Liu, Yue, Luan, Jun, Liu, Rongrong, Wang, Yan, Liu, Yingying, Xu, Ang, Zhou, Bingxin, Han, Fengchan, Shang, Wenjing
Citrate Synthase (Cs) gene mutation (locus ahL4) has been found to play an important role in progressive hearing loss of A/J mice. HEI-OC1 cells have been widely used as an in vitro system to study cellular and molecular mechanisms related to hearing lose. We previously reported the increased apoptosis and the accumulation of reactive oxygen species in shRNACs-1429 cells, a Cs low-expressed cell model
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Tear proteomics analysis of patient suffered from delayed mustard gas keratopathy Proteome Sci. (IF 2.0) Pub Date : 2022-08-10 Parvin, Shahram, Shahriary, Alireza, Aghamollaei, Hossein, Gh, B. Fatemeh Nobakht M., Bagheri, Hasan, Ghanei, Mostafa, Daryabari, Seyed-Hashem, Jadidi, Khosrow, Arabfard, Masoud
Understanding the molecular and cellular mechanisms involved in the pathogenesis of ocular injured induced by mustard gas can help better identify complications and discover appropriate therapies. This study aimed to analyze the proteomics of tears of chemical warfare victims with mustard gas ocular injuries and compare it with healthy individuals. In this case-control research, 10 mustard gas victims
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Phosphoproteome profiling of mouse liver during normal aging Proteome Sci. (IF 2.0) Pub Date : 2022-08-05 Liu, Jiang-Feng, Wu, Yue, Yang, Ye-Hong, Wu, Song-Feng, Liu, Shu, Xu, Ping, Yang, Jun-Tao
Aging is a complex biological process accompanied by a time-dependent functional decline that affects most living organisms. Omics studies help to comprehensively understand the mechanism of aging and discover potential intervention methods. Old mice are frequently obese with a fatty liver. We applied mass spectrometry-based phosphoproteomics to obtain a global phosphorylation profile of the liver
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A risk score model based on TGF-β pathway-related genes predicts survival, tumor microenvironment and immunotherapy for liver hepatocellular carcinoma Proteome Sci. (IF 2.0) Pub Date : 2022-06-22 Liao, Jingsheng, Liu, Qi, Chen, Jingtang, Lu, Zhibin, Mo, Huiting, Jia, Jun
Transforming growth factor-beta (TGF-β) signal is an important pathway involved in all stages of liver hepatocellular carcinoma (LIHC) initiation and progression. Therefore, targeting TGF- β pathway may be a potential therapeutic strategy for LIHC. Prediction of patients’ tumor cells response requires effective biomarkers. From 54 TGF-β-related genes, this research determined the genes showing the
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Identification of different proteins binding to Na, K-ATPase α1 in LPS-induced ARDS cell model by proteomic analysis Proteome Sci. (IF 2.0) Pub Date : 2022-06-09 Wen, Xu-Peng, Long, Guo, Zhang, Yue-Zhong, Huang, He, Liu, Tao-Hua, Wan, Qi-Quan
Acute respiratory distress syndrome (ARDS) is characterized by refractory hypoxemia caused by accumulation of pulmonary fluid, which is related to inflammatory cell infiltration, impaired tight junction of pulmonary epithelium and impaired Na, K-ATPase function, especially Na, K-ATPase α1 subunit. Up until now, the pathogenic mechanism at the level of protein during lipopolysaccharide- (LPS-) induced
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A novel nanobody as therapeutics target for EGFR-positive colorectal cancer therapy: exploring the effects of the nanobody on SW480 cells using proteomics approach Proteome Sci. (IF 2.0) Pub Date : 2022-05-16 Lamtha, Thomanai, Krobthong, Sucheewin, Yingchutrakul, Yodying, Samutrtai, Pawitrabhorn, Gerner, Christopher, Tabtimmai, Lueacha, Choowongkomon, Kiattawee
The epidermal growth factor receptor (EGFR) overexpression is found in metastatic colorectal cancer (mCRC). Targeted molecular therapies such as monoclonal antibodies (mAbs) and tyrosine kinase inhibitors (TKI) are becoming more precise, targeting specifically for cancer therapeutics. However, there are adverse effects of currently available anti-EGFR drugs, including drug-resistant and side effects
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Quantitative proteomic analysis of cerebrospinal fluid reveals CD163, A2M and full-length APP as potential diagnostic biomarkers of paediatric bacterial meningitis Proteome Sci. (IF 2.0) Pub Date : 2022-05-06 Luo, Ting, Yang, Sai, Chen, Yan, Liu, Shulei, Yang, Liming, Hu, Nanfei, Ma, Ye, Qiu, Jun, Wang, Kewei, Li, Liping, Tan, Lihong
Bacterial meningitis (BM) is a life-threatening infectious disease of the central nervous system in infants and children. To date, no diagnostic methods for the early and precise diagnosis of paediatric BM have been developed. A label-free cerebrospinal fluid (CSF) quantitative proteomic analysis of 8 patients with confirmed or suspected BM, 9 patients with confirmed or suspected viral meningitis (VM)
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Long noncoding RNA Ftx regulates the protein expression profile in HCT116 human colon cancer cells Proteome Sci. (IF 2.0) Pub Date : 2022-04-30 Jia, Ruzhen, Song, Lulu, Fei, Zhiqiang, Qin, Chengyong, Zhao, Qi
The long noncoding RNA (lncRNA) five prime to Xist (Ftx) is involved in distant metastasis in colorectal cancer (CRC). This study aimed to investigate Ftx alteration-induced proteomic changes in the highly metastatic CRC cell line HCT116. Tandem mass tag (TMT)-based proteomics analysis was performed to detect the differential protein expression in Ftx-overexpressing and Ftx-silenced HCT116 cells. The
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TMT-based proteomics analysis of the cerebral cortex of TauT knockout rats Proteome Sci. (IF 2.0) Pub Date : 2022-04-25 Xia, Yiming, Huang, Xiaoling, Mo, Lidong, Wang, Chen, Fan, Weijia, Huang, Huiling
Taurine serves a variety of nutritional and physiological roles, and it is mostly transported in cells via taurine transporter (TauT). The effect of taurine transporter in cerebral cortex is still unknown. We employed TMT label-based proteomics to find differences in proteins in the cerebral cortex of TauT knockout rats in this investigation. The goal of this research was to see how TauT deletion affected
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Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer Proteome Sci. (IF 2.0) Pub Date : 2022-04-09 Li, Lingling, Liu, Hui, Li, Yan, Guo, Chunmei, Wang, Bing, Shen, Dan, Zhang, Qiao, Ding, Chen
The surveillance and therapy of early-stage cancer would be better for patients’ prognosis. However, the extreme trace amount of tissue samples in different stages have limited in portraying the characterization of early-stage cancer. Therefore, we focused on and presented comprehensive proteomic and phosphoproproteomic profiling of the trace FFPE samples from early-stage gastrointestinal cancer, and
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Predicting protein–protein interactions between banana and Fusarium oxysporum f. sp. cubense race 4 integrating sequence and domain homologous alignment and neural network verification Proteome Sci. (IF 2.0) Pub Date : 2022-03-29 Fang, Hui, Zhong, Cheng, Tang, Chunyan
The pathogen of banana Fusarium oxysporum f. sp. cubense race 4(Foc4) infects almost all banana species, and it is the most destructive. The molecular mechanism of the interactions between Fusarium oxysporum and banana still needs to be further investigated. We use both the interolog and domain-domain method to predict the protein–protein interactions (PPIs) between banana and Foc4. The predicted protein
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Identification and validation of serum autoantibodies in children with B-cell acute lymphoblastic leukemia by serological proteome analysis Proteome Sci. (IF 2.0) Pub Date : 2022-02-02 Yu, Runhong, Yang, Shiwei, Liu, Yufeng, Zhu, Zunmin
B-cell acute lymphoblastic leukemia (B-ALL) is the most common malignancy of childhood. Even though significant progresses have been made in the treatment of B-ALL, some pediatric B-ALL have still poor prognosis. The identification of tumor autoantibodies may have utility in early cancer diagnosis and immunotherapy. In this study, we used serological proteome analysis (SERPA) to screen serum autoantibodies
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Analysis of plasma proteins using 2D gels and novel fluorescent probes: in search of blood based biomarkers for Alzheimer’s disease Proteome Sci. (IF 2.0) Pub Date : 2022-01-26 Laffoon, Scott B., Doecke, James D., Roberts, Anne M., Vance, Jennifer A., Reeves, Benjamin D., Pertile, Kelly K., Rumble, Rebecca L., Fowler, Chris J., Trounson, Brett, Ames, David, Martins, Ralph, Bush, Ashley I., Masters, Colin L., Grieco, Paul A., Dratz, Edward A., Roberts, Blaine R.
The Australian Imaging and Biomarker Lifestyle (AIBL) study of aging is designed to aid the discovery of biomarkers. The current study aimed to discover differentially expressed plasma proteins that could yield a blood-based screening tool for Alzheimer’s disease. The concentration of proteins in plasma covers a vast range of 12 orders of magnitude. Therefore, to search for medium to low abundant biomarkers
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TMT-based quantitative proteomic profiling of human monocyte-derived macrophages and foam cells Proteome Sci. (IF 2.0) Pub Date : 2022-01-03 Zhang, Yali, Fu, Yu, Jia, Linying, Zhang, Chenyang, Cao, Wenbin, Alam, Naqash, Wang, Rong, Wang, Weirong, Bai, Liang, Zhao, Sihai, Liu, Enqi
Cardiovascular diseases remain the leading cause of morbidity and mortality worldwide, most of which are caused by atherosclerosis. Discerning processes that participate in macrophage-to-foam cell formation are critical for understanding the basic mechanisms underlying atherosclerosis. To explore the molecular mechanisms of foam cell formation, differentially expressed proteins were identified. Human
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First comprehensive proteome analysis of lysine crotonylation in Streptococcus agalactiae, a pathogen causing meningoencephalitis in teleosts Proteome Sci. (IF 2.0) Pub Date : 2021-11-10 Chen, Xinjin, Fan, Bolin, Fan, Chenlong, Wang, Zhongliang, Wangkahart, Eakapol, Huang, Yucong, Huang, Yu, Jian, Jichang, Wang, Bei
Streptococcus agalactiae is a common colonizer of the rectovaginal tract and lead to infectious diseases of neonatal and non-pregnant adults, which also causes infectious disease in fish and a zoonotic risk as well. Lysine crotonylation (Kcr) is a kind of histone post-translational modifications discovered in 2011. In yeast and mammals, Kcr function as potential enhancers and promote gene expression
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The proteomics analysis of the effects of Zhishi Rhubarb soup on ischaemic stroke Proteome Sci. (IF 2.0) Pub Date : 2021-11-10 Zhang, Jing-Hua, Shao, Yue-Jia, Hui, Zhen, Wang, Su-Lei, Huang, Chi, Zhao, Yang
Stroke has always been a major threat worldwide but is most severe in China, with 2.5 million new stroke cases each year and 7.5 million stroke survivors, placing a heavy burden on the social and national health care systems. Zhishi Rhubarb Soup (ZRS) is a traditional Chinese medicine (TCM) that has been used clinically for many years in China. To explore the potential mechanism of ZRS in the treatment
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Quantitative proteomics by iTRAQ-PRM based reveals the new characterization for gout Proteome Sci. (IF 2.0) Pub Date : 2021-10-11 Chen, Guangqi, Cheng, Jiafen, Yu, Hanjie, Huang, Xiao, Bao, Hui, Qin, Ling, Wang, Ling, Song, Yaxiang, Liu, Xinying, Peng, Ai
Gout is a common and complex form of immunoreactive arthritis based on hyperuricemia, while the symptoms would turn to remission or even got worse. So, it is hard to early identify whether an asymptomatic hyperuricemia (AHU) patient will be susceptible to get acute gout attack and it is also hard to predict the process of gout remission to flare. Here, we report that the plasma proteins profile can
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Comparison of false-discovery rates of various decoy databases Proteome Sci. (IF 2.0) Pub Date : 2021-09-18 Lee, Sangjeong, Park, Heejin, Kim, Hyunwoo
The target-decoy strategy effectively estimates the false-discovery rate (FDR) by creating a decoy database with a size identical to that of the target database. Decoy databases are created by various methods, such as, the reverse, pseudo-reverse, shuffle, pseudo-shuffle, and the de Bruijn methods. FDR is sometimes over- or under-estimated depending on which decoy database is used because the ratios
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Analysis of allergen components and identification of bioactivity of HSP70 in pollen of Populus deltoides Proteome Sci. (IF 2.0) Pub Date : 2021-09-03 Guo, Wei, Zhan, Xiaodong, Jiang, Feng, Xi, Yilong
Allergies caused by pollen from Populus deltoides are common, but the allergic components are still unclear. The total proteins in pollen of P. deltoides were analyzed by proteomics, and the potential allergens were identified via the WHO/IUIS database and the allergenOnline database retrieval. One target protein was screened by bioinformatics and expressed in Escherichia coli. The biological activity
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iTRAQ-based proteomic analysis of sperm reveals candidate proteins that affect the quality of spermatozoa from boars on plateaus Proteome Sci. (IF 2.0) Pub Date : 2021-07-30 Zhao, Yanling, Wang, Yaomei, Guo, Feipeng, Lu, Bo, Sun, Jiale, Wang, Jianzhou, Ren, Zili
Tibetan pigs (TP) exhibit heritable adaptations to their hypoxic environments as a result of natural selection. However, candidate proteins that affect the sperm quality of boars on plateaus have not yet been clearly investigated. In this study, to reveal the candidate proteins that affect the quality of spermatozoa of boars on plateaus, we analyzed the sperm quality using computer-assisted semen analysis
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Comparative proteomics analysis reveals differentially accumulated proteins associated with male and female A. chinensis var. chinensis bud development Proteome Sci. (IF 2.0) Pub Date : 2021-04-22 Yu Zhang, Yuexing Wang, Wanying Zhou, Shimao Zheng, Wenhui Zhang
Kiwifruit (Actinidia chinensis var. Chinensis) is abundant with vitamin C and is a rapidly developing crop in China, New Zealand, and other countries. It has been widely used as a raw material for food and kiwifruit wine. Among these, A. chinensis var. chinensis and A. chinensis var. deliciosa are the most valuable kiwifruit in production. Kiwifruit is a typical dioecious plant and its female and male
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Proteomics and ultrastructural analysis of Hermetia illucens (Diptera: Stratiomyidae) larval peritrophic matrix Proteome Sci. (IF 2.0) Pub Date : 2021-04-09 Yu-Bo Lin, Jing-Jing Rong, Xun-Fan Wei, Zhuo-Xiao Sui, Jinhua Xiao, Da-Wei Huang
The black soldier fly (Hermetia illucens) has significant economic potential. The larvae can be used in financially viable waste management systems, as they are voracious feeders able to efficiently convert low-quality waste into valuable biomass. However, most studies on H. illucens in recent decades have focused on optimizing their breeding and bioconversion conditions, while information on their
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Label-free quantitative proteomics of Sorghum bicolor reveals the proteins strengthening plant defense against insect pest Chilo partellus Proteome Sci. (IF 2.0) Pub Date : 2021-04-02 Vaijayanti A. Tamhane, Surhud S. Sant, Abhilash R. Jadhav, Abdul R. War, Hari C. Sharma, Abdul Jaleel, Akanksha S. Kashikar
Spotted stem borer- Chilo partellus - a Lepidopteran insect pest of Sorghum bicolor is responsible for major economic losses. It is an oligophagous pest, which bores through the plant stem, causing ‘deadheart’ and hampering the development of the main cob. We applied a label-free quantitative proteomics approach on three genotypes of S. bicolor with differential resistance/ susceptibility to insect
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Non-targeted proteomics of acute respiratory distress syndrome: clinical and research applications Proteome Sci. (IF 2.0) Pub Date : 2021-03-20 Xu-Peng Wen, Yue-Zhong Zhang, Qi-Quan Wan
Acute respiratory distress syndrome (ARDS) is characterized by refractory hypoxemia caused by accumulation of pulmonary fluid with a high mortality rate, but the underlying mechanism is not yet fully understood, causing absent specific therapeutic drugs to treat with ARDS. In recent years, more and more studies have applied proteomics to ARDS. Non-targeted studies of proteomics in ARDS are just beginning
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Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture Proteome Sci. (IF 2.0) Pub Date : 2021-03-09 Huiyi Song, Ni Lou, Jianjun Liu, Hong Xiang, Dong Shang
Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. To explore the relevant protein abundance changes after E. coli and LGG coculture
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Quantitative proteomic profiling of Cervicovaginal fluid from pregnant women with term and preterm birth Proteome Sci. (IF 2.0) Pub Date : 2021-02-15 Young Eun Kim, Kwonseong Kim, Han Bin Oh, Sung Ki Lee, Dukjin Kang
Preterm birth (PTB) is one of major causes of perinatal mortality and neonatal morbidity, but knowledge of its complex etiology is still limited. Here we present cervicovaginal fluid (CVF) protein profiles of pregnant women who subsequently delivered at spontaneous preterm or term, aiming to identify differentially expressed CVF proteins in PTB and term birth. The CVF proteome of women who sequentially
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ITRAQ-based quantitative proteomic analysis of Fusarium moniliforme (Fusarium verticillioides) in response to Phloridzin inducers Proteome Sci. (IF 2.0) Pub Date : 2021-01-14 Rong Zhang, Weitao Jiang, Xin Liu, Yanan Duan, Li Xiang, Yanfang Wang, Yuanmao Jiang, Xiang Shen, Xuesen Chen, Chengmiao Yin, Zhiquan Mao
Apple replant disease (ARD) has been reported from all major fruit-growing regions of the world, and is often caused by biotic factors (pathogen fungi) and abiotic factors (phenolic compounds). In order to clarify the proteomic differences of Fusarium moniliforme under the action of phloridzin, and to explore the potential mechanism of F. moniliforme as the pathogen of ARD, the role of Fusarium spp
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Malonyl-proteome profiles of Staphylococcus aureus reveal lysine malonylation modification in enzymes involved in energy metabolism Proteome Sci. (IF 2.0) Pub Date : 2021-01-12 Yanan Shi, Jingjing Zhu, Yan Xu, Xiaozhao Tang, Zushun Yang, Aixiang Huang
Protein lysine malonylation, a novel post-translational modification (PTM), has been recently linked with energy metabolism in bacteria. Staphylococcus aureus is the third most important foodborne pathogen worldwide. Nonetheless, substrates and biological roles of malonylation are still poorly understood in this pathogen. Using anti-malonyl-lysine antibody enrichment and high-resolution LC-MS/MS analysis
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A quantitative proteomics analysis for small molecule Stemazole’s effect on human neural stem cells Proteome Sci. (IF 2.0) Pub Date : 2020-12-09 Huajun Li, Yubo Zhang, Jing Zhang, Chaoran Zhao, Yizi Zhu, Mei Han
Stemazole is a novel small molecule that has been suggested to have the ability to protect multiple stem cells. The proliferation-promoting activity and promising neuroprotective effects of stemazole make it a prospective drug for neurodegenerative disease treatment. Since previous studies have shown that it protective effect in extreme conditions, to understand more aspects of stemazole, in this study