Integrated proteogenomic characterization of ampullary adenocarcinoma by Qiao Zhang, Xiaomeng Xu, Dongxian Jiang, Yunzhi Wang, Haixing Wang, Jiajun Zhu, Shaoshuai Tang, Ronghua Wang, Shuang Zhao, Kai Li, Jinwen Feng, Hang Xiang, Zhenmei Yao, Ning Xu, Rundong Fang, Wenjia Guo, Yu Liu, Yingyong Hou, Chen Ding

“…Genomic data illustrate that 4q loss causes fatty acid accumulation and cell proliferation. Proteomic analysis has revealed three distinct clusters (C-FAM, C-AD, C-CC), among which the most aggressive cluster, C-AD, is associated with the poorest prognosis and is characterized by focal adhesion. …”
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Hidden route of protein damage through oxygen-confined photooxidation by Seoyoon Kim, Eojin Kim, Mingyu Park, Seong Ho Kim, Byung-Gyu Kim, Seungjin Na, Victor W. Sadongo, W. C. Bhashini Wijesinghe, Yu-Gon Eom, Gwangsu Yoon, Hannah Jeong, Eunhye Hwang, Chaiheon Lee, Kyungjae Myung, Chae Un Kim, Jeong-Mo Choi, Seung Kyu Min, Tae-Hyuk Kwon, Duyoung Min

“…The effects of this photooxidative reaction appear to be extensive, impacting a wide range of cellular proteins, as supported by whole-cell proteomic analysis. This photooxidative mechanism may represent a latent oxidation pathway in human tissues directly exposed to visible light, such as skin and eyes.…”
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Deep phosphoproteomics of Klebsiella pneumoniae reveals HipA-mediated tolerance to ciprofloxacin. by Payal Nashier, Isabell Samp, Marvin Adler, Fiona Ebner, Lisa Thai Lê, Marc Göppel, Carsten Jers, Ivan Mijakovic, Sandra Schwarz, Boris Macek

“…Importantly, HipAkp overproduction leads to increased tolerance against ciprofloxacin, a commonly used antibiotic in the treatment of K. pneumoniae infections. Proteome and phosphoproteome analyses in the absence and presence of ciprofloxacin confirm that HipAkp has Ser/Thr kinase activity, auto-phosphorylates at S150, and shares multiple substrates with HipAec, thereby providing a valuable resource to clarify the molecular basis of tolerance and the role of Ser/Thr phosphorylation in this human pathogen.…”
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Proteostasis and Mitochondrial Role on Psychiatric and Neurodegenerative Disorders: Current Perspectives by Pablo Olivero, Carlo Lozano, Ramón Sotomayor-Zárate, Nicolás Meza-Concha, Marcelo Arancibia, Claudio Córdova, Wilfredo González-Arriagada, Ricardo Ramírez-Barrantes, Ivanny Marchant

“…Proteostasis alterations in the prefrontal cortex implicate proteome instability and accumulation of misfolded proteins. …”
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Alternative 3′ UTR polyadenylation is disrupted in the rNLS8 mouse model of ALS/FTLD by Randall J. Eck, Paul N. Valdmanis, Nicole F. Liachko, Brian C. Kraemer

“…Here, we identify significant disruptions to 3` UTR polyadenylation in the ALS/FTLD-TDP mouse model rNLS8 that correlate with changes in gene expression and protein levels through the re-analysis of published RNA sequencing and proteomic data. A subset of these changes are shared with TDP-43 knock-down mice suggesting depletion of endogenous mouse TDP-43 is a contributor to polyadenylation dysfunction in rNLS8 mice. …”
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Cytokine Patterns in Brain Tumour Progression by Radu Albulescu, Elena Codrici, Ionela Daniela Popescu, Simona Mihai, Laura Georgiana Necula, Daniel Petrescu, Mihaela Teodoru, Cristiana Pistol Tanase

“…The body’s response to cancer has many parallels with inflammation and repair; the inflammatory cells and cytokines present in tumours are more likely to contribute to tumour growth, progression, and immunosuppression, rather than in building an effective antitumour defence. Using new proteomic technology, we have investigated serum profile of pro- (IL-1β, IL-6, IL-8, IL-12, GM-CSF, and TNF-α) and anti-inflammatory cytokines (IL-4, IL-10), along with angiogenic factors (VEGF, bFGF) in order to assess tumoural aggressiveness. …”
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Molecular correlates for HPV-negative head and neck cancer engraftment prognosticate patient outcomes by Matthew Waas, Christina Karamboulas, Benson Z. Wu, Shahbaz Khan, Stephanie Poon, Jalna Meens, Meinusha Govindarajan, Amanda Khoo, Salvador Mejia-Guerrero, Annie Ha, Lydia Y. Liu, Kevin C. J. Nixon, Joseph Walton, Scott V. Bratman, Shao Hui Huang, David Goldstein, Federico Gaiti, Laurie Ailles, Thomas Kislinger

“…Here, we perform transcriptomic and proteomic profiling of 88 HNSCC patients and find the relationship between engraftment and clinical outcomes is recapitulated by molecular phenotype. …”
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The caterpillar Manduca sexta brain shows changes in gene expression and protein abundance correlating with parasitic manipulation of behaviour by McMillan LEM, Herbison RH, Biron DG, A Barkhouse, DW Miller, N Raun, Adamo SA

“…The host’s behaviour remains unchanged until the wasps exit the caterpillar, and then the caterpillar becomes a non-feeding “bodyguard” for the wasp cocoons. Using proteomic, transcriptomic and qPCR studies, we discovered an increase in antimicrobial peptide gene expression and protein abundance in the host central nervous system at the time of wasp emergence, correlating with the change in host behaviour. …”
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High-Dimensional Cox Regression Analysis in Genetic Studies with Censored Survival Outcomes by Jinfeng Xu

“…With the advancement of high-throughput technologies, nowadays high-dimensional genomic and proteomic data are easy to obtain and have become ever increasingly important in unveiling the complex etiology of many diseases. …”
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Activators of the 26S proteasome when protein degradation increases by Donghoon Lee

“…Abstract In response to extra- and intracellular stimuli that constantly challenge and disturb the proteome, cells rapidly change their proteolytic capacity to maintain proteostasis. …”
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Diagnostic and Prognostic Significance of Exosomes and Their Components in Patients With Cancers by Zinnat Ara Moni, Zahid Hasan, Md. Shaheen Alam, Nitai Roy, Farhadul Islam

“…On the contrary, tumor cells release more exosomes than normal cells, and these tumor‐specific exosomes can carry the genomic and proteomic signature contents of the tumor cells, which can act as tools for the diagnosis and prognosis of patients with cancers. …”
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Integrated multi-omics profiling reveals neutrophil extracellular traps potentiate Aortic dissection progression by Yu-Fei Zhao, Zi-Ang Zuo, Zhe-Yun Li, Ye Yuan, Shi-Chai Hong, Wei-Guo Fu, Bin Zhou, Li-Xin Wang

“…It is imperative to delve into the exploration of prognostic indicators to streamline the identification of individuals at elevated risk for postoperative AAEs, and therapeutic targets to optimize the efficacy of TEVAR for patients with AD. Here, we perform proteomic and single-cell transcriptomic analyses of peripheral blood and aortic lesions, respectively, from patients with AD and healthy subjects. …”
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Secretomes from Mesenchymal Stem Cells against Acute Kidney Injury: Possible Heterogeneity by Kenji Tsuji, Shinji Kitamura, Jun Wada

“…Over the past few decades, many studies identified trophic factors from MSCs, which attenuate renal injury in a variety of animal acute kidney injury models, including renal ischemia-reperfusion injury and drug-induced renal injury, using microarray and proteomic analysis. Nevertheless, these studies have revealed the heterogeneity of trophic factors from MSCs that depend on the cell origins and different stimuli including hypoxia, inflammatory stimuli, and aging. …”
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Cardiac repair using regenerating neonatal heart tissue-derived extracellular vesicles by Hanjing Li, Yining Liu, Yuqing Lin, Sijia Li, Chenlu Liu, Ao Cai, Wei Li, Wanyu Zhang, Xinlu Gao, Zhongyu Ren, Haoyu Ji, Yang Yu, Xiuxiu Wang, Wenya Ma, Ning Wang, Dan Zhao, Tianlong Li, Yu Liu, Benzhi Cai

“…Here, we report that EVs from regenerating neonatal heart tissues, after apical resection surgery (AR-Neo-EVs), exhibit stronger pro-proliferative, anti-apoptotic, and pro-angiogenesis activities than EVs from neonatal mouse cardiac tissues (Neo-EVs), effects which are absent in adult mouse heart-derived EVs (Adu-EVs). Proteomic analysis reveals the expression of Wdr75 protein, a regulator of p53, is higher in AR-Neo-EVs than in Neo-EVs. …”
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Harnessing Tumor Cell‐Derived Exosomes for Immune Rejection Management in Corneal Transplantation by Jieru Yang, Huanmin Kang, Yingyi Liu, Shan Lu, Huihui Wu, Bikui Zhang, Yan He, Wenhu Zhou

“…Utilizing murine corneal transplantation as a model, it is demonstrated that B16‐Exo significantly reduces immune rejection, evidenced by decreased corneal opacity, neovascularization, and immune dysregulation, while enhancing postoperative survival. Proteomic analyses reveal differential expression of pivotal proteins in B16‐Exo, notably the JAK2 protein within the JAK‐STAT signaling pathway, which has been mechanistically demonstrated to amplify the activity of myeloid‐derived suppressor cells (MDSCs) and inhibit T cell proliferation. …”
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<i>Helicobacter pylori</i> HP0135 Is a Small Lipoprotein That Has a Role in Outer Membrane Stability by Doreen Nguyen, Rachel G. Ivester, Kyle Rosinke, Timothy R. Hoover

“…The filament of the <i>H. pylori</i> flagellum is surrounded by a membranous sheath that is contiguous with the outer membrane. Proteomic analysis of isolated sheathed flagella from <i>H. pylori</i> B128 identified the lipoprotein HP0135 as a potential component of the flagellar sheath. …”
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An updated reference genome of Barbatula barbatula (Linnaeus, 1758) by Levente Laczkó, Nikoletta Andrea Nagy, Ágnes Nagy, Ágnes Maroda, Péter Sály

“…We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). …”
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Analysis of Toll-Like Receptors in Human Milk: Detection of Membrane-Bound and Soluble Forms by Chiara Cattaneo, Alice Caramaschi, Elena Uga, Michela Braghin, Gianluca Cosi, Chiara Peila, Maria C. Strozzi, Miriam Sabatini, Diego Gazzolo, Marcello Manfredi, Maria Cavaletto

“…Here, we investigated the presence of Toll-like receptors TLR1/2/4/6 in colostrum and mature milk of women who delivered before (preterm) or after (term) 37 weeks of gestational age, integrating classical immune-related techniques with proteomic LC-MS/MS analysis. We have detected immunoreactivity for TLRs mostly in preterm samples, even for TLR1 and TLR6, until now not described in human milk. …”
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Molecular Characterization of the Onset and Progression of Colitis in Inoculated Interleukin-10 Gene-Deficient Mice: A Role for PPARα by Bianca Knoch, Matthew P. G. Barnett, Janine Cooney, Warren C. McNabb, Diane Barraclough, William Laing, Shuotun Zhu, Zaneta A. Park, Paul MacLean, Scott O. Knowles, Nicole C. Roy

“…The aims were to (1) characterize colitis onset and progression using a histopathological, transcriptomic, and proteomic approach and (2) investigate links between PPARα and IL10 using gene network analysis. …”
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Targeting protein-protein interactions in drug discovery: Modulators approved or in clinical trials for cancer treatment by Cristina Camps-Fajol, Debora Cavero, Jordi Minguillón, Jordi Surrallés

“…Despite the development of PPI modulators is challenging, advances in the genetic, proteomic and computational level have facilitated their discovery and optimization. …”
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