Therapeutic effects of platelet-derived extracellular vesicles on viral myocarditis correlate with biomolecular content by Danielle J. Beetler, Danielle J. Beetler, Danielle J. Beetler, Presley Giresi, Damian N. Di Florio, Damian N. Di Florio, Damian N. Di Florio, Jessica J. Fliess, Elizabeth J. McCabe, Molly M. Watkins, Molly M. Watkins, Molly M. Watkins, Vivian Xu, Matthew E. Auda, Katelyn A. Bruno, Katelyn A. Bruno, Emily R. Whelan, Emily R. Whelan, Emily R. Whelan, Stephen P. C. Kocsis, Brandy H. Edenfield, Sierra A. Walker, Sierra A. Walker, Sierra A. Walker, Logan P. Macomb, Kevin C. Keegan, Angita Jain, Angita Jain, Angita Jain, Andrea C. Morales-Lara, Isha Chekuri, Anneliese R. Hill, Houssam Farres, Joy Wolfram, Joy Wolfram, Atta Behfar, Atta Behfar, Paul G. Stalboerger, Andre Terzic, Andre Terzic, Leslie T. Cooper, DeLisa Fairweather, DeLisa Fairweather, DeLisa Fairweather

“…Proteome and miR sequencing of EVs revealed that PEV miRs specifically targeted antiviral, Toll-like receptor (TLR)4, and inflammasome pathways known to contribute to myocarditis while pmPEV contained general immunoregulatory miRs.DiscussionThese differences in EV content corresponded to the differing anti-inflammatory effects of the two types of EVs on viral myocarditis.…”
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Chromosome-level genome assembly of Monolepta hieroglyphica, two-spotted leaf beetle (Coleoptera: Chrysomelidae) by Hao He, Yongxin Zhao, Dengyu Zheng, Huiyun Kuang, Fei Shen, Kang He, Haiyan Zhang, Changjiang Zhao, Lu Jiang, Da Xiao, Su Wang, Zhenying Wang, Shuai Zhan, Jianhua Wei, Xiaozeng Yang, Zhongyi Wu, Chun Zhang

“…The completeness of the final reported genome and proteome were assessed by BUSCO and show high values of 99.4% and 95.2%, respectively. …”
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Transcriptomic analysis of Andrias davidianus meat and experimental validation for exploring its bioactive components as functional foods by Changge Guan, Zhenglin Tan, Shucheng Li, Yi Wang, Naoyuki Yamamoto, Chong Zhang, Songjun Wang, Junjie Chen, Xin-Hui Xing

“…In this study, we illustrated full-length transcriptome sequencing to interpret the proteome of CGS meat and obtain 10703 coding DNA sequences. …”
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Inhibition of tumour necrosis factor alpha by Etanercept attenuates Shiga toxin-induced brain pathology by Robin Christ, Devon Siemes, Shuo Zhao, Lars Widera, Philippa Spangenberg, Julia Lill, Stephanie Thiebes, Jenny Bottek, Lars Borgards, Andreia G. Pinho, Nuno A. Silva, Susana Monteiro, Selina K. Jorch, Matthias Gunzer, Bente Siebels, Hannah Voss, Hartmut Schlüter, Olga Shevchuk, Jianxu Chen, Daniel R. Engel

“…In this study, we investigated the role of tumour necrosis factor alpha (TNF-α) for microglial activation and brain pathology using a preclinical mouse model of EHEC infection. LC–MS/MS proteomics of mice injected with a combination of Shiga toxin (Stx) and lipopolysaccharide (LPS) revealed extensive alterations of the brain proteome, in particular enrichment of pathways involved in complement activation and coagulation cascades. …”
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Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands by Dekker, Joannes A. A., Mylopotamitaki, Dorothea, Verbaas, Annemieke, Sinet-Mathiot, Virginie, Presslee, Samantha, McCarthy, Morgan L., Olsen, Morten Tange, Olsen, Jesper V., van den Hurk, Youri, Brattinga, Joris, Welker, Frido

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Multi-omics analysis of hexaploid triticale that show molecular responses to salt stress during seed germination by Dongxia Wang, Jiedong Li, Shiming Li, Jiongjie Fu, Baolong Liu, Baolong Liu, Baolong Liu, Dong Cao, Dong Cao, Dong Cao

“…After integrating GWAS-target genes with transcriptomics and proteomics approaches that the candidate gene late embryogenesis abundant protein 14 (LEA14) was up-regulated at the transcriptomic and proteomic levels. …”
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Overexpressing the ClpC AAA+ unfoldase accelerates developmental cycle progression in Chlamydia trachomatis by Aaron A. Jensen, Saba Firdous, Lei Lei, Derek J. Fisher, Scot P. Ouellette

“…We hypothesize that proteases are essential for mediating differentiation by allowing remodeling of the proteome as the organism transitions from one functional form to another. …”
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hnRNPU-mediated pathogenic alternative splicing drives gastric cancer progression by Guoguo Jin, Yanming Song, Shaobo Fang, Mingyang Yan, Zhaojie Yang, Yang Shao, Kexin Zhao, Meng Liu, Zhenwei Wang, Zhiping Guo, Zigang Dong

“…Abstract Background Alternative splicing (AS) is a process that facilitates the differential inclusion of exonic sequences from precursor messenger RNAs, significantly enhancing the diversity of the transcriptome and proteome. In cancer, pathogenic AS events are closely related to cancer progression. …”
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APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence by Jingyi Xie, Daniel G. Chen, William Chour, Rachel H. Ng, Rongyu Zhang, Dan Yuan, Jongchan Choi, Michaela McKasson, Pamela Troisch, Brett Smith, Lesley Jones, Andrew Webster, Yusuf Rasheed, Sarah Li, Rick Edmark, Sunga Hong, Kim M. Murray, Jennifer K. Logue, Nicholas M. Franko, Christopher G. Lausted, Brian Piening, Heather Algren, Julie Wallick, Andrew T. Magis, Kino Watanabe, Phil Mease, Philip D. Greenberg, Helen Chu, Jason D. Goldman, Yapeng Su, James R. Heath

“…Starting with 951 putative antigens representing a comprehensive survey of the SARS-CoV-2 viral proteome, we utilize APMAT for the capture and single cell analysis of CD8 T cells from 62 HLA A*02:01 COVID-19 participants. …”
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Bioelectric stimulation outperforms brain derived neurotrophic factor in promoting neuronal maturation by María del Pilar Diego-Santiago, María Ujué González, Esther María Zamora Sánchez, Nuria Cortes-Carrillo, Carlos Dotti, Francesc Xavier Guix, Sahba Mobini

“…ES with large enough accumulated charge significantly enriched EV proteome associated with neural development and function. …”
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Discovery of a novel highly specific, fully human PSCA antibody and its application as an antibody-drug conjugate in prostate cancer by Xiaojie Chu, Seungmin Shin, Du-San Baek, Liyong Zhang, Alex Conard, Megan Shi, Ye-Jin Kim, Cynthia Adams, Maggie Hines, Xianglei Liu, Chuan Chen, Zehua Sun, Dontcho V. Jelev, John W. Mellors, Dimiter S. Dimitrov, Wei Li

“…The structure-based affinity maturation yielded a high-affinity binder, F12, which is highly specific and does not bind to 6,000 human membrane proteins based on a membrane proteome array assay. F12 targets PSCA amino acids 63–69 as tested by the peptide scanning microarray, and it cross-reacts with the murine PSCA. …”
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Biochemical characterization of the Escherichia coli surfaceome: a focus on type I fimbriae and flagella by Devon W. Kavanaugh, Adeline Sivignon, Yannick Rossez, Zina Chouit, Christophe Chambon, Christophe Chambon, Louane Béal, Mathilde Bonnet, Michel Hébraud, Michel Hébraud, Yann Guérardel, Hang Thi Thu Nguyen, Nicolas Barnich

“…While the exact identity of the glycan(s) and their site of attachment currently elude detection by conventional glycomics/glycoproteomics, the current findings highlight a potential additional layer of complexity of the surface (glyco) proteome of the commensal or adhesive and invasive E. coli strains studied.…”
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Kaempferol protects against high-salt-induced hypertension and vascular endothelial injury by inhibiting ferroptosis through the ATF4/ACSL4 pathway by Qiuer Liang, Minghao Chen, Guangtian Chen, Pengli Xu, Lai Kwan Lam, Pengcheng Xie, Ting Xie, Wanqing Tu, Tianhao Liu, Xiaopeng Peng, Haoyao Yuan, Liguo Chen, Ya Xiao

“…Surface plasmon resonance and molecular docking analyses revealed that Kae directly binds to ATF4, while proteome microarray and co-immunoprecipitation assays demonstrated that ATF4 interacts with ACSL4 in HAECs. …”
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Prediction of potential drug targets and key inhibitors (ZINC67974679, ZINC67982856, and ZINC05668040) against Rickettsia felis using integrated computational approaches by Sudais Rahman, Hsien Liu, Mohibuallah Shah, Mashal M. Almutairi, Iram Liaqat, Tetsuya Tanaka, Chien-Chin Chen, Chien-Chin Chen, Chien-Chin Chen, Chien-Chin Chen, Abdulaziz Alouffi, Abid Ali

“…This study employed a comprehensive subtractive proteomics analysis of the R. felis proteome, aiming to identify essential, non-host homologous, and pathogen-specific proteins, which were subsequently evaluated as potential new drug targets. …”
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Extracellular vesicles (EVs) in seminal plasma of buffalo bulls possess spermatozoa specific fertility associated proteins and enzymes by Rakesh Kumar, Mir Ahmad, Bala Subramaniam, Ankit Pal, Aditya Patel, Shiva Shiva, Vitika Chauhan, Seema Karanwal, Mukesh Bhakat, Tirtha K. Datta

“…Finally, LC-MS/MS-based high throughput proteome was performed to identify the differential abundance of protein cargo in seminal EVs of contrasting fertility bulls. …”
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Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins by Rodriguez Palomo, Ismael, Nair, Bharath, Chiang, Yun, Dekker, Joannes, Dartigues, Benjamin, Mackie, Meaghan, Evans, Miranda, Macleod, Ruairidh, Olsen, Jesper V., Collins, Matthew J.

“…We tested different reference database choices, a targeted dairy protein one, and the whole bovine proteome and the three digestion options (tryptic-, semi-tryptic- and non-specific searches), in order to evaluate the effects of search space and the identification of peptides. …”
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Rational Design of Biocompatible Ir(III) Photosensitizer to Overcome Drug‐Resistant Cancer via Oxidative Autophagy Inhibition by Mingyu Park, Jung Seung Nam, Taehyun Kim, Gwangsu Yoon, Seoyoon Kim, Chaiheon Lee, Chae Gyu Lee, Sungjin Park, Kochan S. Bejoymohandas, Jihyeon Yang, Yoon Hee Kwon, Yoo Jin Lee, Jeong Kon Seo, Duyoung Min, Taiho Park, Tae‐Hyuk Kwon

“…Also, the biological mechanisms for autophagy inhibition via lysosomal oxidation are explored. Proteome analyses reveal significant oxidation of proteins essential for autophagy, including lysosomal and fusion‐mediator proteins. …”
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ERK activation waves coordinate mechanical cell competition leading to collective elimination via extrusion of bacterially infected cells by Lara Hundsdorfer, Marie Muenkel, Raul Aparicio-Yuste, Julio Cesar Sanchez-Rendon, Maria Jose Gomez-Benito, Aylin Balmes, Tilman E. Schäffer, Ana Velic, Yi-Ting Yeh, Iordania Constantinou, Kathryn Wright, Gizem Özbaykal Güler, Dominik Brokatzky, Boris Maček, Serge Mostowy, Effie E. Bastounis

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Longitudinal omics data and preclinical treatment suggest the proteasome inhibitor carfilzomib as therapy for ibrutinib-resistant CLL by Lavinia Arseni, Gianluca Sigismondo, Haniyeh Yazdanparast, Johanne U. Hermansen, Norman Mack, Sibylle Ohl, Verena Kalter, Murat Iskar, Mathias Kalxdorf, Dennis Friedel, Mandy Rettel, Yashna Paul, Ingo Ringshausen, Eric Eldering, Julie Dubois, Arnon P. Kater, Marc Zapatka, Philipp M. Roessner, Eugen Tausch, Stephan Stilgenbauer, Sascha Dietrich, Mikhail M. Savitski, Sigrid S. Skånland, Jeroen Krijgsveld, Peter Lichter, Martina Seiffert

“…A comparative analysis of exome, transcriptome and proteome of sorted leukemic murine cells during treatment and after relapse suggests alterations in the proteasome activity as a driver of ibrutinib resistance. …”
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Mitochondrial dysfunction-driven AMPK-p53 axis activation underpins the anti-hepatocellular carcinoma effects of sulfane sulfur by Xue Zheng, Yuhua Luo, Rui Huo, Yiwen Wang, Youbang Chen, Mianrong Chen, Qi Zhao, Kexin Li, Hanyi Zhang, Xiaotong Li, Xiang Li, Hui Zhang, Zaopeng He, Li Huang, Chun-tao Yang

“…We utilized bioinformatics algorithms for clustering, function enrichment, feature screening and survival analysis on proteomic data from the Cancer Proteome Atlas (CPTAC) and transcriptomic data from the Cancer Genome Atlas (TCGA). …”
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