Towards designing improved cancer immunotherapy targets with a peptide-MHC-I presentation model, HLApollo by William John Thrift, Nicolas W. Lounsbury, Quade Broadwell, Amy Heidersbach, Emily Freund, Yassan Abdolazimi, Qui T. Phung, Jieming Chen, Aude-Hélène Capietto, Ann-Jay Tong, Christopher M. Rose, Craig Blanchette, Jennie R. Lill, Benjamin Haley, Lélia Delamarre, Richard Bourgon, Kai Liu, Suchit Jhunjhunwala

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Acquisition of Fc-afucosylation of PfEMP1-specific IgG is age-dependent and associated with clinical protection against malaria by Mary Lopez-Perez, Zakaria Seidu, Mads Delbo Larsen, Wenjun Wang, Jan Nouta, Manfred Wuhrer, Gestur Vidarsson, Michael F. Ofori, Lars Hviid

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The role of multiomics in revealing the mechanism of skin repair and regeneration by Shaoyan Shi, Xuehai Ou, Jafeng Long, Xiqin Lu, Siqi Xu, Gang Li

“…Multiomics, an integrated approach combining genomics, transcriptomics, proteomics, and metabolomics, offers unprecedented insights into the complex molecular and cellular mechanisms involved in skin healing. …”
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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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CLOCK Genes and Circadian Rhythmicity in Alzheimer Disease by J. Thome, A. N. Coogan, A. G. Woods, C. C. Darie, F. Häßler

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NHSL3 controls single and collective cell migration through two distinct mechanisms by Nikita M. Novikov, Jinmei Gao, Artem I. Fokin, Nathalie Rocques, Giovanni Chiappetta, Karina D. Rysenkova, Diego Javier Zea, Anna Polesskaya, Joelle Vinh, Raphael Guerois, Alexis M. Gautreau

“…We identify the partner repertoire of each isoform using proteomics and predict direct partners and their binding sites using an AlphaFold2-based pipeline. …”
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Discovery of novel serum peptide biomarkers for cholangiocarcinoma recurrence through MALDI-TOF MS and LC–MS/MS peptidome analysis by Vasin Thanasukarn, Piya Prajumwongs, Nattha Muangritdech, Watcharin Loilome, Nisana Namwat, Poramate Klanrit, Arporn Wangwiwatsin, Sawanya Charoenlappanit, Janthima Jaresitthikunchai, Sittiruk Roytrakul, Attapol Titapun

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The Role of PDGFs and PDGFRs in Colorectal Cancer by Roberta M. Manzat Saplacan, Loredana Balacescu, Claudia Gherman, Romeo I. Chira, Anca Craiu, Petru A. Mircea, Cosmin Lisencu, Ovidiu Balacescu

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Effect of potato glycoside alkaloids on mitochondria energy metabolism of Fusarium solani, the root rot pathogen of Lycium barbarum by Ruiyun Li, Bin Wang, Wei Chen, Chongqing Zhang, Nan Li, Yupeng Wang, Yuke Yan, Yuyan Sun, Jing He, Jing He

“…The results from both parallel reaction monitoring (PRM) and real-time RT-qPCR were consistent with the overall trends observed in TMT proteomics, thereby confirming the validity of the TMT proteomics analysis. …”
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Executioner caspases degrade essential mediators of pathogen-host interactions to inhibit growth of intracellular Listeria monocytogenes by Marilyne Lavergne, Raffael Schaerer, Sara De Grandis, Safaa Bouheraoua, Oluwadamilola Adenuga, Tanja Muralt, Tiffany Schaerer, Léa Chèvre, Alessandro Failla, Patricia Matthey, Michael Stumpe, Dieter Kressler, Pierre-Yves Mantel, Michael Walch

“…Here, by means of chemical and genetical modifications, we show that the executioner caspases-3 and -7 efficiently inhibit growth of intracellular Listeria monocytogenes in host cells. Comprehensive proteomics revealed multiple caspase-3 substrates in the Listeria secretome, including LLO, Iap and various other proteins crucially involved in pathogen-host interactions. …”
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Enantioselective OTUD7B fragment discovery through chemoproteomics screening and high-throughput optimisation by Aini Vuorinen, Cassandra R. Kennedy, Katherine A. McPhie, William McCarthy, Jonathan Pettinger, J. Mark Skehel, David House, Jacob T. Bush, Katrin Rittinger

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Widespread release of translational repression across Plasmodium's host-to-vector transmission event. by Kelly T Rios, James P McGee, Aswathy Sebastian, Sanjaya Aththawala Gedara, Robert L Moritz, Marina Feric, Sabrina Absalon, Kristian E Swearingen, Scott E Lindner

“…Therefore, we have conducted the first quantitative, comparative transcriptomics and DIA-MS proteomics of Plasmodium parasites across the host-to-vector transmission event to document the global release of translational repression. …”
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Protocol for generating protein profiles and distance-based network analysis of murine tissue slices by Luisa Schmidt, Philipp Antczak, Marcus Krüger

“…Summary: We introduce a protocol for spatial proteomics using thin cryotome sections of mouse skeletal muscle tissue. …”
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The Role of Organelle Stresses in Diabetes Mellitus and Obesity: Implication for Treatment by Yi-Cheng Chang, Siow-Wey Hee, Meng-Lun Hsieh, Yung-Ming Jeng, Lee-Ming Chuang

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The Mycobacterium ulcerans toxin mycolactone causes destructive Sec61-dependent loss of the endothelial glycocalyx and vessel basement membrane to drive skin necrosis by Louise Tzung-Harn Hsieh, Belinda S Hall, Jane Newcombe, Tom A Mendum, Sonia Santana Varela, Yagnesh Umrania, Michael J Deery, Wei Q Shi, Josué Diaz-Delgado, Francisco J Salguero, Rachel E Simmonds

“…Unbiased quantitative proteomics identified a profound effect on proteoglycans, driven by rapid loss of type II transmembrane proteins of the Golgi, including enzymes required for glycosaminoglycan (GAG) synthesis, combined with a reduction in the core proteins themselves. …”
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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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Toward measurements of absolute membrane potential in Bacillus subtilis using fluorescence lifetime by Debjit Roy, Xavier Michalet, Evan W. Miller, Kiran Bharadwaj, Shimon Weiss

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Aminoglycoside tolerance in Vibrio cholerae engages translational reprogramming associated with queuosine tRNA modification by Louna Fruchard, Anamaria Babosan, Andre Carvalho, Manon Lang, Blaise Li, Magalie Duchateau, Quentin Giai Gianetto, Mariette Matondo, Frederic Bonhomme, Isabelle Hatin, Hugo Arbes, Céline Fabret, Enora Corler, Guillaume Sanchez, Virginie Marchand, Yuri Motorin, Olivier Namy, Valérie de Crécy-Lagard, Didier Mazel, Zeynep Baharoglu

“…We characterized its impact on the overall bacterial proteome, and elucidated the molecular mechanisms underlying the effects of Q34 modification in antibiotic translational stress response. …”
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High-Density Lipoprotein Reduction Differentially Modulates to Classical and Nonclassical Monocyte Subpopulations in Metabolic Syndrome Patients and in LPS-Stimulated Primary Human... by Johanna L. Grün, Aaron N. Manjarrez-Reyna, Angélica Y. Gómez-Arauz, Sonia Leon-Cabrera, Felix Rückert, José M. Fragoso, Nallely Bueno-Hernández, Sergio Islas-Andrade, Guillermo Meléndez-Mier, Galileo Escobedo

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Nonclinical immunogenicity risk assessment for knobs-into-holes bispecific IgG1 antibodies by Wen-Ting K. Tsai, Yinyin Li, Zhaojun Yin, Peter Tran, Qui Phung, Zhenru Zhou, Kun Peng, Dan Qin, Sien Tam, Christoph Spiess, Jochen Brumm, Manda Wong, Zhengmao Ye, Patrick Wu, Sivan Cohen, Paul J. Carter

“…Assay methods used include dendritic cell internalization, T cell proliferation, and T cell epitope identification by in silico prediction and MHC-associated peptide proteomics. Data from each method were considered independently and then together for an overall integrated immunogenicity risk assessment. …”
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