Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response in pancreatic cancer by Lukas Klein, Mengyu Tu, Niklas Krebs, Laura Urbach, Daniela Grimm, Muhammad Umair Latif, Frederike Penz, Anna Blandau, Xueyan Wu, Rebecca Diya Samuel, Stefan Küffer, Florian Wegwitz, Nathan Chan, Kazeera Aliar, Foram Vyas, Uday Kishore, Elisabeth Hessmann, Andreas Trumpp, Elisa Espinet, Argyris Papantonis, Rama Khokha, Volker Ellenrieder, Barbara T. Grünwald, Shiv K. Singh

“…Here, by combining preclinical models, multi-center clinical, transcriptomic, proteomic, and patient bioimaging data, we identify an interplay between neoplastic intrinsic AP1 transcription factor dichotomy and extrinsic macrophages driving subtype co-existence and an immunosuppressive microenvironment. …”
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Zika virus modulates human fibroblasts to enhance transmission success in a controlled lab-setting by Raimondas Mozūraitis, Karsten Cirksena, Mohammad Raftari, Melika Hajkazemian, Musa Mustapha Abiodun, Juela Brahimi, Sandra Radžiutė, Violeta Apšegaitė, Rasa Bernotienė, Lech Ignatowicz, Tessy Hick, Andreas Kirschning, Annasara Lenman, Gisa Gerold, S. Noushin Emami

“…The findings are complemented by an extensive meta-proteome analysis. Overall, we demonstrate a multifaceted role of virus-host interaction and shed light on how arboviruses may influence the behaviour of their vectors as an evolved means of improving transmission-success.…”
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Cross-trait multivariate GWAS confirms health implications of pubertal timing by Siquan Zhou, Yujie Xu, Jingyuan Xiong, Guo Cheng

“…We find 266 independent variants in 197 loci, including 18 novel variants. Transcriptomic, proteome imputation and fine-mapping analyses reveal genes causal for pubertal timing, including KDM4C, LEPR, CCNC, ACP1, and PCSK1. …”
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Isolation of Viral Biofilms From HTLV-1 Chronically Infected T Cells and Integrity Analysis by Coline Arone, Hélène Dutartre, Delphine Muriaux

“…In this study, we optimized a protocol to isolate HTLV-1 biofilms from chronically infected T cells, facilitating their structural and molecular characterization using proteomic and super-resolution microscopy analyses. …”
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Lipopolysaccharide affects metabolic processes and energy homeostasis in the corpus luteum by Karol Mierzejewski, Robert Stryiński, Iwona Bogacka, Monika Golubska, Mónica Carrera, Aleksandra Kurzynska

“…Understanding the intricate interplay between inflammatory processes and reproductive organ’s function is crucial for the development of effective therapeutic strategies to alleviate reproductive disorders and improve fertility.MethodsThe aim of this study was to determine the in vitro effects of lipopolysaccharide (LPS) on the proteomic profile of the porcine CL in the mid-luteal phase of the estrous cycle using LC-MS/MS analysis. …”
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Integrative multi-omics analysis reveals the translational landscape of the plant-parasitic nematode Meloidogyne incognita by Zhaolu Zhu, Dexin Bo, Chuanshuai Xie, Dadong Dai, Donghai Peng, Ming Sun, Jinshui Zheng

“…In this study, we elucidated the translational landscape of Meloidogyne incognita through the integration of translatome, transcriptome and quantitative proteome analyses. Our findings revealed numerous previously unannotated translation events and refined the genome annotation. …”
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Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis by Célia Alecki, Javeria Rizwan, Phuong Le, Suleima Jacob-Tomas, Mario Fernandez Comaduran, Morgane Verbrugghe, Jia Ming Stella Xu, Sandra Minotti, James Lynch, Jeetayu Biswas, Tad Wu, Heather D. Durham, Gene W. Yeo, Maria Vera

“…However, this is challenging in neuronal projections because of their polarized morphology and constant synaptic proteome remodeling. Using high-resolution fluorescence microscopy, we discover that hippocampal and spinal cord motor neurons of mouse and human origin localize a subset of chaperone mRNAs to their dendrites and use microtubule-based transport to increase this asymmetric localization following proteotoxic stress. …”
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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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Downregulation of S100 Calcium Binding Protein A9 in Esophageal Squamous Cell Carcinoma by Harsh Pawar, Srinivas M. Srikanth, Manoj Kumar Kashyap, Gajanan Sathe, Sandip Chavan, Mukul Singal, H. C. Manju, Kariyanakatte Veeraiah Veerendra Kumar, M. Vijayakumar, Ravi Sirdeshmukh, Akhilesh Pandey, T. S. Keshava Prasad, Harsha Gowda, Rekha V. Kumar

“…We had previously employed a quantitative proteomic approach to identify differentially expressed proteins in ESCC tumors. …”
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Characterization of the Protective HIV-1 CTL Epitopes and the Corresponding HLA Class I Alleles: A Step towards Designing CTL Based HIV-1 Vaccine by Sajib Chakraborty, Taibur Rahman, Rajib Chakravorty

“…High mutation rate in the viral genome underlying the antigenic variability of the viral proteome is the major hindrance as far as the antibody based vaccine development is concerned. …”
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Molecular Basis of GABA Hypofunction in Adolescent Schizophrenia-Like Animals by Xiaodan Wang, Ying Hu, Wenxin Liu, Yuanyuan Ma, Xi Chen, Ting Xue, Donghong Cui

“…Slice recording showed reduced GABA transmission and PVI+ hypofunction, indicating GABAergic hypofunction. Cortical proteomic evaluation combined with analysis of single cell data from the Allen Brain showed that various metabolic processes were enriched in top ranks and differentially altered in excitatory neurons, GABAergic interneurons, and glial cells. …”
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Profiling protease cleavage patterns in plasma for pancreatic cancer detection by Morgan R. Stewart, Arnaud Quentel, Elise Manalo, Jose Montoya Mira, Srivathsan Ranganathan, Bruce P. Branchaud, Jared M. Fischer, Eugene Tu, Fehmi Civitci, Yu-Jui Chiu, Adem Yildirim

“…However, the complexity of the human proteome makes it challenging to develop sensitive and selective tests against a specific protease biomarker. …”
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Comparative analysis of microbial contamination in diesel fuels using MALDI-TOF MS by Agnieszka Ludwiczak, Tomasz Zieliński, Ewelina Sibińska, Grażyna Czeszewska-Rosiak, Michał Złoch, Joanna Rudnicka, Andrzej Tretyn, Paweł Pomastowski

“…The 16 S rDNA sequencing confirmed proteomic identifications by the MALDI systems with high accuracy. …”
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Influence of Acute High Glucose on Protein Abundance Changes in Murine Glomerular Mesangial Cells by Michelle T. Barati, James C. Gould, Sarah A. Salyer, Susan Isaacs, Daniel W. Wilkey, Michael L. Merchant

“…The effects of acute exposure to high glucose levels as experienced by glomerular mesangial cells in postprandial conditions and states such as in prediabetes were investigated using proteomic methods. Two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry methods were used to identify protein expression patterns in immortalized rat mesangial cells altered by 2 h high glucose (HG) growth conditions as compared to isoosmotic/normal glucose control (NG⁎) conditions. …”
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smu_1558c-mediated regulation of growth and biofilm formation in Streptococcus mutans by Jing Zhou, Jing Zhou, Qizhao Ma, Qizhao Ma, Jingou Liang, Jingou Liang, Yangyang Pan, Yangyang Pan, Yang Chen, Yang Chen, Shuxing Yu, Shuxing Yu, Yaqi Liu, Yaqi Liu, Qiong Zhang, Qiong Zhang, Yuqing Li, Jing Zou, Jing Zou

“…The deletion of smu_1558c resulted in impaired growth, reduced biofilm formation, and diminished synthesis of water-insoluble extracellular polysaccharides (EPS). Proteomic analysis revealed 166 differentially expressed proteins in the deletion mutant, with significant enrichment in pathways related to carbohydrate transport and metabolism, and translation. …”
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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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Predicting the hub interactome of COVID-19 and oral squamous cell carcinoma: uncovering ALDH-mediated Wnt/β-catenin pathway activation via salivary inflammatory proteins by Pradeep Kumar Yadalam, Deepavalli Arumuganainar, Prabhu Manickam Natarajan, Carlos M. Ardila

“…The gradient boosting model outperformed all models with an accuracy of 95% and class accuracy of 95%. Salivary proteomic interactome analysis revealed novel hub proteins as potential common biomarkers.…”
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Expression Profiling of Long Noncoding RNA Splice Variants in Human Microvascular Endothelial Cells: Lipopolysaccharide Effects In Vitro by Imran H. Chowdhury, Hema P. Narra, Abha Sahni, Kamil Khanipov, Casey L. C. Schroeder, Jignesh Patel, Yuriy Fofanov, Sanjeev K. Sahni

“…Endothelial cell interactions with lipopolysaccharide (LPS) involve both activating and repressing signals resulting in pronounced alterations in their transcriptome and proteome. Noncoding RNAs are now appreciated as posttranscriptional and translational regulators of cellular signaling and responses, but their expression status and roles during endothelial interactions with LPS are not well understood. …”
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PMA1-containing extracellular vesicles of Candida albicans triggers immune responses and colitis progression by Zhen Xu, Shuping Qiao, Zelin Wang, Chen Peng, Yayi Hou, Baorui Liu, Guochun Cao, Tingting Wang

“…Compared to WT-C.a, ΔPMA1-C.a could not aggravate colitis. Proteomic analysis showed that PMA1 was transported by extracellular vesicles (EVs) of C. albicans. …”
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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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