Cellular senescence induced by cholesterol accumulation is mediated by lysosomal ABCA1 in APOE4 and AD by Shaowei Wang, Boyang Li, Jie Li, Zhiheng Cai, Cristelle Hugo, Yi Sun, Lu Qian, Julia TCW, Helena C. Chui, Dante Dikeman, Isaac Asante, Stan G. Louie, David A. Bennett, Zoe Arvanitakis, Alan T. Remaley, Bilal E. Kerman, Hussein N. Yassine

“…Methods We examined the association between cellular senescence and ABCA1 expression in human postmortem brain samples using transcriptomic, histological, and biochemical analyses. Unbiased proteomic screening was performed to identify the proteins that mediate cellular ABCA1 trafficking. …”
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Polygenic prediction of human longevity on the supposition of pervasive pleiotropy by M. Reza Jabalameli, Jhih-Rong Lin, Quanwei Zhang, Zhen Wang, Joydeep Mitra, Nha Nguyen, Tina Gao, Mark Khusidman, Sanish Sathyan, Gil Atzmon, Sofiya Milman, Jan Vijg, Nir Barzilai, Zhengdong D. Zhang

“…Together, our approach demonstrates a promising framework for polygenic modeling of additive liability conferred by ARTs in defining exceptional longevity and assisting the identification of individuals at a higher risk of mortality for targeted lifestyle modifications earlier in life. Furthermore, the proteomic signature associated with iLGS highlights the functional pathway upstream of the PI3K-Akt that can be effectively targeted to slow down aging and extend lifespan.…”
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Amyloids in bladder cancer hijack cancer-related proteins and are positive correlated to tumor stage by Diego Alem, César X. García-Laviña, Francisco Garagorry, Dardo Centurión, Joaquina Farias, Hany Pazos-Espinosa, María Noel Cuitiño-Mendiberry, Carolina Villadóniga, Susana Castro-Sowinski, Martín Fló, Federico Carrión, Brenda Iglesias, Kevin Madauss, Lucía Canclini

“…Subsequently, the amyloid proteome of the RT4 non-invasive and HT1197 invasive bladder cancer cell lines was identified and included oncogenes, tumor suppressors, and highly expressed cancer-related proteins. …”
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Mechanistic insights into PROS1 inhibition of bladder cancer progression and angiogenesis via the AKT/GSK3β/β-catenin pathway by Xin-peng Fan, Ji-rong Wang, Si-yu Chen, Xiao-ran Li, Jin-long Cao, Hua-bin Wang, Li-yun Ding, Tuan-jie Che, Li Yang

“…However, the deregulation of PROS1 and its specific function in BLCA is not well understood. By combining proteomic and transcriptomic datasets, we discovered PROS1 expression was significantly reduced in BLCA tissues and revealed the clinical relevance of PROS1 with BLCA. …”
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Nanobody-thioesterase chimeras to specifically target protein palmitoylation by Chien-Wen Kuo, Caglar Gök, Hannah Fulton, Eleanor Dickson-Murray, Samuel Adu, Emily K. Gallen, Sheon Mary, Alan D. Robertson, Fiona Jordan, Emma Dunning, William Mullen, Godfrey L. Smith, William Fuller

“…Abstract The complexity of the cellular proteome is massively expanded by a repertoire of chemically distinct reversible post-translational modifications (PTMs) that control protein localisation, interactions, and function. …”
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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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TGF-β induces cholesterol accumulation to regulate the secretion of tumor-derived extracellular vesicles by Dorival Mendes Rodrigues-Junior, Chrysoula Tsirigoti, Konstantina Psatha, Dimitris Kletsas, Michalis Aivaliotis, Carl-Henrik Heldin, Aristidis Moustakas

“…To this end, we used a large number of cancer cell models, coupled to EV cell biological assays, unbiased proteomic and transcriptomic screens, followed by signaling and cancer biology analyses, including drug resistance assays. …”
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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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The nonlinear cysteine redox dynamics in the i-space: A proteoform-centric theory of redox regulation by James N. Cobley, Panagiotis N. Chatzinikolaou, Cameron A. Schmidt

“…In support, even 90%-reduced proteomes can house vast numbers of unique, potentially functioanlly diverse, oxiforms. …”
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Disorders in brassinosteroids signal transduction triggers the profound molecular alterations in the crown tissue of barley under drought. by Anetta Kuczyńska, Martyna Michałek, Piotr Ogrodowicz, Michał Kempa, Paweł Krajewski, Vladimiro Cardenia, Maria Teresa Rodriguez-Estrada, Marina Pérez-Llorca, Sergi Munné-Bosch, Krzysztof Mikołajczak

“…Large-scale transcriptomic and proteomic profiling confirmed the specific re-modeling of behavior of the BRs-insensitive barley uzu1.a mutant under drought. …”
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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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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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Unlocking biological complexity: the role of machine learning in integrative multi-omics by Ravindra Kumar, Rajrani Ruhel, Andre J. van Wijnen

“…Integrative multi-omics approaches use multi-layered datasets such as genomic, transcriptomic, proteomic, and metabolomic data to understand biological processes much more comprehensively compared to the single-omics analysis and to provide a comprehensive view of cellular and molecular processes. …”
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Prediction of inhibitory peptides against E.coli with desired MIC value by Nisha Bajiya, Nishant Kumar, Gajendra P. S. Raghava

“…Additionally, we screened anti-E. coli proteins in the proteomes of three probiotic bacterial strains and created a web-based platform, “EIPpred”, enabling users to design peptides with desired MIC values ( https://webs.iiitd.edu.in/raghava/eippred ).…”
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SHASI-ML: a machine learning-based approach for immunogenicity prediction in Salmonella vaccine development by Ottavia Spiga, Ottavia Spiga, Ottavia Spiga, Anna Visibelli, Francesco Pettini, Bianca Roncaglia, Annalisa Santucci, Annalisa Santucci, Annalisa Santucci

“…When applied to the Salmonella enterica serovar Typhimurium proteome, the model identified 292 novel immunogenic protein candidates. …”
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Exploring BCL2 regulation and upstream signaling transduction in venetoclax resistance in multiple myeloma: potential avenues for therapeutic intervention by Rodrigo Fonseca, Yuan Xiao Zhu, Laura A. Bruins, Joseph Ahmann, Cecilia de Bonolo Campos, Esteban Braggio, Xianfeng Chen, Mariano Arribas, Susie Darvish, Seth Welsh, Erin Meermeier, Kiran K. Mangalaparthi, Richard K. Kandasamy, Greg Ahmann, J. Erin Wiedmeier-Nutor, Akhilesh Pandey, Marta Chesi, P. Leif Bergsagel, Rafael Fonseca

“…We conducted a multi-omic characterization of established VTX-resistant isogenic human myeloma cell lines (HMCL) and primary MM patient samples pre- and post-VTX treatment. Transcriptomic and proteomic analysis revealed that resistance was largely associated with BCL-2 family protein dysregulation, including upregulation of anti-apoptotic proteins such as MCL-1, BCL-XL, BCL-2, and downregulation of pro-apoptotic members. …”
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PfFBXO1 is essential for inner membrane complex formation in Plasmodium falciparum during both asexual and transmission stages by Sreelakshmi K. Sreenivasamurthy, Carlos Gustavo Baptista, Christopher M. West, Ira J. Blader, Jeffrey D. Dvorin

“…PfFBXO1-deficient gametocytes are abnormally shaped and fail to fully mature. Proteomic analysis identified PfSKP1 as one of PfBXO1’s stable interacting partners, while other major proteins included multiple IMC pellicle and membrane proteins. …”
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Pan-caspase inhibitors induce secretion of HIV-1 latency reversal agent lymphotoxin-alpha from cytokine-primed NK cells by Zamaneh Hajikhezri, Ioannis Zygouras, Anders Sönnerborg, Robert van Domselaar

“…Here, we aimed to identify this LRA using a targeted proteomic approach. We identified lymphotoxin-α (LTα) as the key LRA secreted by NK cells following pan-caspase inhibitor treatment. …”
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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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Immune monitoring of trabectedin therapy in refractory soft tissue sarcoma patients - the IMMUNYON study by Paulo Rodrigues-Santos, Paulo Rodrigues-Santos, Paulo Rodrigues-Santos, Paulo Rodrigues-Santos, Paulo Rodrigues-Santos, Paulo Rodrigues-Santos, Jani Sofia Almeida, Jani Sofia Almeida, Jani Sofia Almeida, Jani Sofia Almeida, Jani Sofia Almeida, Jani Sofia Almeida, Luana Madalena Sousa, Luana Madalena Sousa, Luana Madalena Sousa, Patrícia Couceiro, Patrícia Couceiro, Patrícia Couceiro, Patrícia Couceiro, António Martinho, Joana Rodrigues, Ruben Fonseca, Manuel Santos-Rosa, Manuel Santos-Rosa, Manuel Santos-Rosa, Manuel Santos-Rosa, Manuel Santos-Rosa, Paulo Freitas-Tavares, José Manuel Casanova, José Manuel Casanova, José Manuel Casanova, José Manuel Casanova, José Manuel Casanova

“…Immune monitoring included deep immunophenotyping (200+ parameters), gene expression profiling (103 genes), and soluble proteome analysis (99 analytes). Using RECIST1.1 criteria, 68.2% of patients achieved stable disease (SD), while 31.8% exhibited progression disease (PD). …”
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