Cytotoxic mechanisms of pemetrexed and HDAC inhibition in non-small cell lung cancer cells involving ribonucleotides in DNA by Tobias Solli Iveland, Lars Hagen, Mirta Mittelstedt Leal de Sousa, Nina Beate Liabakk, Per Arne Aas, Animesh Sharma, Bodil Kavli, Geir Slupphaug

“…To explore this further, A549 NSCLC cells were treated with various combinations of pemetrexed and the HDACi MS275 (Entinostat), and subsequently assessed for cell viability, cell cycle changes, and genotoxic markers. Proteomic alterations were analyzed using label-free shotgun and targeted LC–MS/MS. …”
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In vitro effect of hCG on cryptorchid patients’ gubernacular cells: a predictive model for adjuvant personalized therapy by Andrea Errico, Giulia Ambrosini, Sara Vinco, Emanuela Bottani, Elisa Dalla Pozza, Nunzio Marroncelli, Jessica Brandi, Daniela Cecconi, Ilaria Decimo, Filippo Migliorini, Nicola Zampieri, Ilaria Dando

“…Furthermore, from the proteomic analysis, we show that hCG regulates the intra- and extra-cellular organization of gubernacular cells together with a massive regulation of the antioxidant response. …”
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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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Bioprocess exploitation of microaerobic auto-induction using the example of rhamnolipid biosynthesis in Pseudomonas putida KT2440 by Jakob Grether, Holger Dittmann, Leon Willems, Tabea Schmiegelt, Elvio Henrique Benatto Perino, Philipp Hubel, Lars Lilge, Rudolf Hausmann

“…Proteomics indicated a remodeling of the respiratory chain and the regulation of stress-related proteins under oxygen limitation. …”
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Toward spatial glycomics and glycoproteomics: Innovations and applications by Patcharaporn Boottanun, Sayaka Fuseya, Atsushi Kuno

“…We discuss glycopathology and tissue glycomic profiling using highly sensitive lectin-based analyses and introduce deep visual proteomics for glycomic/glycoproteomic sample preparation. …”
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Development of an in vitro model to study muscle maladaptation to overtraining by Giuseppe Sirago, Clément Lanfranchi, Justin Carrard, Vincent Gremeaux, Nadège Zanou, Nicolas Place

“…Mitochondrial biogenesis biomarkers have been measured, alongside proteomics analysis and mitochondrial respiration. …”
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Editorial: Agrobiodiversity at different scales for improving conservation strategies by Carmine Guarino, Guido Cipriani, Jesus V. Jorrin-Novo, Domenico Carputo, Claudio Di Vaio

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Functions of Fasciculation and Elongation Protein Zeta-1 (FEZ1) in the Brain by Andrés D. Maturana, Toshitsugu Fujita, Shun'ichi Kuroda

“…Suppression of FEZ1 expression in cultured embryonic neurons causes deficiency of neuronal differentiation. Recently, proteomic techniques revealed that FEZ1 interacts with various intracellular partners, such as signaling, motor, and structural proteins. …”
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The effect of triple CFTR modulator therapy and azithromycin on ion channels and inflammation in cystic fibrosis by Suhad Bani Melhim, Lisa E.J. Douglas, James A. Reihill, Damian G. Downey, S. Lorraine Martin

“…AZ reduced IL-8 in NuLi-1 but not CuFi-1 cells. The Proteome Profiler™ screen identified several disease-relevant cytokines that were modulated by treatment. …”
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Characterizing Antimicrobial Effects of Radiation and Antibiotic Interactions on <i>Staphylococcus aureus</i> and <i>Escherichia coli</i> Using MALDI-TOF MS by Ali Haider, Renáta Homlok, Csilla Mohácsiné Farkas, Tamás Kocsis

“…The findings highlight MALDI-TOF MS as a valuable tool in detecting proteomic biomarkers linked to bacterial resistance and stress adaptation.…”
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Effects of GS-CA1 on nuclear envelope-associated early HIV-1 infection steps by Amita Singh, Victor Fourcassié, Victor Fourcassié, Karen Cristine Gonçalves Dos Santos, Hocine Chelbi, Natacha Merindol, Arnaud Droit, Arnaud Droit, Hugo Germain, Lionel Berthoux

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Nutrigenomics: A promising frontier in chronic disease prevention by Seyed Morteza Hosseiniara, Solmaz Sadat Hosseini Zijoud

“…These include the integration of diverse and complex datasets from various sources -such as genomics, metabolomics, and proteomics- the development of robust bioinformatics tools for data analysis and interpretation, and careful consideration of ethical implications, including privacy concerns and the potential for genetic discrimination.Moving forward, the integration of multi-omics approaches -encompassing a comprehensive analysis of an individual's genetic, epigenetic, metabolic, and proteomic profiles- will be crucial for advancing the field of nutrigenomics. …”
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Triple-negative breast cancer modifies the systemic immune landscape and alters neutrophil functionality by Noor A. M. Bakker, Hannah Garner, Ewald van Dyk, Elisa Champanhet, Chris Klaver, Maxime Duijst, Leonie Voorwerk, Iris Nederlof, Rosie Voorthuis, Marte C. Liefaard, Marja Nieuwland, Iris de Rink, Onno B. Bleijerveld, Hendrika M. Oosterkamp, Lodewyk F. A. Wessels, Marleen Kok, Karin E. de Visser

“…Chemotherapy-naïve mTNBC patients showed increased classical monocytes and neutrophils. Transcriptional, proteomic, and functional analyses revealed that neutrophils in mTNBC exhibited enhanced migratory capacity, elevated granule proteins, and higher ROS production. …”
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Evaluation of ovarian stiffness and its biological mechanism using shear wave elastography in polycystic ovary syndrome by Yifang He, Shuangping Deng, Yanli Wang, Xiali Wang, Qingqing Huang, Jing Cheng, Dandan Wang, Guorong Lyu

“…Histological analysis, enzyme-linked immunosorbent assay, quantitative reverse transcription-polymerase chain reaction, western blotting, transcriptomics, and proteomics were performed to assess alterations in fibrosis and basement membrane (BM) gene expression. …”
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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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Overview on signal transduction cascades regulation roles of garlic and its bioactive constituents by Ammad Ahmad Farooqi, Iqra Mobeen, Rukset Attar, Khalida I. Noel, Baojun Xu, William C. Cho

“…High-throughput technologies in combination with modern exciting advancements in mass spectrometry-based proteomics and data analysis pipelines have empowered comprehensive characterization of disease phenotypes and their mechanistic regulation by dietary agents and bioactive molecules at unprecedented dimensionality and resolution. …”
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Targeting eEF1A reprograms translation and uncovers broad-spectrum antivirals against cap or m6A protein synthesis routes by Elisa Molina Molina, Joan Josep Bech-Serra, Eloi Franco-Trepat, Ignasi Jarne, Daniel Perez-Zsolt, Roger Badia, Eva Riveira-Muñoz, Edurne Garcia-Vidal, Lluís Revilla, Sandra Franco, Ferran Tarrés-Freixas, Núria Roca, Gerardo Ceada, Karl Kochanowski, Dàlia Raïch-Regué, Itziar Erkizia, Rytis Boreika, Antoni E. Bordoy, Laia Soler, Sonia Guil, Jorge Carrillo, Julià Blanco, Miguel Ángel Martínez, Roger Paredes, Alejandro Losada, Pablo Aviles, Carmen Cuevas, Júlia Vergara-Alert, Joaquim Segalés, Bonaventura Clotet, Ester Ballana, Carolina de la Torre, Nuria Izquierdo-Useros

“…Here we detect that plitidepsin decreases de novo cap-dependent translation of SARS-CoV-2 and non-viral RNAs but affects less than 13% of the host proteome, thus preserving cellular viability. In response to plitidepsin, cells upregulate EIF2AK3 and proteins that reduce translation, but also proteins that support proteostasis via ribosome synthesis and cap-independent translation by eIF4G2 and IGF2BP2. …”
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Protocol for generating liver metastasis microtissues to decipher cellular interactions between metastatic intestinal cancer and liver tissue by Maria Lamprou, Ana Krotenberg Garcia, Saskia Jacoba Elisabeth Suijkerbuijk

“…Here, we present a protocol for generating matrix-free microtissues recapitulating cellular interactions between intestinal cancer and hepatocyte-like cells using microscopy or transcriptomics/proteomics. We describe steps for generating and differentiating liver progenitor organoids and microtissue formation. …”
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Accurate Identification of Cancerlectins through Hybrid Machine Learning Technology by Jieru Zhang, Ying Ju, Huijuan Lu, Ping Xuan, Quan Zou

“…Our work provides a basis for the computational identification of cancerlectins and reveals the power of hybrid machine learning techniques in computational proteomics.…”
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Single-Cell Sequencing in Cancer: Recent Applications to Immunogenomics and Multi-omics Tools by Michael C. Sierant, Jungmin Choi

“…The application of single-cell sequencing, in concert with existing genomics methods, has enabled high-resolution interrogation of the genome, transcriptome, epigenome, and proteome. Applied to cancers, these single-cell multi-omics methods bypass previous limitations on data resolution and have enabled a more nuanced understanding of the evolutionary dynamics of tumor progression, immune evasion, metastasis, and treatment resistance. …”
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