Vitamin D sensitizes cervical cancer to radiation-induced apoptosis by inhibiting autophagy through degradation of Ambra1 by Zhaoming zhang, Xinyue Yu, Guanghui Cheng

“…We examined conventional radiation-induced cell death, such as DNA damage and cell cycle arrest, in vitamin D–treated cells to detect the underlying mechanism, but no association was observed between them. Subsequently, our proteome analysis exhibited that autophagy was reduced in irradiated CCs treated with vitamin D, and apoptosis displayed the opposite effect. …”
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Tracing the paths of modular evolution by quantifying rearrangement events of protein domains by Abdulbaki Coban, Erich Bornberg-Bauer, Carsten Kemena

“…Therefore, these events can be used to characterize and reconstruct major events of molecular adaptation by comparing large data sets of proteomes. Results Here we determine, at unprecedented completeness, the rates of fusion, fission, emergence and loss of domains in five eukaryotic clades (monocots, eudicots, fungi, insects, vertebrates). …”
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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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Isovitexin targets SIRT3 to prevent steroid-induced osteonecrosis of the femoral head by modulating mitophagy-mediated ferroptosis by Yinuo Fan, Zhiwen Chen, Haixing Wang, Mengyu Jiang, Hongduo Lu, Yangwenxiang Wei, Yunhao Hu, Liang Mo, Yuhao Liu, Chi Zhou, Wei He, Zhenqiu Chen

“…In this study, we analyzed clinical samples obtained from SIONFH patients using proteomic and bioinformatic approaches. We found an imbalance in mitochondrial homeostasis and ferroptosis-induced impairment of osteogenic capacity in SIONFH. …”
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Detection of HIV-1 and Human Proteins in Urinary Extracellular Vesicles from HIV+ Patients by Samuel I. Anyanwu, Akins Doherty, Michael D. Powell, Chamberlain Obialo, Ming B. Huang, Alexander Quarshie, Claudette Mitchell, Khalid Bashir, Gale W. Newman

“…Conclusion. Differences in the proteomic profile of EVs from HIV+ versus HIV− samples were found. …”
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Subclinical Inflammatory Status in Rett Syndrome by Alessio Cortelazzo, Claudio De Felice, Roberto Guerranti, Cinzia Signorini, Silvia Leoncini, Alessandra Pecorelli, Gloria Zollo, Claudia Landi, Giuseppe Valacchi, Lucia Ciccoli, Luca Bini, Joussef Hayek

“…., “pseudo-autistic”) RTT patients by routine haematology/clinical chemistry and proteomic 2-DE/MALDI-TOF analyses as a function of four major MECP2 gene mutation types (R306C, T158M, R168X, and large deletions). …”
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Integrating AI into Cancer Immunotherapy—A Narrative Review of Current Applications and Future Directions by David B. Olawade, Aanuoluwapo Clement David-Olawade, Temitope Adereni, Eghosasere Egbon, Jennifer Teke, Stergios Boussios

“…Results: AI has significantly contributed to identifying biomarkers that predict immunotherapy efficacy by analyzing genomic, transcriptomic, and proteomic data. It also optimizes combination therapies by predicting the most effective treatment protocols. …”
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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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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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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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Inhibition of glutathione peroxidase 4 suppresses gastric cancer peritoneal metastasis via regulation of RCC2 homeostasis by Can Hu, Jingli Xu, Yanqiang Zhang, Ruolan Zhang, Siwei Pan, Jiahui Chen, Yan Wang, Qianyu Zhao, Yuqi Wang, Weiwei Zhu, Mengxuan Cao, Shengjie Zhang, Dan Zu, Zhiyuan Xu, Ji Jing, Xiangdong Cheng

“…GPx4 knockdown suppressed GC invasion, migration and peritoneal metastasis in vitro and in vivo. Proteomic analysis revealed that GPx4 expression regulated the Homeostasis of RCC2, an oncogene link to epithelial-mesenchymal transition (EMT). …”
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Wogonin effects on the efflux transporters BCRP and MRP2, explain its effectiveness in ulcerative colitis: Implications for metabolic and transport interactions by Yuanyuan Liu, Zerong Zhang, Xiaoyan Li, Qinghong Hu, Zhangyu Jiang, Jia Lv, Jiayi Xue, Dongyu Wang, Jianxiong Cao, Lingyu Li, Xiaowen Ou, Lijun Zhu, Zhongqiu Liu, Tao Su

“…These indicate that inhibiting efflux transporters suppresses cellular and mitochondrial glucuronidation metabolism. Interestingly, proteomic sequencing of mitochondrial subcellular organelles revealed that wogonin exhibited anti-UC effects by inhibiting afamin (AFM), with these effects modulated by BCRP and MRP2. …”
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Antihypertensive effects of whey protein hydrolysate involve reshaping the gut microbiome in spontaneously hypertension rats by Peipei Dou, Xiaoyi Li, Xiaoxiao Zou, Kai Wang, Lei Yao, Zhuo Sun, Hui Hong, Yongkang Luo, Yuqing Tan

“…The heart weight and cardiomyocyte injuries (hypertrophy and degeneration) were alleviated by WPH. The proteomic results revealed that 19 protein expressions in the heart mainly associated with the wingless/integrated (Wnt) signaling pathway and Apelin signaling pathway were altered after WPH supplementation. …”
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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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Methyl-Arginine Profile of Brain from Aged PINK1-KO+A53T-SNCA Mice Suggests Altered Mitochondrial Biogenesis by Georg Auburger, Suzana Gispert, Nadine Brehm

“…Now we studied brain hemispheres of DM mice at age of 18 months in a hypothesis-free approach, employing a quantitative label-free global proteomic mass spectrometry scan of posttranslational modifications focusing on methyl-arginine. …”
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Plasmatic Membrane Expression of Adhesion Molecules in Human Cardiac Progenitor/Stem Cells Might Explain Their Superior Cell Engraftment after Cell Transplantation by Imelda Ontoria-Oviedo, Itziar Palacios, Joaquín Panadero, Belén Sánchez, Francisco García-García, Adolfo López-Cerdán, Akaitz Dorronsoro, Delia Castellano, Luis Rodríguez-Borlado, Antonio Bernad, Pilar Sepúlveda

“…The CPC and BM-MSC receptome were analyzed by proteomic analysis of biotin-labeled surface proteins. …”
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Reprogramming of iPSCs to NPCEC-like cells by biomimetic scaffolds for zonular fiber reconstruction by Tianhui Chen, Zhongxing Chen, Juan Du, Min Zhang, Zexu Chen, Qingyi Gao, Aodong Chen, Qinghao Meng, Yang Sun, Yan liu, Linghao Song, Xinyue Wang, Pranav Prakash Edavi, Chen Xu, Hongmei Zhang, Jinhai Huang, Yongxiang Jiang

“…Ocular tissue and aqueous humour samples from patients with EL were subjected to RNA sequencing and Olink high-throughput proteomic analysis, revealing the downregulation of pathogenic genes (FBN1, MFAP2) and upregulation of secretory proteins (IL-12, MMP-1). …”
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Bilayer 3D co‐culture platform inducing the differentiation of normal fibroblasts into cancer‐associated fibroblast like cells: New in vitro source to obtain cancer‐associated fibr... by Yeon Ju Kim, Hyeon Song Lee, Dohyun Kim, Hwa Kyung Byun, Woong Sub Koom, Won‐Gun Koh

“…The mRNA expression levels of CAF‐related markers were significantly upregulated in 3D, but not in 2D co‐culture. Proteomic analysis identified upregulated proteins associated with CAFs, further confirming the transformation of normal fibroblasts into CAF within the proposed 3D co‐culture platform. …”
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RSK4 promotes the metastasis of clear cell renal cell carcinoma by activating RUNX1-mediated angiogenesis by Jing Ma, Yanru Yang, Kaijing Wang, Jin Liu, Junyi Feng, Gongcheng Wang, Shuangping Guo, Linni Fan

“…We analyzed changes in the expression of target genes through transcriptomic and proteomic assessments. We also conducted tube formation assays and VEGF ELISAs to understand the role of RSK4 in angiogenesis. …”
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The metabolomic approach to the assessment of cultivar specificity of Brassica napus L. seeds by G. N. Smolikova, A. L. Shavarda, I. V. Alekseichuk, V. V. Chantseva, S. S. Medvedev

“…Recent biomolecular studies tend to involve combinations of different methods and approaches that allow analyzing organisms on the genomic and proteomic levels, as well as on the level of metabolomics. …”
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