Anti-PD-1 amplifies costimulation in melanoma-infiltrating Th1-like Foxp3+ regulatory T cells to alleviate local immunosuppression by Fernando Alvarez, Fan Huang, Sonia V Del Rincon, Mikhaël Attias, Tho-Alfakar Al-Aubodah, Roman Istomine, Paige McCallum, Abrahim Sleiman, Tamiko Nishimura, Yasser Riazalhosseini, Ciriaco A Piccirillo

“…Treg cell responses in tumors and lymphoid compartments were examined throughout tumor growth or therapy and were assessed ex vivo by multiparametric flow cytometry analysis, with in vitro suppression assays using tumor-infiltrating lymphocytes isolated by fluorescence-activated cell sorting (FACS) and in situ through spatial proteomic and transcriptomic profiling.Results In this highly immunogenic melanoma model, anti-PD-1 monotherapy yielded high responders (HRs) and low responders (LRs). …”
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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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Systemic regulation of retinal medium-chain fatty acid oxidation repletes TCA cycle flux in oxygen-induced retinopathy by Almut Heinken, John M. Asara, Gopalan Gnanaguru, Charandeep Singh

“…Our systems level in vivo RNA-seq, proteomics, and lipidomic profiling and ex-vivo retinal explant studies show that the medium-chain fatty acids serves as an alternative source to feed the TCA cycle. …”
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Nutrigenomics: Definitions and Advances of This New Science by N. M. R. Sales, P. B. Pelegrini, M. C. Goersch

“…Hence, Nutrigenomics corresponds to the use of biochemistry, physiology, nutrition, genomics, proteomics, metabolomics, transcriptomics, and epigenomics to seek and explain the existing reciprocal interactions between genes and nutrients at a molecular level. …”
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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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Cancer multi-omics-based differential expression analysis and prognostic potential of identified hub targets of myco-metabolites for breast carcinoma and lung carcinoma by Singh Shreya, Debadatta Mohapatra, Gaurav Gopal Naik, Pooja Kathait, Soki Malang, Pradeep Patel, Shambhavi, Gulzar Alam, Alakh N. Sahu

“…In the present work, web servers UALCAN, GEPIA2, and KM plotter were used to explore the genomic and proteomic expression of these hub targets, along with their prognosis potential in BC and LC. …”
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A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment by Bokai Zhu, Yunhao Bai, Yao Yu Yeo, Xiaowei Lu, Xavier Rovira-Clavé, Han Chen, Jason Yeung, Dingani Nkosi, Jonathan Glickman, Antonio Delgado-Gonzalez, Georg K. Gerber, Mike Angelo, Alex K. Shalek, Garry P. Nolan, Sizun Jiang

“…We demonstrate MicroCart by investigating gut host and microbiome changes in a murine colitis model, using spatial proteomics, transcriptomics, and glycomics. Our findings reveal a global but systematic transformation in tissue immune responses, encompassing tissue-level remodeling in response to host immune and epithelial cell state perturbations, bacterial population shifts, localized inflammatory responses, and metabolic process alterations during colitis. …”
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Usefulness of the Vitreous Fluid Analysis in the Translational Research of Diabetic Retinopathy by Olga Simó-Servat, Cristina Hernández, Rafael Simó

“…The usefulness of new technologies such as flow cytometry and proteomics in identifying new candidates involved in the inflammatory process that occurs in DR will be overviewed. …”
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Cdk6’s functions are critically regulated by its unique C-terminus by Alessia Schirripa, Helge Schöppe, Sofie Nebenfuehr, Markus Zojer, Thorsten Klampfl, Valentina Kugler, Belinda S. Maw, Huriye Ceylan, Iris Z. Uras, Lisa Scheiblecker, Elisabeth Gamper, Ulrich Stelzl, Eduard Stefan, Teresa Kaserer, Veronika Sexl, Karoline Kollmann

“…C-terminally truncated Cdk6 (Cdk6 ΔC) shows reduced nuclear translocation and therefore chromatin interaction and fails to enhance proliferation and disease progression. The combination of proteomic analysis and protein modeling highlights that Cdk6’s C-terminus is essential for protein flexibility and for its binding potential to cyclin D, p27Kip1 and INK4 proteins but not cyclin B. …”
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Integrated proteogenomic characterization of ampullary adenocarcinoma by Qiao Zhang, Xiaomeng Xu, Dongxian Jiang, Yunzhi Wang, Haixing Wang, Jiajun Zhu, Shaoshuai Tang, Ronghua Wang, Shuang Zhao, Kai Li, Jinwen Feng, Hang Xiang, Zhenmei Yao, Ning Xu, Rundong Fang, Wenjia Guo, Yu Liu, Yingyong Hou, Chen Ding

“…Genomic data illustrate that 4q loss causes fatty acid accumulation and cell proliferation. Proteomic analysis has revealed three distinct clusters (C-FAM, C-AD, C-CC), among which the most aggressive cluster, C-AD, is associated with the poorest prognosis and is characterized by focal adhesion. …”
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Inflammatory Mechanisms of Idiopathic Epiretinal Membrane Formation by Malav Joshi, Shivi Agrawal, John Byron Christoforidis

“…Recent advances in proteomics techniques have also elucidated the growth factors and cytokines involved in iERM formation, most notably nerve growth factor, glial cell line-derived growth factor, and transforming growth factor β1.…”
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Melittin, a Potential Natural Toxin of Crude Bee Venom: Probable Future Arsenal in the Treatment of Diabetes Mellitus by Md. Sakib Hossen, Siew Hua Gan, Md. Ibrahim Khalil

“…This review summarizes the various sources, proteomics, biological roles, adverse effects, and medical applications of melittin and its mechanism of action in combating DM.…”
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Systemic factors associated with antler growth promote complete wound healing by Qianqian Guo, Guokun Zhang, Jing Ren, Jiping Li, Zhen Wang, Hengxing Ba, Zihao Ye, Ying Wang, Junjun Zheng, Chunyi Li

“…Interestingly, topical application of systemic factors from ARP (n = 9) promoted regenerative wound healing in rats. Comparative proteomics analysis (n = 3) revealed that PRG4 and IGF-1 were high during ARP, and topical application of PRG4 + IGF-1 promoted restoration in rat FTE wounds. …”
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Hidden route of protein damage through oxygen-confined photooxidation by Seoyoon Kim, Eojin Kim, Mingyu Park, Seong Ho Kim, Byung-Gyu Kim, Seungjin Na, Victor W. Sadongo, W. C. Bhashini Wijesinghe, Yu-Gon Eom, Gwangsu Yoon, Hannah Jeong, Eunhye Hwang, Chaiheon Lee, Kyungjae Myung, Chae Un Kim, Jeong-Mo Choi, Seung Kyu Min, Tae-Hyuk Kwon, Duyoung Min

“…The effects of this photooxidative reaction appear to be extensive, impacting a wide range of cellular proteins, as supported by whole-cell proteomic analysis. This photooxidative mechanism may represent a latent oxidation pathway in human tissues directly exposed to visible light, such as skin and eyes.…”
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Systematic protein–protein interaction mapping for clinically relevant human GPCRs by Kate Sokolina, Saranya Kittanakom, Jamie Snider, Max Kotlyar, Pascal Maurice, Jorge Gandía, Abla Benleulmi‐Chaachoua, Kenjiro Tadagaki, Atsuro Oishi, Victoria Wong, Ramy H Malty, Viktor Deineko, Hiroyuki Aoki, Shahreen Amin, Zhong Yao, Xavier Morató, David Otasek, Hiroyuki Kobayashi, Javier Menendez, Daniel Auerbach, Stephane Angers, Natasa Pržulj, Michel Bouvier, Mohan Babu, Francisco Ciruela, Ralf Jockers, Igor Jurisica, Igor Stagljar

“…Abstract G‐protein‐coupled receptors (GPCRs) are the largest family of integral membrane receptors with key roles in regulating signaling pathways targeted by therapeutics, but are difficult to study using existing proteomics technologies due to their complex biochemical features. …”
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Mechanism for microbial population collapse in a fluctuating resource environment by Serdar Turkarslan, Arjun V Raman, Anne W Thompson, Christina E Arens, Mark A Gillespie, Frederick von Netzer, Kristina L Hillesland, Sergey Stolyar, Adrian López García de Lomana, David J Reiss, Drew Gorman‐Lewis, Grant M Zane, Jeffrey A Ranish, Judy D Wall, David A Stahl, Nitin S Baliga

“…We have characterized the mechanism for collapse by conducting RNA‐seq analysis, proteomics, microcalorimetry, and single‐cell transcriptome analysis. …”
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Alternative 3′ UTR polyadenylation is disrupted in the rNLS8 mouse model of ALS/FTLD by Randall J. Eck, Paul N. Valdmanis, Nicole F. Liachko, Brian C. Kraemer

“…Here, we identify significant disruptions to 3` UTR polyadenylation in the ALS/FTLD-TDP mouse model rNLS8 that correlate with changes in gene expression and protein levels through the re-analysis of published RNA sequencing and proteomic data. A subset of these changes are shared with TDP-43 knock-down mice suggesting depletion of endogenous mouse TDP-43 is a contributor to polyadenylation dysfunction in rNLS8 mice. …”
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Biological Aging and Venous Thromboembolism: A Review of Telomeres and Beyond by Rafaela Vostatek, Cihan Ay

“…Techniques such as high-throughput genomics, epigenomics, transcriptomics, proteomics, and metabolomics analyses identified and quantified numerous epigenetic markers, transcripts, proteins, and metabolites. …”
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Cytokine Patterns in Brain Tumour Progression by Radu Albulescu, Elena Codrici, Ionela Daniela Popescu, Simona Mihai, Laura Georgiana Necula, Daniel Petrescu, Mihaela Teodoru, Cristiana Pistol Tanase

“…The body’s response to cancer has many parallels with inflammation and repair; the inflammatory cells and cytokines present in tumours are more likely to contribute to tumour growth, progression, and immunosuppression, rather than in building an effective antitumour defence. Using new proteomic technology, we have investigated serum profile of pro- (IL-1β, IL-6, IL-8, IL-12, GM-CSF, and TNF-α) and anti-inflammatory cytokines (IL-4, IL-10), along with angiogenic factors (VEGF, bFGF) in order to assess tumoural aggressiveness. …”
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Molecular correlates for HPV-negative head and neck cancer engraftment prognosticate patient outcomes by Matthew Waas, Christina Karamboulas, Benson Z. Wu, Shahbaz Khan, Stephanie Poon, Jalna Meens, Meinusha Govindarajan, Amanda Khoo, Salvador Mejia-Guerrero, Annie Ha, Lydia Y. Liu, Kevin C. J. Nixon, Joseph Walton, Scott V. Bratman, Shao Hui Huang, David Goldstein, Federico Gaiti, Laurie Ailles, Thomas Kislinger

“…Here, we perform transcriptomic and proteomic profiling of 88 HNSCC patients and find the relationship between engraftment and clinical outcomes is recapitulated by molecular phenotype. …”
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