Brown Adipose Tissue undergoes pathological perturbations and shapes C2C12 myoblast homeostasis in the SOD1-G93A mouse model of Amyotrophic Lateral Sclerosis by Marco Rosina, Silvia Scaricamazza, Flaminia Riggio, Gianmarco Fenili, Flavia Giannessi, Alessandro Matteocci, Valentina Nesci, Illari Salvatori, Daniela F. Angelini, Katia Aquilano, Valerio Chiurchiù, Daniele Lettieri Barbato, Nicola Biagio Mercuri, Cristiana Valle, Alberto Ferri

“…In this study, we employed a multi-omics approach, including RNA sequencing (GEO identifier GSE273052) and proteomics (ProteomeXchange identifier PXD054147), to investigate the alterations in BAT and its EVs in the SOD1-G93A mouse model of ALS. …”
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Podophyllotoxin mediates hepatic toxicity via the C5a/C5aR/ROS/NLRP3 and cGMP/PKG/mTOR axis in rats based on toxicological evidence chain (TEC) concept by phosphoproteomic analysis by Chuanxin Liu, Xiaobin Huang, Jiao Kong, Xuejiao Li, Yuming Wang, Fangfang Zhang, Jiajia Duan

“…Histopathological examination revealed liver sinusoidal congestion in the liver tissue (AOE). Omics analysis revealed that hepatotoxicity primarily affected the complement-pyroptosis and cGMP-PKG-autophagy pathways. …”
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Slow Metabolism–Driven Amplification of Hepatic PPARγ Agonism Mediates Benzbromarone‐Induced Obesity‐Specific Liver Injury by Guanting Li, Yourong Hu, Han Zhao, Ziyu Peng, Xin Shang, Jia Zhang, Kunxin Xie, Meiwei Li, Xiaohang Zhou, Qinyao Zhou, Kai Li, Fang Zhou, Heyao Wang, Zhijian Xu, Jiali Liu, Peng Sun

“…In this study, through a combined multi‐omics, pharmacological, and pharmacokinetic approaches, it is found that BBR‐induced obesity‐specific DILI is primarily through the potentiation of peroxisome proliferator‐activated receptor gamma (PPARγ) signaling pathways. …”
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Multilevel plasticity and altered glycosylation drive aggressiveness in hypoxic and glucose-deprived bladder cancer cells by Andreia Peixoto, Dylan Ferreira, Andreia Miranda, Marta Relvas-Santos, Rui Freitas, Tim S. Veth, Andreia Brandão, Eduardo Ferreira, Paula Paulo, Marta Cardoso, Cristiana Gaiteiro, Sofia Cotton, Janine Soares, Luís Lima, Filipe Teixeira, Rita Ferreira, Carlos Palmeira, Albert J.R. Heck, Maria José Oliveira, André M.N. Silva, Lúcio Lara Santos, José Alexandre Ferreira

“…The molecular mechanisms facilitating cellular adaptation to these stimuli remain largely elusive. Employing a multi-omics approach, we discovered that hypoxic and glucose-deprived cancer cells enter a quiescent state supported by mitophagy, fatty acid β-oxidation, and amino acid catabolism, concurrently enhancing their invasive capabilities. …”
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Understanding the Immune System and Biospecimen-Based Response in Glioblastoma: A Practical Guide to Utilizing Signal Redundancy for Biomarker and Immune Signature Discovery by Luke R. Jackson, Anna Erickson, Kevin Camphausen, Andra V. Krauze

“…The key to understanding the true nature of these interactions is through multi-omic analysis of tumor progression and treatment response. …”
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Engineering dual-driven pro-angiogenic nanozyme based on porous silicon for synergistic acceleration of burn infected wound healing by Wei Duan, Yue Gao, Ruru Xu, Sheng Huang, Xueqian Xia, Jingwen Zhao, Longhuan Zeng, Qiaolin Wei, Jia-Wei Shen, Jianmin Wu, Yongke Zheng

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Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink by Lejla Gul, Anna Julia Elias, Tanvi Tambaku, Marton Olbei, Emily Watters, Balazs Bohar, Dezso Modos, Matthew Madgwick, Tamas Korcsmaros

“…The protocol outlines procedures for predicting protein-protein interactions through domain-motif interactions, integrating multi-omic datasets to map downstream effects, performing network analyses to identify key regulatory pathways, and visualizing multi-layered networks for systems-level data interpretation.For complete details on the use and execution of this protocol, please refer to Gul et al.1 and Poletti et al.2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
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Lipid metabolism and microbial regulation analyses provide insights into the energy-saving strategies of hibernating snakes by Yuting Wei, Huirong Mao, Qiuhong Liu, Wenjie Fang, Tianxiang Zhang, Yongtao Xu, Weiwei Zhang, Biao Chen, Yunlin Zheng, Xiaolong Hu

“…In order to provide insights into the energy metabolism and potential microbial regulatory mechanisms in hibernating snakes, the serum, liver, gut content samples were measured by multi-omic methods. Here we show the active snakes have more vigorous lipid metabolism, whereas snakes in hibernation groups have higher sphingolipid metabolism. …”
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Cell-Sonar, an Easy and Low-cost Method to Track a Target Protein by Expression Changes of Specific Protein Markers by Sabrina Brockmöller, Lara Molitor, Franz Worek, Simone Rothmiller

“…Detailed microscopy for protein co-localization detection or omic technologies, which provide holistic network data, are elaborate, mostly complex, and expensive to apply. …”
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A Novel PET Imaging Using 64Cu-Labeled Monoclonal Antibody against Mesothelin Commonly Expressed on Cancer Cells by Kazuko Kobayashi, Takanori Sasaki, Fumiaki Takenaka, Hiromasa Yakushiji, Yoshihiro Fujii, Yoshiro Kishi, Shoichi Kita, Lianhua Shen, Hiromi Kumon, Eiji Matsuura

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Using multiomic integration to improve blood biomarkers of major depressive disorder: a case-control studyResearch in context by Amazigh Mokhtari, El Chérif Ibrahim, Arnaud Gloaguen, Claire-Cécile Barrot, David Cohen, Margot Derouin, Hortense Vachon, Guillaume Charbonnier, Béatrice Loriod, Charles Decraene, Ipek Yalcin, Cynthia Marie-Claire, Bruno Etain, Raoul Belzeaux, Andrée Delahaye-Duriez, Pierre-Eric Lutz

“…Case-control comparisons were conducted for each omic layer. We also defined gene coexpression networks, followed by step-by-step annotations across omic layers. …”
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Biological correlates associated with high-risk breast cancer patients identified using a computational method by Jung Hun Oh, Fresia Pareja, Rena Elkin, Kaiming Xu, Larry Norton, Joseph O. Deasy

“…Abstract Using a novel unsupervised method to integrate multi-omic data, we previously identified a breast cancer group with a poor prognosis. …”
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Distinct immune cell infiltration patterns in pancreatic ductal adenocarcinoma (PDAC) exhibit divergent immune cell selection and immunosuppressive mechanisms by Shivan Sivakumar, Ashwin Jainarayanan, Edward Arbe-Barnes, Piyush Kumar Sharma, Maire Ni Leathlobhair, Sakina Amin, David J. Reiss, Lara Heij, Samarth Hegde, Assaf Magen, Felicia Tucci, Bo Sun, Shihong Wu, Nithishwer Mouroug Anand, Hubert Slawinski, Santiago Revale, Isar Nassiri, Jonathon Webber, Gerard D. Hoeltzel, Adam E. Frampton, Georg Wiltberger, Ulf Neumann, Philip Charlton, Laura Spiers, Tim Elliott, Maria Wang, Suzana Couto, Thomas Lila, Pallavur V. Sivakumar, Alexander V. Ratushny, Mark R. Middleton, Dimitra Peppa, Benjamin Fairfax, Miriam Merad, Michael L. Dustin, Enas Abu-Shah, Rachael Bashford-Rogers

“…A comprehensive analysis of single-cell multi-omic data from matched tumour-infiltrated CD45+ cells and peripheral blood in 12 patients, and two published datasets, reveals a complex immune infiltrate. …”
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Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM12 mice reveals pathogen-specific host and microbiota responses by Mathias K.-M. Herzog, Audrey Peters, Nizar Shayya, Monica Cazzaniga, Kardokh Kaka Bra, Trisha Arora, Manja Barthel, Ersin Gül, Luca Maurer, Patrick Kiefer, Philipp Christen, Katharina Endhardt, Julia A. Vorholt, Gad Frankel, Markus M. Heimesaat, Stefan Bereswill, Cormac G. M. Gahan, Marcus J. Claesson, Xavier Domingo-Almenara, Wolf-Dietrich Hardt

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Improving Geldanamycin Production in <i>Streptomyces geldanamycininus</i> Through UV Mutagenesis of Protoplast by Yuan Yuan, Lu Yang, Zhikai Fang, Haimin Chen, Fei Sun, Hong Jiang, Jian Zhou

“…A mutant strain that produced 3742 μg/mL geldanamycin was generated by protoplast UV mutagenesis, with a 36% higher yield than the initial strain. Multi-omic analysis revealed that the high-yielding geldanamycin in mutant strain 53 could upregulate <i>GdmG</i> and <i>GdmX</i> by 1.59 and 2.38 times in the ansamycin synthesis pathway, and downregulate <i>pks12</i>, <i>pikAI</i>, and <i>pikAII</i> by 0.25, 0.37, and 0.48 times in the fatty acid synthesis pathway, which was crucial for geldanamycin production. …”
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Covariation Between Microbiome Composition and Host Transcriptome in the Gut of Wild Drosophila melanogaster: A Re‐Analysis by Frances Llanwarne, Adam J. Dobson

“…The fruitfly Drosophila melanogaster is a preeminent model organism, amenable to field investigation by ‘omic analyses. Previous work in wild male D. melanogaster guts analysed paired measurements of (A) bacterial diversity and abundance, measured by 16S amplicon sequencing; and (B) the host gut transcriptome, but no signature of covariation was detected. …”
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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

“…Abstract Investigating venetoclax (VTX) resistance in multiple myeloma (MM) is crucial for the development of novel therapeutic strategies to tackle resistance. 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. …”
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Advancing precision medicine: the transformative role of artificial intelligence in immunogenomics, radiomics, and pathomics for biomarker discovery and immunotherapy optimization by Luchen Chang, Jiamei Liu, Jialin Zhu, Shuyue Guo, Yao Wang, Zhiwei Zhou, Xi Wei

“…In immunogenomics, AI can process vast amounts of genomic and multi-omic data to identify biomarkers associated with immunotherapy responses and disease prognosis, thus providing strong support for personalized treatments. …”
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Perspectives on Structural, Physiological, Cellular, and Molecular Responses to Desiccation in Resurrection Plants by Yathisha Neeragunda Shivaraj, Plancot Barbara, Bruno Gugi, Maïté Vicré-Gibouin, Azeddine Driouich, Sharatchandra Ramasandra Govind, Akash Devaraja, Yogendra Kambalagere

“…Current progress in “-omic” technologies has enabled quantitative monitoring of the plethora of biological molecules in a high throughput routine, making it possible to compare their levels between desiccation-sensitive and DT species. …”
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Exome sequencing of UK birth cohorts [version 2; peer review: 2 approved, 1 approved with reservations] by Petr Danecek, Amy Hough, John Wright, Karen Ho, Nicholas J. Timpson, Sarah J. Lindsay, Davide Bonfanti, Daniel S. Malawsky, Rafaq Azad, Deborah Plowman, Sara Widaa, Gemma Shireby, Emla Fitzsimons, David Bann, Matthew E. Hurles, Hilary C. Martin, Susan M. Ring, Dan Mason, Michael A. Quail, Wei Huang, Vivek Iyer, Mahmoud Koko, Iaroslav Popov, Laurie Fabian, Gennadii Zakharov, Ruth Y. Eberhardt, Emma E. Wade, Qin Qin Huang

“…They collect information useful for a wide range of life course research domains, and biological samples which can be used to derive data from an increasing collection of omic technologies. This rich source of longitudinal data, when combined with genomic data, offers the scientific community valuable insights ranging from population genetics to applications across the social sciences. …”
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