Using ExpressAnalyst for Comprehensive Gene Expression Analysis in Model and Non‐Model Organisms DOI Creative Commons
Jessica Ewald,

Guangyan Zhou,

Yao Lü

и другие.

Current Protocols, Год журнала: 2023, Номер 3(11)

Опубликована: Ноя. 1, 2023

Abstract ExpressAnalyst is a web‐based platform that enables intuitive, end‐to‐end transcriptomics and proteomics data analysis. Users can start from FASTQ files, gene/protein abundance tables, or lists. will perform read quantification, gene expression table processing normalization, differential analysis, meta‐analysis with complex study designs. The results are presented via various interactive visualizations such as volcano plots, heatmaps, networks, ridgeline charts, built‐in functional enrichment analysis to allow flexible exploration understanding. currently contains support for 29 common organisms. For non‐model organisms without good reference genomes, it comprehensive transcriptome profiling directly RNA‐seq reads. These tasks covered in 11 Basic Protocols. © 2023 Authors. Current Protocols published by Wiley Periodicals LLC. Protocol 1 : count uploading, processing, normalization 2 Differential linear models 3 Functional plot, network, visualization 4 Hierarchical clustering of using heatmaps 5 Cross‐species based on ortholog mapping 6 Proteomics microarray 7 Preparing multiple tables 8 Statistical 9 signatures 10 Dose‐response time‐series reads quantification transcriptomes

Язык: Английский

A sustainable approach to universal metabolic cancer diagnosis DOI
Ruimin Wang, Shouzhi Yang, Mengfei Wang

и другие.

Nature Sustainability, Год журнала: 2024, Номер 7(5), С. 602 - 615

Опубликована: Апрель 22, 2024

Язык: Английский

Процитировано

29

Selenium reduction of ubiquinone via SQOR suppresses ferroptosis DOI
Namgyu Lee, Sung Jin Park,

Mike Lange

и другие.

Nature Metabolism, Год журнала: 2024, Номер 6(2), С. 343 - 358

Опубликована: Фев. 13, 2024

Язык: Английский

Процитировано

23

Reproducible mass spectrometry data processing and compound annotation in MZmine 3 DOI
Steffen Heuckeroth, Tito Damiani, Aleksandr Smirnov

и другие.

Nature Protocols, Год журнала: 2024, Номер 19(9), С. 2597 - 2641

Опубликована: Май 20, 2024

Язык: Английский

Процитировано

22

A non‐metal single atom nanozyme for cutting off the energy and reducing power of tumors DOI
Junjie Cheng, Li Li,

Duo Jin

и другие.

Angewandte Chemie International Edition, Год журнала: 2024, Номер 63(16)

Опубликована: Фев. 16, 2024

Enzymes are considered safe and effective therapeutic tools for various diseases. With the increasing integration of biomedicine nanotechnology, artificial nanozymes offer advanced controllability functionality in medical design. However, several notable gaps, such as catalytic diversity, specificity biosafety, still exist between their native counterparts. Here we report a non-metal single-selenium (Se)-atom nanozyme (SeSAE), which exhibits potent nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-mimetic activity. This novel single atom provides alternative to conventional metal-based catalysts effectively cuts off cellular energy reduction equivalents through its distinctive function tumors. In this study, have demonstrated substantial efficacy SeSAE an antitumor nanomedicine across diverse mouse models without discernible systemic adverse effects. The mechanism NADPH oxidase-like activity was rationalized by density functional theory calculations. Furthermore, comprehensive elucidation biological functions, cell death pathways, metabolic remodeling effects conducted, aiming provide valuable insights into development with clinical translation potential.

Язык: Английский

Процитировано

17

The critical role that spectral libraries play in capturing the metabolomics community knowledge DOI
Wout Bittremieux, Mingxun Wang, Pieter C. Dorrestein

и другие.

Metabolomics, Год журнала: 2022, Номер 18(12)

Опубликована: Ноя. 19, 2022

Язык: Английский

Процитировано

63

Engineered Extracellular Vesicles Derived from Dermal Fibroblasts Attenuate Inflammation in a Murine Model of Acute Lung Injury DOI Creative Commons
Ana I. Salazar‐Puerta, María A. Rincon‐Benavides, Tatiana Z. Cuellar‐Gaviria

и другие.

Advanced Materials, Год журнала: 2023, Номер 35(28)

Опубликована: Апрель 29, 2023

Acute respiratory distress syndrome (ARDS) represents a significant burden to the healthcare system, with ≈200 000 cases diagnosed annually in USA. ARDS patients suffer from severe refractory hypoxemia, alveolar-capillary barrier dysfunction, impaired surfactant function, and abnormal upregulation of inflammatory pathways that lead intensive care unit admission, prolonged hospitalization, increased disability-adjusted life years. Currently, there is no cure or FDA-approved therapy for ARDS. This work describes implementation engineered extracellular vesicle (eEV)-based nanocarriers targeted nonviral delivery anti-inflammatory payloads inflamed/injured lung. The results show ability protein A (SPA)-functionalized IL-4- IL-10-loaded eEVs promote intrapulmonary retention reduce inflammation, both vitro vivo. Significant attenuation observed tissue damage, proinflammatory cytokine secretion, macrophage activation, influx protein-rich fluid, neutrophil infiltration into alveolar space as early 6 h post-eEVs treatment. Additionally, metabolomics analyses eEV treatment causes changes metabolic profile inflamed lungs, driving secretion key metabolites. Altogether, these establish potential derived dermal fibroblasts prevalence/progression injury during via genes/transcripts.

Язык: Английский

Процитировано

39

L-arginine metabolism inhibits arthritis and inflammatory bone loss DOI
Shan Cao, Yixuan Li, Rui Song

и другие.

Annals of the Rheumatic Diseases, Год журнала: 2023, Номер 83(1), С. 72 - 87

Опубликована: Сен. 29, 2023

Objectives To investigate the effect of L-arginine metabolism on arthritis and inflammation-mediated bone loss. Methods was applied to three models (collagen-induced arthritis, serum-induced human TNF transgenic mice). Inflammation assessed clinically histologically, while changes were quantified by μCT histomorphometry. In vitro, effects osteoclast differentiation analysed RNA-seq mass spectrometry (MS). Seahorse, Single Cell ENergetIc profilIng Translation inHibition transmission electron microscopy used for detecting metabolic in osteoclasts. Moreover, arginine-associated metabolites measured serum rheumatoid (RA) pre-RA patients. Results inhibited loss all directly blocked TNFα-induced murine osteoclastogenesis. MS analyses indicated that switched glycolysis oxidative phosphorylation inflammatory osteoclasts leading increased ATP production, purine elevated inosine hypoxanthine levels. Adenosine deaminase inhibitors blocking production abolished inhibition osteoclastogenesis vitro vivo. Altered arginine levels also found RA Conclusion Our study demonstrated ameliorates erosion through reprogramming perturbation

Язык: Английский

Процитировано

35

Metabolomics and transcriptomics based multi-omics integration reveals radiation-induced altered pathway networking and underlying mechanism DOI Creative Commons
Kiran Maan, Ruchi Baghel, Seema Dhariwal

и другие.

npj Systems Biology and Applications, Год журнала: 2023, Номер 9(1)

Опубликована: Сен. 9, 2023

Recent advancement in integrated multi-omics has significantly contributed to many areas of the biomedical field. Radiation research also grasped uprising omics technologies biomarker identification aid triage management. Herein, we have used a combinatorial approach based on transcriptomics together with metabolomics and lipidomics blood from murine exposed 1 Gy (LD) 7.5 (HD) total-body irradiation (TBI) for comprehensive understanding biological processes through pathways networking. Both displayed demarcation HD group controls using multivariate analysis. Dysregulated amino acids, various PC, PE carnitine were observed along dysregulated genes (Nos2, Hmgcs2, Oxct2a, etc.). Joint-Pathway Analysis STITCH interaction showed radiation exposure resulted changes acid, carbohydrate, lipid, nucleotide, fatty acid metabolism. Elicited immune response was by Gene Ontology. BioPAN predicted Elovl5, Elovl6 Fads2 pathways, only group. Collectively, combined facilitated better uncovering metabolic pathways. Presumably, this is first that utilized an following TBI mice. Our work integration could be valuable tool comprehending mechanism as well molecular interactions.

Язык: Английский

Процитировано

32

Parallel CRISPR-Cas9 screens identify mechanisms of PLIN2 and lipid droplet regulation DOI Creative Commons

Melissa A. Roberts,

Kirandeep K. Deol,

Alyssa J. Mathiowetz

и другие.

Developmental Cell, Год журнала: 2023, Номер 58(18), С. 1782 - 1800.e10

Опубликована: Июль 25, 2023

Despite the key roles of perilipin-2 (PLIN2) in governing lipid droplet (LD) metabolism, mechanisms that regulate PLIN2 levels remain incompletely understood. Here, we leverage a set genome-edited human reporter cell lines series CRISPR-Cas9 loss-of-function screens, identifying genetic modifiers influence expression and post-translational stability under different metabolic conditions types. These regulators include canonical genes control metabolism as well involved ubiquitination, transcription, mitochondrial function. We further demonstrate role for E3 ligase MARCH6 regulating triacylglycerol biosynthesis, thereby influencing LD abundance stability. Finally, our CRISPR screens several published provide foundation CRISPRlipid (http://crisprlipid.org), an online data commons lipid-related functional genomics data. Our study identifies regulation provides extensive resource exploration biology metabolism.

Язык: Английский

Процитировано

30

Multi-omics blood atlas reveals unique features of immune and platelet responses to SARS-CoV-2 Omicron breakthrough infection DOI Creative Commons
Hong Wang, Cuicui Liu, Xiaowei Xie

и другие.

Immunity, Год журнала: 2023, Номер 56(6), С. 1410 - 1428.e8

Опубликована: Май 17, 2023

Язык: Английский

Процитировано

29