Mass spectrometry imaging for spatially resolved multi-omics molecular mapping DOI Creative Commons
Hua Zhang,

K. Lu,

Malik Ebbini

et al.

npj Imaging, Journal Year: 2024, Volume and Issue: 2(1)

Published: July 17, 2024

Abstract The recent upswing in the integration of spatial multi-omics for conducting multidimensional information measurements is opening a new chapter biological research. Mapping landscape various biomolecules including metabolites, proteins, nucleic acids, etc., and even deciphering their functional interactions pathways believed to provide more holistic nuanced exploration molecular intricacies within living systems. Mass spectrometry imaging (MSI) stands as forefront technique spatially mapping metabolome, lipidome, proteome diverse tissue cell samples. In this review, we offer systematic survey delineating different MSI techniques resolved analysis, elucidating principles, capabilities, limitations. Particularly, focus on advancements methodologies aimed at augmenting sensitivity specificity MSI; depict burgeoning MSI-based metabolomics, lipidomics, proteomics, encompassing synergy with other modalities. Furthermore, speculative insights into potential trajectory technology future.

Language: Английский

Gene regulatory network inference in the era of single-cell multi-omics DOI
Pau Badia-i-Mompel, Lorna Wessels, Sophia Müller‐Dott

et al.

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(11), P. 739 - 754

Published: June 26, 2023

Language: Английский

Citations

188
Using clusterProfiler to characterize multiomics data DOI
Shuangbin Xu, Erqiang Hu, Yantong Cai

et al.

Nature Protocols, Journal Year: 2024, Volume and Issue: 19(11), P. 3292 - 3320

Published: July 17, 2024

Language: Английский

Citations

150
Current insights and future perspectives of ultraviolet radiation (UV) exposure: Friends and foes to the skin and beyond the skin DOI Creative Commons
X. Tang,

Tingyi Yang,

Daojiang Yu

et al.

Environment International, Journal Year: 2024, Volume and Issue: 185, P. 108535 - 108535

Published: Feb. 27, 2024

Ultraviolet (UV) radiation is ubiquitous in the environment, which has been classified as an established human carcinogen. As largest and outermost organ of body, direct exposure skin to sunlight or UV can result sunburn, inflammation, photo-immunosuppression, photoaging even cancers. To date, there are tactics protect by preventing reducing amount skin. Nevertheless, deciphering essential regulatory mechanisms may pave way for therapeutic interventions against UV-induced disorders. Additionally, light considered beneficial specific skin-related conditions medical therapy. Recent evidence indicates that biological effects extend beyond include treatment inflammatory diseases, solid tumors certain abnormal behaviors. This review mainly focuses on Moreover, novel findings other organs systems also summarized. through affects organism remain be fully elucidated achieve a more comprehensive understanding its effects.

Language: Английский

Citations

92
A Review of Single-Cell RNA-Seq Annotation, Integration, and Cell–Cell Communication DOI Creative Commons
Changde Cheng, Wenan Chen, Hongjian Jin

et al.

Cells, Journal Year: 2023, Volume and Issue: 12(15), P. 1970 - 1970

Published: July 30, 2023

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular biology at an unprecedented resolution, enabling the characterization of heterogeneity, identification rare but significant cell types, and exploration cell-cell communications interactions. Its broad applications span both basic clinical research domains. In this comprehensive review, we survey current landscape scRNA-seq analysis methods tools, focusing on count modeling, cell-type annotation, data integration, including spatial transcriptomics, inference communication. We review challenges encountered in analysis, issues sparsity or low expression, reliability assumptions discuss potential impact suboptimal clustering differential expression tools downstream analyses, particularly identifying subpopulations. Finally, recent advancements future directions enhancing analysis. Specifically, highlight development novel annotating single-cell data, integrating interpreting multimodal datasets covering epigenomics, proteomics, inferring communication networks. By elucidating latest progress innovation, provide overview rapidly advancing field

Language: Английский

Citations

70
Guidelines for minimal information on cellular senescence experimentation in vivo DOI Creative Commons
Mikołaj Ogrodnik, Juan Carlos Acosta, Peter D. Adams

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(16), P. 4150 - 4175

Published: Aug. 1, 2024

Cellular senescence is a cell fate triggered in response to stress and characterized by stable cell-cycle arrest hypersecretory state. It has diverse biological roles, ranging from tissue repair chronic disease. The development of new tools study vivo paved the way for uncovering its physiological pathological roles testing senescent cells as therapeutic target. However, lack specific broadly applicable markers makes it difficult identify characterize tissues living organisms. To address this, we provide practical guidelines called "minimum information cellular experimentation vivo" (MICSE). presents an overview rodent tissues, transgenic models, non-mammalian systems, human tumors their use identification specification cells. These uniform, state-of-the-art, accessible toolset improve our understanding vivo.

Language: Английский

Citations

68
Benchmarking spatial clustering methods with spatially resolved transcriptomics data DOI
Zhiyuan Yuan, Fangyuan Zhao, Senlin Lin

et al.

Nature Methods, Journal Year: 2024, Volume and Issue: 21(4), P. 712 - 722

Published: March 15, 2024

Language: Английский

Citations

54
SpatialData: an open and universal data framework for spatial omics DOI Creative Commons
Luca Marconato, Giovanni Palla, Kevin A. Yamauchi

et al.

Nature Methods, Journal Year: 2024, Volume and Issue: unknown

Published: March 20, 2024

Abstract Spatially resolved omics technologies are transforming our understanding of biological tissues. However, the handling uni- and multimodal spatial datasets remains a challenge owing to large data volumes, heterogeneity types lack flexible, spatially aware structures. Here we introduce SpatialData, framework that establishes unified extensible multiplatform file-format, lazy representation larger-than-memory data, transformations alignment common coordinate systems. SpatialData facilitates annotations cross-modal aggregation analysis, utility which is illustrated in context multiple vignettes, including integrative analysis on Xenium Visium breast cancer study.

Language: Английский

Citations

54
Transitioning single-cell genomics into the clinic DOI
Jennifer Lim, Venessa Chin, Kirsten A. Fairfax

et al.

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(8), P. 573 - 584

Published: May 31, 2023

Language: Английский

Citations

49
Cell–cell communication: new insights and clinical implications DOI Creative Commons

Jimeng Su,

Ying Song,

Zhipeng Zhu

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2024, Volume and Issue: 9(1)

Published: Aug. 7, 2024

Multicellular organisms are composed of diverse cell types that must coordinate their behaviors through communication. Cell-cell communication (CCC) is essential for growth, development, differentiation, tissue and organ formation, maintenance, physiological regulation. Cells communicate direct contact or at a distance using ligand-receptor interactions. So cellular encompasses two processes: signal conduction generation intercellular transmission signals, transduction reception procession signals. Deciphering networks critical understanding metabolism. First, we comprehensively review the historical milestones in CCC studies, followed by detailed description mechanisms molecule importance main signaling pathways they mediate maintaining biological functions. Then systematically introduce series human diseases caused abnormalities progress clinical applications. Finally, summarize various methods monitoring interactions, including imaging, proximity-based chemical labeling, mechanical force analysis, downstream analysis strategies, single-cell technologies. These aim to illustrate how functions depend on these interactions complexity regulatory regulate crucial processes, homeostasis, immune responses diseases. In addition, this enhances our processes occur after cell-cell binding, highlighting its application discovering new therapeutic targets biomarkers related precision medicine. This collective provides foundation developing targeted drugs personalized treatments.

Language: Английский

Citations

46
A Comprehensive Review of Artificial Intelligence Approaches in Omics Data Processing: Evaluating Progress and Challenges DOI Creative Commons

Ali Mahmoud Ali,

Mazin Abed Mohammed

International Journal of Mathematics Statistics and Computer Science, Journal Year: 2023, Volume and Issue: 2, P. 114 - 167

Published: Dec. 25, 2023

The primary objective of this study is to review and assess the best available research on omics-related artificial intelligence (AI) methods. Furthermore, it seeks demonstrate promise AI approaches in omics data analysis identify critical problems that must be solved achieve potential fully. There are many moving parts when trying make sense a plethora through literature review. Essential components include, for instance, clinical applications collections. Other researchers have faced challenges, existing highlights them. Using systematic strategy, we searched all relevant articles utilizing multiple keyword variations. We also seek additional research, such as guidelines, studies comparison, studies. Challenges with AI, preprocessing, datasets, validation models, testbed arose was used analyze data. To solve these problems, several pertinent investigations were carried out. Our work offers unique insights into intersection model fields, setting apart from prior articles. anticipate practitioners seeking an all-encompassing perspective using processing would find study's findings invaluable.

Language: Английский

Citations

45