Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases DOI Creative Commons
Paul Kießling, Christoph Kuppe

Genome Medicine, Journal Year: 2024, Volume and Issue: 16(1)

Published: Jan. 18, 2024

Abstract Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome parallel or even same tissue section. This review focuses on recent advancements spatial multi-omics technologies, including novel computational approaches. We discuss low-resolution high-resolution methods which can resolve up 10,000 individual molecules at subcellular level. By applying integrating these techniques, researchers recently gained valuable insights into molecular circuits mechanisms govern cell biology along cardiovascular disease spectrum. provide an overview current approaches, with focus integration datasets, highlighting strengths weaknesses various pipelines. These tools play crucial role analyzing interpreting facilitating discovery new findings, enhancing translational research. Despite nontrivial challenges, such need for standardization experimental setups, analysis, improved tools, application holds tremendous potential revolutionizing our understanding human processes identification biomarkers therapeutic targets. Exciting opportunities lie ahead field will likely contribute advancement personalized medicine diseases.

Language: Английский

Small molecule metabolites: discovery of biomarkers and therapeutic targets DOI Creative Commons
Shi Qiu, Ying Cai, Hong Yao

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: March 20, 2023

Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks diseases. Metabolite signatures that have close proximity subject's phenotypic informative dimension, are useful for predicting diagnosis prognosis diseases as well monitoring treatments. The lack early biomarkers could poor serious outcomes. Therefore, noninvasive methods with high specificity selectivity desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool biomarker pathway analysis, revealing possible mechanisms human various deciphering therapeutic potentials. It help identify functional related variation delineate biochemical changes indicators pathological damage prior disease development. Recently, scientists established large number profiles reveal underlying networks target exploration in biomedicine. This review summarized analysis on potential value small-molecule candidate metabolites clinical events, may better diagnosis, prognosis, drug screening treatment. We also discuss challenges need be addressed fuel next wave breakthroughs.

Language: Английский

Citations

388
Immune mechanisms linking metabolic injury to inflammation and fibrosis in fatty liver disease – novel insights into cellular communication circuits DOI Creative Commons
Moritz Peiseler, Robert F. Schwabe, Jochen Hampe

et al.

Journal of Hepatology, Journal Year: 2022, Volume and Issue: 77(4), P. 1136 - 1160

Published: June 22, 2022

Language: Английский

Citations

313
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

189
The pentose phosphate pathway in health and disease DOI Open Access
Tara TeSlaa, Markus Ralser, Jing Fan

et al.

Nature Metabolism, Journal Year: 2023, Volume and Issue: 5(8), P. 1275 - 1289

Published: Aug. 23, 2023

Language: Английский

Citations

188
Unbiased spatial proteomics with single-cell resolution in tissues DOI Creative Commons
Andreas Mund, Andreas‐David Brunner, Matthias Mann

et al.

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(12), P. 2335 - 2349

Published: June 1, 2022

Language: Английский

Citations

161
Artificial intelligence-based multi-omics analysis fuels cancer precision medicine DOI Open Access
Xiujing He, Xiaowei Liu,

Fengli Zuo

et al.

Seminars in Cancer Biology, Journal Year: 2022, Volume and Issue: 88, P. 187 - 200

Published: Dec. 31, 2022

Language: Английский

Citations

157
Sphingolipids control dermal fibroblast heterogeneity DOI
Laura Capolupo, Irina Khven, Alex R. Lederer

et al.

Science, Journal Year: 2022, Volume and Issue: 376(6590)

Published: April 14, 2022

Human cells produce thousands of lipids that change during cell differentiation and can vary across individual the same type. However, we are only starting to characterize function these cell-to-cell differences in lipid composition. Here, measured lipidomes transcriptomes human dermal fibroblasts by coupling high-resolution mass spectrometry imaging with single-cell transcriptomics. We found variations specific metabolic pathways contribute establishment states involved organization skin architecture. Sphingolipid composition is shown define fibroblast subpopulations, sphingolipid rewiring driving cell-state transitions. Therefore, heterogeneity affects determination states, adding a new regulatory component self-organization multicellular systems.

Language: Английский

Citations

134
Explainable multiview framework for dissecting spatial relationships from highly multiplexed data DOI Creative Commons
Jovan Tanevski, Ricardo O. Ramirez Flores, Attila Gábor

et al.

Genome biology, Journal Year: 2022, Volume and Issue: 23(1)

Published: April 14, 2022

Abstract The advancement of highly multiplexed spatial technologies requires scalable methods that can leverage information. We present MISTy, a flexible, scalable, and explainable machine learning framework for extracting relationships from any omics data, dozens to thousands measured markers. MISTy builds multiple views focusing on different or functional contexts dissect effects. evaluated in silico breast cancer datasets by imaging mass cytometry transcriptomics. estimated structural interactions coming demonstrated how relate MISTy’s results clinical features.

Language: Английский

Citations

121
Analyzing cell-type-specific dynamics of metabolism in kidney repair DOI Creative Commons
Gangqi Wang, Bram Heijs, Sarantos Kostidis

et al.

Nature Metabolism, Journal Year: 2022, Volume and Issue: 4(9), P. 1109 - 1118

Published: Aug. 25, 2022

Abstract A common drawback of metabolic analyses complex biological samples is the inability to consider cell-to-cell heterogeneity in context an organ or tissue. To overcome this limitation, we present advanced high-spatial-resolution metabolomics approach using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) combined with isotope tracing. This method allows mapping cell-type-specific dynamic changes central carbon metabolism a heterogeneous tissue architecture, such as kidney. Combined multiplexed immunofluorescence staining, can detect and nutrient partitioning targeted cell types, demonstrated bilateral renal ischemia–reperfusion injury (bIRI) experimental model. Our enables us identify region-specific perturbations associated lesion throughout recovery, including unexpected anomalies cells apparently normal phenotype recovery phase. These findings may be relevant understanding homeostatic capacity kidney microenvironment. In sum, achieve resolution at single-cell level situ hence interpret dynamics structure neighboring cells.

Language: Английский

Citations

119
To metabolomics and beyond: a technological portfolio to investigate cancer metabolism DOI Creative Commons
Federica Danzi,

Raffaella Pacchiana,

Andrea Mafficini

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: March 22, 2023

Abstract Tumour cells have exquisite flexibility in reprogramming their metabolism order to support tumour initiation, progression, metastasis and resistance therapies. These reprogrammed activities include a complete rewiring of the bioenergetic, biosynthetic redox status sustain increased energetic demand cells. Over last decades, cancer field has seen an explosion new biochemical technologies giving more tools than ever before navigate this complexity. Within cell or tissue, metabolites constitute direct signature molecular phenotype thus profiling concrete clinical applications oncology. Metabolomics fluxomics, are key technological approaches that mainly revolutionized enabling researchers both qualitative mechanistic model cancer. Furthermore, upgrade from bulk single-cell analysis provided unprecedented opportunity investigate biology at cellular resolution allowing depth quantitative complex heterogenous diseases. More recently, advent functional genomic screening allowed identification pathways, processes, biomarkers novel therapeutic targets concert with other allow patient stratification treatment regimens. This review is intended be guide for metabolism, highlighting current emerging technologies, emphasizing advantages, disadvantages potential leading development innovative anti-cancer

Language: Английский

Citations

111