Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single‐cell metabolomics DOI Creative Commons
Dirk Wevers, Rawi Ramautar, Charles Clark

et al.

Electrophoresis, Journal Year: 2023, Volume and Issue: 44(24), P. 2000 - 2024

Published: Sept. 5, 2023

Abstract Single‐cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques single‐cell analysis. As metabolome provides closest view of status quo cell, studying at resolution may unravel said heterogeneity. A challenge analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes a wide range analyte concentrations. Due high sensitivity resolution, MS preferred metabolomics. Large numbers cells analysed proper statistics; this requires high‐throughput analysis, hence automation workflow. Significant advances (micro)sampling methods, CE ion mobility spectrometry have been made, some which applied analyses. Microfluidics has enabled an cell picking metabolite extraction; image recognition automated identification. Many used data varying from conventional novel combinations advanced chemometric approaches. Steps set making more findable, accessible, interoperable reusable, but significant opportunities improvement remain. Herein, workflows are discussed, recommendations made based on experimental goal.

Language: Английский

Plant and microbial sciences as key drivers in the development of metabolomics research DOI Creative Commons
Asaph Aharoni, Royston Goodacre, Alisdair R. Fernie

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(12)

Published: March 17, 2023

This year marks the 25th anniversary of coinage term metabolome [S. G. Oliver et al ., Trends Biotech. 16 , 373–378 (1998)]. As field rapidly advances, it is important to take stock progress which has been made best inform disciplines future. While a medical-centric perspective on metabolomics recently published [M. Giera Cell Metab. 34 21–34 (2022)], this largely ignores pioneering contributions by plant and microbial science communities. In perspective, we provide contemporary overview all fields in employed with particular emphasis both methodological application breakthroughs sciences that have shaped evolving research discipline from very early days its establishment. will not cover types assays currently but focus mainly those utilizing mass spectrometry–based measurements since they are far most prominent. Having established historical context metabolomics, address key challenges facing offer potential approaches these can be faced. Most salient among fact vast majority features as yet annotated high confidence; what may refer definitive identification. We discuss standard compound libraries artificial intelligence technologies challenge use natural variance–based such genome-wide association studies attempt assign specific functions myriad structurally similar complex specialized metabolites. conclude stating our contention epic need greater cooperative efforts biologists, chemists, computer scientists an interest kingdoms life than date. Ultimately, better linkage genome data likely also needed particularly considering Earth BioGenome Project.

Language: Английский

Citations

30
Advances in single-cell metabolomics to unravel cellular heterogeneity in plant biology DOI Creative Commons
Kanchana Pandian, Minami Matsui, Thomas Hankemeier

et al.

PLANT PHYSIOLOGY, Journal Year: 2023, Volume and Issue: 193(2), P. 949 - 965

Published: June 20, 2023

Single-cell metabolomics is a powerful tool that can reveal cellular heterogeneity and elucidate the mechanisms of biological phenomena in detail. It promising approach studying plants, especially when has an impact on different processes. In addition, metabolomics, which be regarded as detailed phenotypic analysis, expected to answer previously unrequited questions will lead expansion crop production, increased understanding resistance diseases, other applications well. this review, we introduce flow sample acquisition single-cell techniques facilitate adoption metabolomics. Furthermore, summarized reviewed.

Language: Английский

Citations

19
Challenges and recent advances in quantitative mass spectrometry‐based metabolomics DOI Open Access

Nathan Ghafari,

Lekha Sleno

Analytical Science Advances, Journal Year: 2024, Volume and Issue: 5(5-6)

Published: June 1, 2024

Abstract The field of metabolomics has gained tremendous interest in recent years. Whether the goal is to discover biomarkers related certain pathologies or better understand impact a drug contaminant, numerous studies have demonstrated how crucial it variations metabolism. Detailed knowledge metabolic variabilities can lead more effective treatments, as well faster less invasive diagnostics. Exploratory approaches are often employed metabolomics, using relative quantitation look at perturbations between groups samples. Most been based on metabolite profiling quantitation, with very few an approach for absolute quantitation. Using accurate facilitates comparison different studies, enabling longitudinal studies. In this review, we discuss most widely used techniques quantitative mass spectrometry (MS). Various aspects will be addressed, such use external and/or internal standards, derivatization techniques, vivo isotopic labelling, MS imaging. principles, associated limitations and challenges, described each approach.

Language: Английский

Citations

7
Metabolomic and gene networks approaches reveal the role of mitochondrial membrane proteins in response of human melanoma cells to THz radiation DOI
Е. А. Бутикова,

N. V. Basov,

Artem D. Rogachev

et al.

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Journal Year: 2025, Volume and Issue: unknown, P. 159595 - 159595

Published: Jan. 1, 2025

Language: Английский

Citations

1
The complex nature of heterogeneity and its roles in breast cancer biology and therapeutic responsiveness DOI Creative Commons
Karla Andrade de Oliveira, Surojeet Sengupta,

Anil Yadav

et al.

Frontiers in Endocrinology, Journal Year: 2023, Volume and Issue: 14

Published: Feb. 23, 2023

Heterogeneity is a complex feature of cells and tissues with many interacting components. Depending on the nature research context, features cellular, drug response, genetic, molecular, spatial, temporal, vascular heterogeneity may be present. We describe various forms examples their interactions how they play role in affecting cellular phenotype responses breast cancer. While most widely described invoked, are evident within tumor microenvironment affect to endocrine cytotoxic drugs used standard clinical care. Drug response critical determinant curative potential also multifaceted when encountered. The interactive some readily apparent. For example, process metastasis has properties both temporal spatial host, whereas each individual metastatic deposit exhibit heterogeneity. This review describes heterogeneity, integrated activities, offers insights into understood studied future.

Language: Английский

Citations

14
MALDI-2-Enabled Oversampling for the Mass Spectrometry Imaging of Metabolites at Single-Cell Resolution DOI
Jayden C. McKinnon, Rachelle Balez, Reuben S. E. Young

et al.

Journal of the American Society for Mass Spectrometry, Journal Year: 2024, Volume and Issue: 35(11), P. 2729 - 2742

Published: Aug. 13, 2024

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can provide valuable insights into the metabolome of complex biological systems such as organ tissues and cells. However, obtaining metabolite data at single-cell spatial resolutions presents a few technological challenges. Generally, resolution is defined by increment sample stage moves between ablation spots. Stage movements less than diameter focused beam (

Language: Английский

Citations

6
Recent Developments in Single-Cell Metabolomics by Mass Spectrometry─A Perspective DOI Creative Commons
Boryana Petrova, Arzu Tuğçe Güler

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 22, 2024

Recent advancements in single-cell (sc) resolution analyses, particularly sc transcriptomics and proteomics, have revolutionized our ability to probe understand cellular heterogeneity. The study of metabolism through small molecules, metabolomics, provides an additional level information otherwise unattainable by or proteomics shedding light on the metabolic pathways that translate gene expression into functional outcomes. Metabolic heterogeneity, critical health disease, impacts developmental outcomes, disease progression, treatment responses. However, dedicated approaches probing metabolome not reached maturity other omics technologies. Over past decade, innovations metabolomics addressed some practical limitations, including cell isolation, signal sensitivity, throughput. To fully exploit their potential biological research, however, remaining challenges must be thoroughly addressed. Additionally, integrating with orthogonal techniques will required validate relevant results gain systems-level understanding. This perspective offers a broad-stroke overview recent mass spectrometry (MS)-based advancements, focusing ongoing from biologist's viewpoint, aimed at addressing pertinent innovative questions. we emphasize use showcase systems these sophisticated methodologies are apt explore.

Language: Английский

Citations

6
Single-cell metabolomics by mass spectrometry: ready for primetime? DOI Creative Commons

Congrou Zhang,

Sylvia E. Le Dévédec, Ahmed Ali

et al.

Current Opinion in Biotechnology, Journal Year: 2023, Volume and Issue: 82, P. 102963 - 102963

Published: June 24, 2023

Single-cell metabolomics (SCMs) is a powerful tool for studying cellular heterogeneity by providing insight into the differences between individual cells. With development of set promising SCMs pipelines, this maturing technology expected to be widely used in biomedical research. However, before ready primetime, there are some challenges overcome. In review, we summarize trends and SCMs. We also highlight latest methodologies, applications, sketch perspective integration with other omics imaging approaches.

Language: Английский

Citations

13
Integrating ion mobility into comprehensive multidimensional metabolomics workflows: critical considerations DOI
Jody C. May, John A. McLean

Metabolomics, Journal Year: 2022, Volume and Issue: 18(12)

Published: Dec. 6, 2022

Language: Английский

Citations

19
Small molecule mediators of host-T. cruzi-environment interactions in Chagas disease DOI Creative Commons
Godwin Kwakye-Nuako,

Caitlyn E. Middleton,

Laura‐Isobel McCall

et al.

PLoS Pathogens, Journal Year: 2024, Volume and Issue: 20(3), P. e1012012 - e1012012

Published: March 8, 2024

Small molecules (less than 1,500 Da) include major biological signals that mediate host-pathogen-microbiome communication. They also key intermediates of metabolism and critical cellular building blocks. Pathogens present with unique nutritional needs restrict pathogen colonization or promote tissue damage. In parallel, parts host are responsive to immune signaling regulated by cascades. These interactions can trigger both adaptive maladaptive metabolic changes in the host, microbiome-derived contributing disease progression. turn, targeting is an important strategy develop new treatments for infectious diseases. Trypanosoma cruzi a single-celled eukaryotic causative agent Chagas disease, neglected tropical associated cardiac intestinal dysfunction. Here, we discuss role small during T . infection its vector mammalian host. We integrate these findings build theoretical interpretation how drive extrapolate on guide drug development.

Language: Английский

Citations

4