Plant and microbial sciences as key drivers in the development of metabolomics research

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(12)

Опубликована: Март 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.

Язык: Английский

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Advances in single-cell metabolomics to unravel cellular heterogeneity in plant biology

PLANT PHYSIOLOGY, Год журнала: 2023, Номер 193(2), С. 949 - 965

Опубликована: Июнь 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.

Язык: Английский

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Challenges and recent advances in quantitative mass spectrometry‐based metabolomics

Analytical Science Advances, Год журнала: 2024, Номер 5(5-6)

Опубликована: Июнь 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.

Язык: Английский

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MALDI-2-Enabled Oversampling for the Mass Spectrometry Imaging of Metabolites at Single-Cell Resolution

Journal of the American Society for Mass Spectrometry, Год журнала: 2024, Номер 35(11), С. 2729 - 2742

Опубликована: Авг. 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 (

Язык: Английский

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Recent Developments in Single-Cell Metabolomics by Mass Spectrometry─A Perspective

Journal of Proteome Research, Год журнала: 2024, Номер unknown

Опубликована: Окт. 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.

Язык: Английский

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The complex nature of heterogeneity and its roles in breast cancer biology and therapeutic responsiveness

Frontiers in Endocrinology, Год журнала: 2023, Номер 14

Опубликована: Фев. 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.

Язык: Английский

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Single-cell metabolomics by mass spectrometry: ready for primetime?

Current Opinion in Biotechnology, Год журнала: 2023, Номер 82, С. 102963 - 102963

Опубликована: Июнь 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.

Язык: Английский

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Small molecule mediators of host-T. cruzi-environment interactions in Chagas disease

PLoS Pathogens, Год журнала: 2024, Номер 20(3), С. e1012012 - e1012012

Опубликована: Март 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.

Язык: Английский

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Unveiling novel insights in acute myeloid leukemia through single-cell RNA sequencing

Frontiers in Oncology, Год журнала: 2024, Номер 14

Опубликована: Апрель 22, 2024

Acute myeloid leukemia (AML) is a complex and heterogeneous group of aggressive hematopoietic stem cell disease. The presence diverse functionally distinct populations cells within the same patient’s bone marrow or blood poses significant challenge in diagnosing treating AML. A substantial proportion AML patients demonstrate resistance to induction chemotherapy grim prognosis upon relapse. rapid advance next generation sequencing technologies, such as single-cell RNA-sequencing (scRNA-seq), has revolutionized our understanding pathogenesis by enabling high-resolution interrogation cellular heterogeneity ecosystem, their transcriptional signatures at level. New studies have successfully characterized inextricably intertwined interactions among cells, immune microenvironment contributions development, therapeutic These findings deepened broadened complexity AML, which are difficult detect with bulk RNA-seq. This review encapsulates burgeoning body knowledge generated through scRNA-seq, providing novel insights discoveries it unveiled biology. Furthermore, we discuss potential implications scRNA-seq opportunities, focusing on immunotherapy. Finally, highlight current limitations future direction field.

Язык: Английский

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A Single‐Cell Metabolic Profiling Characterizes Human Aging via SlipChip‐SERS

Advanced Science, Год журнала: 2024, Номер unknown

Опубликована: Сен. 4, 2024

Abstract Metabolic dysregulation is a key driver of cellular senescence, contributing to the progression systemic aging. The heterogeneity senescent cells and their metabolic shifts are complex unexplored. A microfluidic SlipChip integrated with surface‐enhanced Raman spectroscopy (SERS), termed SlipChip‐SERS, developed for single‐cell metabolism analysis. This SlipChip‐SERS enables compartmentalization single cells, parallel delivery saponin nanoparticles release intracellular metabolites realize SERS detection simple slipping operations. Analysis different cancer cell lines using demonstrated its capability sensitive multiplexed profiling individual cells. When applied human primary fibroblasts ages, it identified 12 differential metabolites, spermine validated as potent inducer senescence. Prolonged exposure can induce classic senescence phenotype, such increased senescence‐associated β‐glactosidase activity, elevated expression senescence‐related genes reduced LMNB1 levels. Additionally, senescence‐inducing capacity in HUVECs WRL‐68 confirmed, exogenous treatment accumulation H 2 O . Overall, novel system analysis, revealing potential across multiple types, which may offer new strategies addressing ageing ageing‐related diseases.

Язык: Английский

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