Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics

Earl, D.C.N.; Ferrell, P. Brent; Leelatian, Nalin; Froese, Jordan; Reisman, Benjamin J.; Irish, Jonathan M.; Bachmann, Brian O.

doi:10.1038/s41467-017-02470-8

Cited by 38 publications

(33 citation statements)

References 66 publications

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“…We used fluorescent cell barcoding for multiplex flow cytometry to identify differentially regulated markers over time in step or ramp conditions 62,63 . This functional temporal screen allows us to uniquely encode each time point sample with a combination of two dye concentrations ( Figure 2c).…”

Section: Resultsmentioning

confidence: 99%

Kinetics of osmotic stress regulates a cell fate switch of cell survival

Thiemicke

Neuert

2020

Preprint

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Exposure of cells to diverse types of stressful environments differentially regulate cell fate. Although many types of stresses causing this differential regulation are known, it is unknown how changes over time of the same stressor regulate cell fate. Changes in extracellular osmolarity are critically involved in physiological and pathophysiological processes in several tissues. We observe that human cells survive gradual but not acute hyperosmotic stress. We find that stress, caspase, and apoptosis signaling do not activate during gradual stress in contrast to acute treatments. Contrary to the current paradigm, we see a substantial accumulation of proline in cells treated with gradual but not acute stresses. We show that proline can protect cells from hyperosmotic stress similar to the osmoprotection in plants and bacteria. Our studies found a cell fate switch that enables cells to survive gradually changing stress environments by preventing caspase activation and protect cells through proline accumulation.

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Section: Resultsmentioning

confidence: 99%

Kinetics of osmotic stress regulates a cell fate switch of cell survival

Thiemicke

Neuert

2020

Preprint

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“…Furthermore, our study indicates that these signals might serve as an excellent approach to activate SM biosynthesis without genetic engineering. In future, SM production by biomediator and its application to approaches such as single cell multiplexed activity metabolomics might link with the discovery of effector molecules to human cells 31 .…”

Section: Resultsmentioning

confidence: 99%

β-carboline biomediators induce reveromycin production in Streptomyces sp. SN-593

Panthee

Takahashi

Hayashi

et al. 2019

Sci Rep

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The biosynthetic potential of soil-dwelling actinomycetes to produce diverse bioactive molecules that are useful as drug seeds has been achieved in the laboratory by modifying culture conditions. Availability of a small molecule that can induce secondary metabolism in these microbes can greatly facilitate the exploration of bioactive natural products. In this manuscript, through the screening of natural products and chemical modification, we demonstrated that the presence of the β-carboline compound, BR-1, enhanced reveromycin A production in Streptomyces sp. SN-593. BR-1 induced reveromycins production at the wide range of concentrations without affecting cell growth. Our study indicates that BR-1 might serve as an alternative to activate specialized metabolite biosynthesis without genetic engineering.

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“…Thus, a potential future avenue for these techniques is to combine bioactivity measurements with comparative metabolomics data sets. Examples of this combined approach include overlaying bioactivity to molecular networking (65) and our own multiplexed activity metabolomics (MAM) approach (66). In both cases, these methods enable an estimation of the activity of unknown compounds and structure-activity relationships within compound families prior to compound isolation using activity metabolomics techniques (65,66).…”

Section: Discussionmentioning

confidence: 99%

Response of Secondary Metabolism of Hypogean Actinobacterial Genera to Chemical and Biological Stimuli

Covington

Spraggins

Yñigez-Gutierrez

et al. 2018

Appl Environ Microbiol

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Microorganisms within microbial communities respond to environmental challenges by producing biologically active secondary metabolites, yet the majority of these small molecules remain unidentified. We have previously demonstrated that secondary metabolite biosynthesis in actinomycetes can be activated by model environmental chemical and biological stimuli, and metabolites can be identified by comparative metabolomics analyses between stimuli conditions. Herein, we survey the secondary metabolite productivity of a group of 20 phylogenetically diverse actinobacteria isolated from hypogean (cave) environments by applying a battery of stimuli consisting of exposure to antibiotics, metals, and mixed microbial culture. Comparative metabolomics was used to reveal secondary metabolite responses from stimuli. These analyses revealed substantial changes in global metabolomic dynamics with over 30 % of metabolomic features increasing more than 10-fold under at least one stimulus condition. Selected features were isolated and identified via NMR, revealing several known secondary metabolite families including the tetarimycins, aloesaponarins, hypogeamicins, actinomycins, and propeptins. One prioritized metabolite was identified to be a previously unreported aminopolyol polyketide, funisamine, produced by a cave isolate when exposed to mixed culture. The production of funisamine was most significantly increased in mixed culture with sp. The biosynthetic gene cluster responsible for the production of funisamine was identified via genomic sequencing of the producing strain, sp. KDCAGE35, which facilitated deduction of its biosynthesis. Together, these data demonstrate that comparative metabolomics can reveal the stimulus-induced production of natural products from diverse microbial phylogenies. Microbial secondary metabolites are an important source of biologically active and therapeutically relevant small molecules. However, much of this active molecular diversity is challenging to access due to low production levels or difficulty in discerning secondary metabolites within complex microbial extracts prior to isolation. Herein we demonstrate that ecological stimuli increase secondary metabolite production in phylogenetically diverse actinobacteria isolated from understudied hypogean environments. Additionally, we show that comparative metabolomics linking stimuli to metabolite response data can effectively reveal secondary metabolites within complex biological extracts. This approach highlighted secondary metabolites in almost all observed natural product classes, including low abundance analogs of biologically relevant metabolites, as well as a new linear aminopolyol polyketide, funisamine. This study demonstrates the generality of activating stimuli to potentiate secondary metabolite production across diverse actinobacterial genera.

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Discovery of human cell selective effector molecules using single cell multiplexed activity metabolomics

Cited by 38 publications

References 66 publications

Kinetics of osmotic stress regulates a cell fate switch of cell survival

Kinetics of osmotic stress regulates a cell fate switch of cell survival

β-carboline biomediators induce reveromycin production in Streptomyces sp. SN-593

Response of Secondary Metabolism of Hypogean Actinobacterial Genera to Chemical and Biological Stimuli

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