Virus and host interaction: lipidomics and applications
Ampa Suksatu, Ph.D.Department of Microbiology
Faculty of Science, Mahidol University
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Family Flaviviridae• 2 important genera: Flavivirus, and
Hepacivirus (HCV)• Enveloped with a single positive-sense RNA
• Flavivirus genus consists of >50 species, many of them are arthropod-borne human pathogens
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Amplifying host Vector
Birds Mosquito (Culex)
Mosquito (Aedes)
Primates
TickRodents
Flavivirus
Cellular lipids & Flavivirus life cycle
3Martín-Acebes MA. et al. Prog Lipid Res. 2016;64:123-137.
Vesicle packet
Vesicle packets
Vesicle packet
Convoluted membrane
virion
Flavivirus infection and lipid metabolism(cell culture-based)
• WNV infected cells increased proportion of glycerophospholipids and sphingolipids (Martin-Acebes et al. 2014)
• WNV virions enriched in sphingolipids and reduced PC (Martin-Acebes et al., 2014)
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• DENV infections altered size and abundance of lipid droplets (Heaton and Randell 2010, Zhang et al. 2018)
• Evidence of alterations in lipid profiles of mosquito cell lines and midgut cells in response to DENV infection (Perera et al. 2012, Chotiwan et al. 2018)
• DENV NS3 recruited FASN to the replication site, inhibition of FASN reduced viral infection and virion production (Heaton at al. 2010, Tongluan et al., 2017)
Multiple connections of flaviviruseswith lipid metabolism
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Flavivirusinfection
Intracellular membrane remodeling
(ER)
Interaction with
peroxisomes
Interaction with lipid droplets
Regulation of cellular
lipid metabolism
Modulation of
autophagy(lipophagy)
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Cholesterol metabolism
Sphingolipid metabolism
GPL metabolism
Fatty acids
Innate immune evasionMembrane rearrangement
Virion morphogenesis
Energy sourceLipid biosynthesisViral replication
Virion morphogenesisMembrane rearrangement
Virion morphogenesisInnate immunity
Martín-Acebes MA. et al. Prog Lipid Res. 2016;64:123-137.
Flavivirus interaction with lipid metabolism
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Metabolomics & Lipidomics• Aim to study the global changes of small molecule metabolites
and lipids in biological systems in response to biological stimuli or perturbations
• Provide global views of metabolome and lipidome landscapes and implicate metabolic to disease phenotype
1. Potential serum biomarkers of infection/severity
2. Platform of antiviral strategies
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Applications:
Mass Spectrometer(DIMS/LC-MS/GC-MS)
2. Ion separation
1. IonizationElectrospray ionization (ESI) – great for polar
Atmospheric pressure chemical ionization (APCI) – great for nonpolar
There is a trade-off between speedand mass accuracy/resolution
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Ion separation, the big 3 techniques
- Very fast (up to 500 spectra/sec)
- Low mass resolution- Low mass accuracy
Quadrupole
- Fast (10-100 spectra/sec)
- Medium/high mass resolution
- Excellent mass accuracy
Time-of-flight(TOF)
- Slow (1-20 spectra/s)- Very high resolution- Excellent mass
accuracy
Orbitrap
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Untargeted vs. Targeted MS
- Analysis of all the measurable metabolites in a sample, including chemical unknowns
- Usually applied to hypothesis generation
- Rely on high resolution, accurate mass measurement and fragmentation data
- Suitable for Q-TOF/Orbitrap type instrument
Untargeted- Focus on specific compounds of
interest, which means you already know them
- Usually applied to validate novel discovery of a hypothesis
- Rely on characteristic fragmentation of molecules
- Low resolution instruments such as triple quadrupole (QQQ)
Targeted
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Selected metabolites from publications on human infections with DENV
11Byers NM. et al. Viruses. 2019;11(3). pii: E225.
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Healthy Febrile Defervescence convalescenceTemporal serum metabolome profiles with DENV infection
Metabolome was significantly perturbed
during early acute phaseand normalized to control
levels at convalescent stage
Prognostic markers of the disease
60 metabolites
Cui L. et al. PLoS Negl Trop Dis. 2013;7(8):e2373.
Q-TOF
Correlation of serum lipids with specific serological parameters
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SM => Early host response lysoPE => Late recovery response
Cui L. et al. PLoS Negl Trop Dis. 2013;7(8):e2373.
QQQ
Total and LDL-cholesterol levels are lower in serum of patients with severe dengue
14Lima W.G. et al. Rev Med Virol. 2019;29(5):e2056.
Selected metabolites from publications on CHIKV, WNV, and ZIKV
15Byers NM. et al. Viruses. 2019;11(3). pii: E225.
Lipid biomarkers from serum analysis of ZIKV-infected patients
16Melo CFOR. et al. Front Microbiol. 2017;8:1954.
DIMS Orbitrap
Serum concentration of molecular species of PE and pPE in ZIKV infected and controls patients
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6 PE molecular species
12 pPE molecular species
Queiroz A. et al. Front Microbiol. 2019;10:753.
Triple TOF
• Broad variation in response to the infection among individuals makes it difficult to identify markers of severity
• Different control groups, sample preparation methods, and sample collection time
• Types/abilities of mass spectrometer• Various studies showing the association between circulating
metabolite/lipid levels and the severity of infection so far lack consistency
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Problems in metabolome/lipidome studies from human infections with flaviviruses
Examples of lipid-related anti-flaviviral strategies
19Martín-Acebes MA. et al. Prog Lipid Res. 2016;64:123-137.
Sterols
Others
Sphingolipids
Fatty acids
Glycerophospholipids
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Effect of D609 on endogenous SM contents
Treatment with 50 μM of D609 for 16 hrsreduced total SM levels 19.50-43.73% in MEFs
SM with C16 acyl chain length was drastically suppressed by D609
↓23.39%
↓57.20%*
*
*
QQQ
Suksatu A. et al. in publication process
* *
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* *** * *
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Effect of D609 treatment on infectivity of different flaviviruses
Suksatu A. et al. (in publication process)
ZIKV
WNV Kunjin
• Repositioning/repurposing drugs that already licensed, i.e., statins (cardiovascular disease), metformin (diabetes), imipramine (antidepressant),could lead to more affordable broad spectrum, lipid-targeting compounds
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The strong dependency of cellular lipid metabolism for flavivirus infection
Biomarkers of infection/ disease progression
Lipid-based antiviral candidates(broad spectrum potential)
Novel therapeutics Repositioning drugs