Summary of Study ST001900

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001195. The data can be accessed directly via it's Project DOI: 10.21228/M87M55 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001900
Study TitleSystemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites (part II)
Study TypeStudy part 2 of 2 (independent experiment 2; replication experiment of Study part 1)
Study SummaryPrevious reports suggest that the maturation rate of malaria parasites within red blood cells (RBC) is not constant for a given species in vivo. For instance, maturation can be influenced by host nutrient status or circadian rhythm. Here we observed in mice that systemic host inflammation, induced by lipopolysaccharide (LPS) conditioning or ongoing acute malaria infection, slowed the progression of a single cohort of parasites from one generation of RBC to the next. LPS-conditioning and acute infection both triggered substantial changes to the metabolomic composition of plasma in which parasites circulated. This altered plasma directly slowed parasite maturation in a manner that could not be rescued by supplementation, consistent with the presence of inhibitory factors. Single-cell transcriptomic assessment of mixed parasite populations, exposed to a short period of systemic host inflammation in vivo, revealed specific impairment in the transcriptional activity and translational capacity of trophozoites compared to rings or schizonts. Thus, we provide in vivo evidence of transcriptomic and phenotypic plasticity of asexual blood-stage Plasmodium parasites when exposed to systemic host inflammation
Institute
QIMR Berghofer Medical Research Institute
DepartmentCell & Molecular Biology Department
LaboratoryPrecision & Systems Biomedicine
Last NameStoll
First NameThomas
Address300 Herston Road
Emailthomas.stoll@qimrberghofer.edu.au
Phone+61 7 3845 3992
Submit Date2021-08-09
Num Groups5
Total Subjects30
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-06-26
Release Version1
Thomas Stoll Thomas Stoll
https://dx.doi.org/10.21228/M87M55
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001195
Project DOI:doi: 10.21228/M87M55
Project Title:Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites
Project Type:MS untargeted metabolomics analysis
Project Summary:Previous reports suggest that the maturation rate of malaria parasites within red blood cells (RBC) is not constant for a given species in vivo. For instance, maturation can be influenced by host nutrient status or circadian rhythm. Here we observed in mice that systemic host inflammation, induced by lipopolysaccharide (LPS) conditioning or ongoing acute malaria infection, slowed the progression of a single cohort of parasites from one generation of RBC to the next. LPS-conditioning and acute infection both triggered substantial changes to the metabolomic composition of plasma in which parasites circulated. This altered plasma directly slowed parasite maturation in a manner that could not be rescued by supplementation, consistent with the presence of inhibitory factors. Single-cell transcriptomic assessment of mixed parasite populations, exposed to a short period of systemic host inflammation in vivo, revealed specific impairment in the transcriptional activity and translational capacity of trophozoites compared to rings or schizonts. Thus, we provide in vivo evidence of transcriptomic and phenotypic plasticity of asexual blood-stage Plasmodium parasites when exposed to systemic host inflammation
Institute:QIMR Berghofer Medical Research Institute
Department:Cell & Molecular Biology Department
Laboratory:Precision & Systems Biomedicine
Last Name:Stoll
First Name:Thomas
Address:300 Herston Road, Herston QLD 4006, Australia
Email:thomas.stoll@qimrberghofer.edu.au
Phone:+61 7 3845 3992

Subject:

Subject ID:SU001978
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6J, C57BL/6J.rag1−/−
Age Or Age Range:6-8 weeks
Gender:Female

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Treatment
SA176179MP_Blank_01Blank Blank
SA176180MP_Blank_02Blank Blank
SA176181MP_Blank_03Blank Blank
SA176182MP18KO Acute Immune deficient infected control
SA176183MP27KO Acute Immune deficient infected control
SA176184MP11KO Acute Immune deficient infected control
SA176185MP24KO Acute Immune deficient infected control
SA176186MP06KO Acute Immune deficient infected control
SA176187MP08KO Acute Immune deficient infected control
SA176188MP36KO Naïve Immune deficient control
SA176189MP31KO Naïve Immune deficient control
SA176190MP33KO Naïve Immune deficient control
SA176191MP15KO Naïve Immune deficient control
SA176192MP28KO Naïve Immune deficient control
SA176193MP09KO Naïve Immune deficient control
SA176194QC_MP_04QC QC
SA176195QC_MP_05QC QC
SA176196QC_MP_06QC QC
SA176197QC_MP_02QC QC
SA176198QC_MP_03QC QC
SA176199QC_MP_01QC QC
SA176200MP30WT Acute Infected
SA176201MP22WT Acute Infected
SA176202MP02WT Acute Infected
SA176203MP01WT Acute Infected
SA176204MP16WT Acute Infected
SA176205MP21WT Acute Infected
SA176206MP05WT LPS LPS treatment
SA176207MP29WT LPS LPS treatment
SA176208MP12WT LPS LPS treatment
SA176209MP19WT LPS LPS treatment
SA176210MP26WT LPS LPS treatment
SA176211MP10WT LPS LPS treatment
SA176212MP03WT Naïve Control
SA176213MP34WT Naïve Control
SA176214MP13WT Naïve Control
SA176215MP14WT Naïve Control
SA176216MP37WT Naïve Control
SA176217MP07WT Naïve Control
Showing results 1 to 39 of 39

Collection:

Collection ID:CO001971
Collection Summary:Two independent experiments were conducted, each with 6 mice per treatment group (30 individuals in total). Mice were euthanized by CO2 asphyxiation and their blood was taken by cardiac puncture into lithium-heparin coated tubes. Samples were spun for 5 min at 5000 rpm (approx. 7,043 × g) and plasma was immediately aliquoted into 1.5 mL tubes. In addition, a global sample pool containing equal volumes of each sample was prepared as quality control (QC) and four aliquots were transferred into 1.5 mL tubes. Finally, collection tube blank extractions were performed in triplicate by adding 1x PBS (same volume as blood collection) to lithium-heparin tubes and then transferring an aliquot into a 1.5 mL tube
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001990
Treatment Summary:Genotype: Treatment C57BL/6J Naïve: Control, C57BL/6J mice were intraperitoneally injected (200 uL) with saline (0.9%) 9 hours prior to plasma acquisition. C57BL/6J Acute: Infected, C57BL/6J mice were infected with 10^5 Plasmodium berghei ANKA parasitised red blood cells 5 days prior to plasma acquisition and intraperitoneally injected (200 uL) with saline (0.9%) 9 hours prior to plasma acquisition for analysis. C57BL/6J LPS: LPS treatment, C57BL/6J mice were intraperitoneally injected (200 uL) with lipopolysaccharides (LPS) (0.75 mg/mL), from E.coli O127:B8, 9 hours prior to plasma acquisition. rag1-/- Naïve: Immune deficient control, C57BL/6J.rag1-/- mice were intraperitoneally injected (200 uL) with saline (0.9%) 9 hours prior to plasma acquisition. rag1-/- Acute: Immune deficient infected control, C57BL/6J.rag1-/- mice were infected with 10^5 Plasmodium berghei ANKA parasitised red blood cells 5 days prior to plasma acquisition and intraperitoneally injected (200 uL) with saline 9 hours prior to plasma acquisition for analysis.

Sample Preparation:

Sampleprep ID:SP001984
Sampleprep Summary:Ten-times the sample volume of ice-cold butanol/methanol (1:1) containing 50 µg/mL antioxidant 2,6-di-tert-butyl-4-methylphenol (BHT) was added to each sample and vortexed for 10 s. Samples were snap frozen and transported on dry ice. Subsequently, samples were thawed on ice and labelled in a randomized order. Samples were sonicated for 15 min in an ice-cold water bath sonicator, stored for 2 hrs at -30oC and then centrifuged for 15 min at 16,000 × g (4oC). Lastly, samples were aliquoted, dried down using a vacuum concentrator and stored at -80oC until LC/MS analysis

Combined analysis:

Analysis ID AN003087 AN003088
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent 1290 Infinity II Agilent 1290 Infinity II
Column Agilent Zorbax HILIC Plus RRHD (100 x 2.1mm,1.8um,95Å) Agilent Zorbax HILIC Plus RRHD (100 x 2.1mm,1.8um,95Å)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6545 QTOF Agilent 6545 QTOF
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH002279
Chromatography Summary:Metabolite separation was performed on a Zorbax HILIC Plus RRHD (95Å, 1.8 µm, 2.1x100mm) analytical column connected to a 3 x 5 mm Zorbax HILIC Plus UHPLC guard column. The autosampler and column temperature were set to 4°C and 40°C, respectively. In positive and negative mode, eluent A was 10 mM ammonium acetate (pH neutral) in acetonitrile/milliQ water (95:5, v/v) and eluent B was 10 mM ammonium acetate (pH neutral) in acetonitrile/milliQ water (50:50, v/v). Total method runtime was 12 min with the following gradient for both modes: 0 min (1% eluent B) - 3.5 min (50% B) - 5.5 min (99%B) - 6.5 min (99% B) - 6.7 min (1% B) - 12 min (1% B). Flow rate was set to 0.5 mL/min.
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent Zorbax HILIC Plus RRHD (100 x 2.1mm,1.8um,95Å)
Column Temperature:40
Flow Gradient:Total method runtime was 12 min with the following gradient for both modes: 0 min (1% eluent B) - 3.5 min (50% B) - 5.5 min (99%B) - 6.5 min (99% B) - 6.7 min (1% B) - 12 min (1% B). Flow rate was set to 0.5 mL/min.
Flow Rate:0.5 mL/min
Solvent A:95% acetonitrile/5% water; 10 mM ammonium acetate,pH neutral
Solvent B:50% acetonitrile/50% water; 10 mM ammonium acetate,pH neutral
Chromatography Type:HILIC

MS:

MS ID:MS002869
Analysis ID:AN003087
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS acquisition: The LC/MS platform consisted of a 1290 Infinity II UHPLC coupled to a 6545 QTOF mass spectrometer via Dual AJS ESI source (Agilent, Santa Clara, USA) and was controlled using MassHunter data acquisition software (v.10.1). Assessment of MS instrument performance and usage of reference ions were also performed as described previously. Full scan MS data (m/z 50-1700) was acquired at a scan rate of 2.5 spectra/sec (equals 3224 transients/spectrum) with the following source conditions: Gas temperature 250°C, gas flow 13 L/min, sheath gas temperature and flow at 400°C and 12 L/min, respectively, nebulizer 30 psi, fragmentor 135, capillary voltage at +4500 V and -4000 V, nozzle voltage was zero. Data processing: Positive and negative mode data was analysed separately. Data files (30 sample files, 6 QC files and 3 tube blank extraction files) were loaded into MassHunter Profinder (v 10 SP1, Agilent) and assigned to sample groups. Spectral feature extraction was performed using the recursive feature extraction method employing default settings with minor adjustments: Peak extraction was restricted to retention time (Rt) range 0-6.5 min, compound binning and alignment tolerances were set to 1% + 0.3 min for Rt and 20 ppm + 2 mDa for mass, integrator Agile 2 was used for peak integration, peak filters were set to at least 2500 counts and features must have satisfied filter conditions in at least 75 % of files in at least one sample group. Feature peak area was exported and data cleaning was performed using an in-house R script compiled of the following steps. Features were deleted if they: had a mean QC/tube blank area ratio of < 10; were absent across all QC samples; and had duplicates present. In addition, samples with a TIC scaling factor more than 50% above or below the median TIC were removed.
Ion Mode:POSITIVE
  
MS ID:MS002870
Analysis ID:AN003088
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS acquisition: The LC/MS platform consisted of a 1290 Infinity II UHPLC coupled to a 6545 QTOF mass spectrometer via Dual AJS ESI source (Agilent, Santa Clara, USA) and was controlled using MassHunter data acquisition software (v.10.1). Assessment of MS instrument performance and usage of reference ions were also performed as described previously. Full scan MS data (m/z 50-1700) was acquired at a scan rate of 2.5 spectra/sec (equals 3224 transients/spectrum) with the following source conditions: Gas temperature 250°C, gas flow 13 L/min, sheath gas temperature and flow at 400°C and 12 L/min, respectively, nebulizer 30 psi, fragmentor 135, capillary voltage at +4500 V and -4000 V, nozzle voltage was zero. Data processing: Positive and negative mode data was analysed separately. Data files (30 sample files, 6 QC files and 3 tube blank extraction files) were loaded into MassHunter Profinder (v 10 SP1, Agilent) and assigned to sample groups. Spectral feature extraction was performed using the recursive feature extraction method employing default settings with minor adjustments: Peak extraction was restricted to retention time (Rt) range 0-6.5 min, compound binning and alignment tolerances were set to 1% + 0.3 min for Rt and 20 ppm + 2 mDa for mass, integrator Agile 2 was used for peak integration, peak filters were set to at least 2500 counts and features must have satisfied filter conditions in at least 75 % of files in at least one sample group. Feature peak area was exported and data cleaning was performed using an in-house R script compiled of the following steps. Features were deleted if they: had a mean QC/tube blank area ratio of < 10; were absent across all QC samples; and had duplicates present. In addition, samples with a TIC scaling factor more than 50% above or below the median TIC were removed.
Ion Mode:NEGATIVE
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