Summary of Study ST001899
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.
| Study ID | ST001899 |
| Study Title | Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites (part I) |
| Study Type | Study part 1 of 2 (independent experiment 1) |
| Study 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 |
| thomas.stoll@qimrberghofer.edu.au | |
| Phone | +61 7 3845 3992 |
| Submit Date | 2021-08-09 |
| Num Groups | 5 |
| Total Subjects | 30 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-06-26 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | SU001977 |
| 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 |
|---|---|---|---|
| SA176140 | MP_Blank_02 | Blank | Blank |
| SA176141 | MP_Blank_03 | Blank | Blank |
| SA176142 | MP_Blank_01 | Blank | Blank |
| SA176143 | MP20 | KO Acute | Immune deficient infected control |
| SA176144 | MP16 | KO Acute | Immune deficient infected control |
| SA176145 | MP29 | KO Acute | Immune deficient infected control |
| SA176146 | MP11 | KO Acute | Immune deficient infected control |
| SA176147 | MP35 | KO Acute | Immune deficient infected control |
| SA176148 | MP15 | KO Acute | Immune deficient infected control |
| SA176149 | MP37 | KO Naïve | Immune deficient control |
| SA176150 | MP13 | KO Naïve | Immune deficient control |
| SA176151 | MP07 | KO Naïve | Immune deficient control |
| SA176152 | MP17 | KO Naïve | Immune deficient control |
| SA176153 | MP33 | KO Naïve | Immune deficient control |
| SA176154 | MP05 | KO Naïve | Immune deficient control |
| SA176155 | QC_MP_01 | QC | QC |
| SA176156 | QC_MP_03 | QC | QC |
| SA176157 | QC_MP_05 | QC | QC |
| SA176158 | QC_MP_02 | QC | QC |
| SA176159 | QC_MP_04 | QC | QC |
| SA176160 | QC_MP_06 | QC | QC |
| SA176161 | MP32 | WT Acute | Infected |
| SA176162 | MP25 | WT Acute | Infected |
| SA176163 | MP01 | WT Acute | Infected |
| SA176164 | MP10 | WT Acute | Infected |
| SA176165 | MP26 | WT Acute | Infected |
| SA176166 | MP22 | WT Acute | Infected |
| SA176167 | MP36 | WT LPS | LPS treatment |
| SA176168 | MP09 | WT LPS | LPS treatment |
| SA176169 | MP03 | WT LPS | LPS treatment |
| SA176170 | MP21 | WT LPS | LPS treatment |
| SA176171 | MP19 | WT LPS | LPS treatment |
| SA176172 | MP31 | WT LPS | LPS treatment |
| SA176173 | MP34 | WT Naïve | Control |
| SA176174 | MP02 | WT Naïve | Control |
| SA176175 | MP04 | WT Naïve | Control |
| SA176176 | MP08 | WT Naïve | Control |
| SA176177 | MP30 | WT Naïve | Control |
| SA176178 | MP23 | WT Naïve | Control |
| Showing results 1 to 39 of 39 |
Collection:
| Collection ID: | CO001970 |
| 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: | TR001989 |
| 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: | SP001983 |
| 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 | AN003085 | AN003086 |
|---|---|---|
| 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: | CH002278 |
| 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: | MS002867 |
| Analysis ID: | AN003085 |
| 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: | MS002868 |
| Analysis ID: | AN003086 |
| 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 |
