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 ID	ST001900
Study Title	Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites (part II)
Study Type	Study part 2 of 2 (independent experiment 2; replication experiment of Study part 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
Email	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

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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
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Genotype	Treatment
SA176179	MP_Blank_01	Blank	Blank
SA176180	MP_Blank_02	Blank	Blank
SA176181	MP_Blank_03	Blank	Blank
SA176182	MP18	KO Acute	Immune deficient infected control
SA176183	MP27	KO Acute	Immune deficient infected control
SA176184	MP11	KO Acute	Immune deficient infected control
SA176185	MP24	KO Acute	Immune deficient infected control
SA176186	MP06	KO Acute	Immune deficient infected control
SA176187	MP08	KO Acute	Immune deficient infected control
SA176188	MP36	KO Naïve	Immune deficient control
SA176189	MP31	KO Naïve	Immune deficient control
SA176190	MP33	KO Naïve	Immune deficient control
SA176191	MP15	KO Naïve	Immune deficient control
SA176192	MP28	KO Naïve	Immune deficient control
SA176193	MP09	KO Naïve	Immune deficient control
SA176194	QC_MP_04	QC	QC
SA176195	QC_MP_05	QC	QC
SA176196	QC_MP_06	QC	QC
SA176197	QC_MP_02	QC	QC
SA176198	QC_MP_03	QC	QC
SA176199	QC_MP_01	QC	QC
SA176200	MP30	WT Acute	Infected
SA176201	MP22	WT Acute	Infected
SA176202	MP02	WT Acute	Infected
SA176203	MP01	WT Acute	Infected
SA176204	MP16	WT Acute	Infected
SA176205	MP21	WT Acute	Infected
SA176206	MP05	WT LPS	LPS treatment
SA176207	MP29	WT LPS	LPS treatment
SA176208	MP12	WT LPS	LPS treatment
SA176209	MP19	WT LPS	LPS treatment
SA176210	MP26	WT LPS	LPS treatment
SA176211	MP10	WT LPS	LPS treatment
SA176212	MP03	WT Naïve	Control
SA176213	MP34	WT Naïve	Control
SA176214	MP13	WT Naïve	Control
SA176215	MP14	WT Naïve	Control
SA176216	MP37	WT Naïve	Control
SA176217	MP07	WT Naïve	Control

Showing results 1 to 39 of 39

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.

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

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