Summary of Study ST002984

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 PR001859. The data can be accessed directly via it's Project DOI: 10.21228/M8DT65 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	ST002984
Study Title	Amino acid catabolite markers for early prognostication of pneumonia in patients with COVID-19
Study Summary	Effective early-stage markers for predicting which patients are at risk of developing SARS-CoV-2 infection have not been fully investigated. Here, we performed comprehensive serum metabolome analysis of a total of 83 patients from two cohorts to determine that the acceleration of amino acid catabolism within 5 days from disease onset correlated with future disease severity. Increased levels of de-aminated amino acid catabolites involved in the de novo nucleotide synthesis pathway were identified as early prognostic markers that correlated with the initial viral load. We further employed mice models of SARS-CoV2-MA10 and influenza infection to demonstrate that such de-amination of amino acids and de novo synthesis of nucleotides were associated with the abnormal proliferation of airway and vascular tissue cells in the lungs during the early stages of infection. Consequently, it can be concluded that lung parenchymal tissue remodeling in the early stages of respiratory viral infections induces systemic metabolic remodeling and that the associated key amino acid catabolites are valid predictors for excessive inflammatory response in later disease stages.
Institute	Graduate School of Medicine, Kyoto University
Department	Center for Cancer Immunotherapy and Immunobiology
Laboratory	Sugiura-lab
Last Name	Sugiura
First Name	Yuki
Address	Shogoin-Kawaramachi 53,, Sakyo-ku, Kyoto, Kyoto, 160-8582, Japan
Email	yuki.sgi@gmail.com
Phone	+818050027858
Submit Date	2023-11-16
Raw Data Available	Yes
Raw Data File Type(s)	lcd, raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2023-12-04
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001859
Project DOI:	doi: 10.21228/M8DT65
Project Title:	Amino acid catabolite markers for early prognostication of pneumonia in patients with COVID-19
Project Summary:	Effective early-stage markers for predicting which patients are at risk of developing SARS-CoV-2 infection have not been fully investigated. Here, we performed comprehensive serum metabolome analysis of a total of 83 patients from two cohorts to determine that the acceleration of amino acid catabolism within 5 days from disease onset correlated with future disease severity. Increased levels of de-aminated amino acid catabolites involved in the de novo nucleotide synthesis pathway were identified as early prognostic markers that correlated with the initial viral load. We further employed mice models of SARS-CoV2-MA10 and influenza infection to demonstrate that such de-amination of amino acids and de novo synthesis of nucleotides were associated with the abnormal proliferation of airway and vascular tissue cells in the lungs during the early stages of infection. Consequently, it can be concluded that lung parenchymal tissue remodeling in the early stages of respiratory viral infections induces systemic metabolic remodeling and that the associated key amino acid catabolites are valid predictors for excessive inflammatory response in later disease stages.
Institute:	Graduate School of Medicine, Kyoto University
Department:	Center for Cancer Immunotherapy and Immunobiology
Laboratory:	Sugiura-lab
Last Name:	Sugiura
First Name:	Yuki
Address:	Shogoin-Kawaramachi 53, Sakyo-ku, Kyoto 606-8507, Japan
Email:	yuki.sgi@gmail.com
Phone:	+818050027858

Subject:

Subject ID:	SU003097
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Symotons
SA323812	23	asymptomatic
SA323813	24	asymptomatic
SA323814	22	asymptomatic
SA323815	21	asymptomatic
SA323816	20	asymptomatic
SA323817	18	asymptomatic
SA323818	19	asymptomatic
SA323819	34	mild
SA323820	35	mild
SA323821	37	mild
SA323822	40	mild
SA323823	41	mild
SA323824	39	mild
SA323825	38	mild
SA323826	36	mild
SA323827	27	mild
SA323828	25	mild
SA323829	33	mild
SA323830	28	mild
SA323831	26	mild
SA323832	29	mild
SA323833	31	mild
SA323834	32	mild
SA323835	30	mild
SA323836	52	moderate
SA323837	51	moderate
SA323838	56	moderate
SA323839	50	moderate
SA323840	55	moderate
SA323841	54	moderate
SA323842	53	moderate
SA323843	44	moderate
SA323844	43	moderate
SA323845	49	moderate
SA323846	45	moderate
SA323847	42	moderate
SA323848	48	moderate
SA323849	47	moderate
SA323850	46	moderate
SA323795	13	Negative
SA323796	12	Negative
SA323797	14	Negative
SA323798	11	Negative
SA323799	15	Negative
SA323800	1	Negative
SA323801	17	Negative
SA323802	10	Negative
SA323803	16	Negative
SA323804	4	Negative
SA323805	3	Negative
SA323806	9	Negative
SA323807	5	Negative
SA323808	2	Negative
SA323809	8	Negative
SA323810	7	Negative
SA323811	6	Negative
SA323851	68	severe
SA323852	66	severe
SA323853	67	severe
SA323854	70	severe
SA323855	65	severe
SA323856	71	severe
SA323857	69	severe
SA323858	61	severe
SA323859	58	severe
SA323860	57	severe
SA323861	59	severe
SA323862	60	severe
SA323863	63	severe
SA323864	62	severe
SA323865	64	severe

Showing results 1 to 71 of 71

Showing results 1 to 71 of 71

Collection:

Collection ID:	CO003090
Collection Summary:	Residual serum samples for biochemical and immunological tests were collected from patients with suspected SARS-CoV-2 infection who underwent RT-PCR testing of nasopharyngeal swab or saliva samples at Keio University Hospital or Osaka Metropolitan University Hospital from March 2020 to January 2021. The diagnosis of COVID-19 was based on a positive RT-PCR test from a nasopharyngeal swab or saliva sample. The classification of severity was based on the Japanese Ministry of Health, Labour and Welfare’s classification of severity (criteria for evaluation by healthcare professionals) and was defined as follows: asymptomatic, no symptoms associated with COVID-19; mild disease, SARS-CoV-2-positive with no findings of pneumonia; moderate disease, SARS-CoV-2-positive with findings of pneumonia but not requiring a ventilator or intensive care unit (ICU) management; and severe disease, SARS-CoV-2-positive requiring ventilator or ICU management, including death attributed to COVID-19 during the treatment period. For a negative control, residual serum samples were collected from patients who underwent RT-PCR testing using nasopharyngeal swab fluid between April and May 2020 at Keio University Hospital and received negative RT-PCR test results, making them clinically unlikely to have COVID-19. The study included the early patient cohorts of waves 1, 2, and 3 of COVID-19 conducted in Japan from March to December 2020. For cohorts 1 and 2, patients were not excluded because of comorbidities, as the main objective was to include the greatest possible number of severe cases for which specimens were available early after disease onset. Cases in the mild and moderate groups were selected based on matching age and sex distribution with the severe group. No specific exclusions were made in any group during the study period, mainly because the number of samples was limited. Asymptomatic and mildly symptomatic patients were selected for inclusion by balancing the sex ratio. The higher proportion of males in the moderate and severe categories is due to the observed tendency for males to be more severely affected. This was particularly true for patients hospitalized during the study period. Sample collection and utilization were conducted under the approval of the Ethics Committee of the Keio University School of Medicine (approval numbers 20200059 and 20200063) and the Ethics Committee of Osaka Metropolitan University Graduate School of Medicine (approval number 2020-003). The use of residual samples was conducted on an opt-out basis based on the approval of the relevant ethics committees. All samples were stored at -80 °C.
Sample Type:	Blood (serum)
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR003106
Treatment Summary:	No Treatment

Sample Preparation:

Sampleprep ID:	SP003103
Sampleprep Summary:	Frozen serum samples of Cohort-1 participants, together with internal standard compounds were sonicated in ice-cold methanol (500 μL), to which an equal volume of chloroform and 0.4 times the volume of ultrapure water (LC/MS grade, Wako Pure Chemical, Tokyo, Japan) were added. The suspension was centrifuged at 15,000 × g for 15 min at 4 °C. The aqueous phase was then filtered in an ultrafiltration tube (Ultrafree MC-PLHCC, Human Metabolome Technologies, Tsuruoka City, Japan), and the filtrate was concentrated using a vacuum concentrator (SpeedVac; Thermo Fisher Scientific, Waltham, MA, USA). The concentrated filtrate was dissolved in 50 μL ultrapure water and subjected to IC-HR-MS analysis. Methionine sulfone (L-Met) and 2-morpholinoethanesulfonic acid (MES) were used as internal standards for cationic and anionic metabolites, respectively.

Sampleprep ID:

SP003103

Sampleprep Summary:

Frozen serum samples of Cohort-1 participants, together with internal standard compounds were sonicated in ice-cold methanol (500 μL), to which an equal volume of chloroform and 0.4 times the volume of ultrapure water (LC/MS grade, Wako Pure Chemical, Tokyo, Japan) were added. The suspension was centrifuged at 15,000 × g for 15 min at 4 °C. The aqueous phase was then filtered in an ultrafiltration tube (Ultrafree MC-PLHCC, Human Metabolome Technologies, Tsuruoka City, Japan), and the filtrate was concentrated using a vacuum concentrator (SpeedVac; Thermo Fisher Scientific, Waltham, MA, USA). The concentrated filtrate was dissolved in 50 μL ultrapure water and subjected to IC-HR-MS analysis. Methionine sulfone (L-Met) and 2-morpholinoethanesulfonic acid (MES) were used as internal standards for cationic and anionic metabolites, respectively.

Combined analysis:

Analysis ID	AN004903	AN004904
Analysis type	MS	MS
Chromatography type	Ion exchange	Reversed phase
Chromatography system	Thermo Dionex ICS-5000+	Shimadzu Nexera X2
Column	Dionex IonPac AS11-HC (250 x 2mm, 4um)	Sigma-Aldrich Discovery HS F5-3 (150 x 2.1 mm, 3 um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Triple quadrupole
MS instrument name	Thermo Q Exactive Focus	LCMS-8060, Shimadzu Corporation
Ion Mode	UNSPECIFIED	UNSPECIFIED
Units	Peak area/Internal Standard	Peak area/Internal Standard

Chromatography:

Chromatography ID:	CH003698
Chromatography Summary:	Metabolites were detected using an orbitrap-type MS instrument (Q-Exactive focus; Thermo Fisher Scientific) connected to a high-performance IC system (ICS-5000+, Thermo Fisher Scientific) that enabled highly selective and sensitive metabolite quantification owing to the IC separation and Fourier transfer MS principle. The IC instrument was equipped with an anion electrolytic suppressor (Dionex AERS 500; Thermo Fisher Scientific) to convert the potassium hydroxide gradient into pure water before the sample entered the MS instrument. Separation was performed using a Dionex IonPac AS11-HC 4 μm particle size column (Thermo Fisher Scientific). The IC flow rate was 0.25 mL/min, supplemented post-column with 0.18 mL/min makeup flow of MeOH. The potassium hydroxide gradient conditions for IC separation were as follows: from 1 mM to 100 mM (0–40 min) to 100 mM (40–50 min) and to 1 mM (50.1–60 min) at a column temperature of 30 °C. The mass spectrometer was operated in the ESI-positive and negative mode with polarity switching, for all detections. A full mass scan (m/z 70–900) was performed at a resolution of 70,000. The automatic gain control target was set at 3 × 106 ions, and the maximum ion injection time was 100 ms. The source ionization parameters were optimized with a spray voltage of 3 kV, and other parameters were as follows: transfer temperature, 320 °C; S-Lens level, 50; heater temperature, 300 °C; sheath gas, 36; and aux gas, 10.
Instrument Name:	Thermo Dionex ICS-5000+
Column Name:	Dionex IonPac AS11-HC (250 x 2mm, 4um)
Column Temperature:	30 °C
Flow Gradient:	From 1 mM to 100 mM (0–40 min) to 100 mM (40–50 min) and to 1 mM (50.1–60 min)
Flow Rate:	0.25 mL/min, supplemented post-column with 0.18 mL/min makeup flow of MeOH
Solvent A:	The potassium hydroxide gradient conditions
Solvent B:	N/A
Chromatography Type:	Ion exchange

Chromatography ID:	CH003699
Chromatography Summary:	Cationic metabolite concentrations were determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In essence, we employed a triple-quadrupole mass spectrometer equipped with an electrospray ionization (ESI) ion source (LCMS-8060, Shimadzu Corporation, Kyoto, Japan) operated in both positive and negative-ESI and in multiple reaction monitoring (MRM) modes. Analyte separation was achieved on a Discovery HS F5-3 column (2.1 mm I.D. × 150 mm L, 3 μm particle size; Sigma-Aldrich, St. Louis, MO, USA) through a gradient elution with mobile phase A (0.1% formate) and mobile phase B (0.1% acetonitrile). The elution profile was as follows: 100:0 (0–5 min), 75:25 (5–11 min), 65:35 (11–15 min), 5:95 (15–20 min), and 100:0 (20–25 min), with a constant flow rate of 0.25 mL/min and a column oven set at 40 °C.
Instrument Name:	Shimadzu Nexera X2
Column Name:	Sigma-Aldrich Discovery HS F5-3 (150 x 2.1 mm, 3 um)
Column Temperature:	40 °C
Flow Gradient:	100:0 (0–5 min), 75:25 (5–11 min), 65:35 (11–15 min), 5:95 (15–20 min), and 100:0 (20–25 min)
Flow Rate:	0.25 mL/min
Solvent A:	0.1% formate
Solvent B:	acetonitrile with 0.1% formate
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004646
Analysis ID:	AN004903
Instrument Name:	Thermo Q Exactive Focus
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	For IC-HR-MS data analysis, the Trace Finder compound identification and confirmation setup parameters included a molecular ion intensity threshold override of 10,000, S/N 5, and mass tolerance of 5 ppm. Isotope pattern analysis using a 90% fit threshold, 30% allowable relative intensity deviation, and 5 ppm mass deviation was also performed to ensure that the relative intensities of the M + 1 and/or M + 2 isotope peaks for each compound were consistent with the theoretical relative intensities.
Ion Mode:	UNSPECIFIED

MS ID:	MS004647
Analysis ID:	AN004904
Instrument Name:	LCMS-8060, Shimadzu Corporation
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	For LC-MS/MS analysis, chromatographic peaks obtained with compound-specific SRM channels were integrated and manually reviewed. For a single target compound, one or more confirmatory SRM channels were set (if available) to confirm peak compound identification. Chromatograms were acquired using Lab Solutions (ver. 5.113, Shimadzu). Peak areas were determined using Data browser software.
Ion Mode:	UNSPECIFIED