Summary of Study ST002328

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001492. The data can be accessed directly via it's Project DOI: 10.21228/M8VX2Q This work is supported by NIH grant, U2C- DK119886.


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 IDST002328
Study TitleMetabolome and transcriptome analysis of oral mucosa of HIV+ patients reveal a role for polyamine metabolic pathway in T cell dysfunction
Study SummaryMetabolic changes of immune cells contribute to both physiological and pathophysiological outcomes of immune reactions. How viruses alter the metabolic states of mucosal T cells and the precise mechanisms underlying the persisting immune dysfunction during chronic viral infections are key questions that have not been fully addressed. Here, by comparing transcriptome and salivary metabolome profiles of the uninfected individuals and people living with HIV (PLWH) on treatment, we found a role of polyamine metabolism in immune perturbations of the oral mucosa of HIV+ patients. Flow cytometry analysis confirmed the higher expression of ornithine decarboxylase (ODC-1) and eukaryotic translation initiation factor 5A (EIF5A), the polyamine metabolism intermediates in CD4+ T cells in PLWH. Mechanistic studies using an in vitro human tonsil organoid infection model revealed that HIV infection of activated T cells also resulted in increased polyamine synthesis, which was dependent on the activities of caspase-1, IL-1β, and ODC-1. HIV-1 also led to elevated dysfunctional regulatory T cells (TregDys) /Thelper 17 (Th17) cell ratios as well as heightened expression of ODC-1, EIF5A, and hypusinated EIF5A. Blockade of caspase-1, ODC-1, and EIF5A hypusination and not HIF-1⍺ or NLRP3 reversed the frequency of TregDys showing the direct impact of polyamine pathway in Treg dysfunction during HIV-1 infection. The addition of exogenous polyamines increased TregDys percentages independent of HIV-1 infection in vitro. Finally, oral mucosal TregDys/Th17 ratios and CD4 hyperactivation positively correlated with the increases in salivary putrescine levels, which were found to be elevated in the saliva of PLWH. Thus, by revealing the role of aberrantly increased polyamine synthesis during HIV infection, our study unveils a new mechanism by which chronic viral infections could drive distinct T cell effector programs and Treg dysfunction.
Case Western Reserve University
DepartmentBiological Sciences
LaboratoryPushpa Pandiyan
Last NamePandiyan
First NamePushpa
AddressDepartment of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, Ohio, 44106
Submit Date2022-08-29
Num Groups2
Total Subjects66
Num Males41
Num Females25
PublicationsUnder revision
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2022-12-01
Release Version1
Pushpa Pandiyan Pushpa Pandiyan application/zip

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Sample Preparation:

Sampleprep ID:SP002421
Sampleprep Summary:100 μl of saliva samples were thawed, transferred to new tubes, extracted with 200 μl of 80% methanol, and vortexed for 30 seconds. Then the samples were kept at -40 °C for 1 hour, vortexed for 30 s, and centrifuged at 12000 rpm, 4 °C for 15 minutes. Finally, 200 μl of supernatant and 5 μl of DL-o-Chlorophenylalanine (1 mg/ml) were transferred to the vial for LC-MS analysis. Quality control (QC) samples were used to evaluate the methodology. The same amount of extract was obtained from each sample and mixed with QC samples. The QC sample was prepared using the same sample preparation procedure. Instrumental setup Separation was performed by Ultimate 3000LC combined with Q Exactive MS (Thermo) and screened with ESI-MS (targeted MS/MS mode). The LC system is comprised of an ACQUITY UPLC HSS T3 (100 × 2.1mm 1.8 μm) with Ultimate 3000LC. The mobile phase was composed of solvent A (0.05% formic acid-water) and solvent B (acetonitrile) with a gradient elution (0-1.0 min, 95% A; 1.0-12.0 min,95%-5% A; 12.0-13.5 min,5% A; 13.5-13.6 min, 5%-95% A; 13.6-16 min, 95% A). The flow rate of the mobile phase was 0.3 ml/min. The column temperature was maintained at 40 °C, and the sample manager temperature is set at 4 °C. Mass spectrometry parameters in ESI+ and ESI- mode are listed as follows: ESI+: Heater Temp 300 °C; Sheath Gas Flow rate, 45 arb; Aux Gas Flow Rate, 15 arb; Sweep Gas Flow Rate, 1 arb; spray voltage, 3.0 kV; Capillary Temp, 350 °C; S-Lens RF Level, 30%. ESI-: Heater Temp 300 °C, Sheath Gas Flow rate, 45 arb; Aux Gas Flow Rate, 15arb; Sweep Gas Flow Rate, 1 arb; spray voltage, 3.2 kV; Capillary Temp,350 °C; S-Lens RF Level, 60%. Bioinformatic data analysis included multivariate statistical analysis, single variable analysis, cluster analysis, and correlation network of differential metabolites. Statistically significant metabolites (FC >1.5) were integrated with differentially expressed genes obtained from the RNAseq data and the combined data was visualized with Metaboanalyst ( and Cytoscape v3.8 via Metscape v3.1 plugin (
Sampleprep Protocol Filename:Sample_preparation.pdf
Processing Storage Conditions:Described in summary
Extract Storage:Described in summary