Summary of Study ST004309
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 PR002725. The data can be accessed directly via it's Project DOI: 10.21228/M8DV7W 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 | ST004309 |
| Study Title | Metabolic reprogramming by caloric restriction enhances acute-phase virologic control and reduces chronic inflammation in SIV-infected rhesus macaques |
| Study Type | Non-human primate study |
| Study Summary | Nutrient metabolism influences HIV-1 replication, immunity, and chronic inflammation, yet is difficult to leverage for therapeutic gain. We sought to modulate metabolism in the non-human primate model of HIV-1 by caloric restriction (CR) without causing malnutrition, a modality canonically known for its anti-aging benefits. Four months of 30% CR was safe and resulted in broad metabolic reprogramming in healthy male and female rhesus macaques. Relative to that of ad libitum-fed animals, CR reduced acute phase viremia upon infection with SIV and notably enhanced the cycling of memory CD8⁺ T cells and NK cells in lymphoid tissues. During virologic suppression with antiretroviral therapy (ART), CR reduced the densities of activated lymphocytes in the GI tract and caused a systemic down-regulation of soluble inflammatory media-tors. Interrogating the plasma metabolome across infection revealed a contribution of distinct metabolic states to outcome, with glycolytic signatures associated with im-proved virologic control during acute SIV, and tricarboxylic acid cycle metabolites linked to an anti-inflammatory state during ART. These data highlight that manipulating metabolism through diet can enhance immunity and limit pathology in a primate lentiviral infection and reveal context-dependent metabolic programs associated with improved outcomes in SIV. |
| Institute | Tulane National Biomedical Research Center |
| Department | Immunology |
| Last Name | Naveen |
| First Name | Suresh Babu |
| Address | 18703 Three Rivers Road, Covington, Louisiana, USA, 70433. |
| nsureshbabu@tulane.edu | |
| Phone | 4126264523 |
| Submit Date | 2025-10-17 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-11-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002725 |
| Project DOI: | doi: 10.21228/M8DV7W |
| Project Title: | Plasma metabolomics study on calorie restriction in rhesus macaques |
| Project Summary: | This project aimed to assess plasma metabolite concentrations using LC-MS in two cohorts of rhesus macaques. The ad-libitum (AL, n = 11) cohort consisted of animals fed without restriction, while the calorie-restricted (CR, n = 6) cohort received a diet restricted by up to 30% of their baseline intake. Plasma samples were collected at three time points: uninfected baseline (labeled in the study design as Ad-libitum and CR), 14 days post-SIV infection (labelled as Ad-libitum+SIV, CR+SIV), and 11 months post-ART (labelled as Ad-libitum+SIV+ART, CR+SIV+ART). LC-MS metabolomics was performed on all six CR animals at every time point. In the AL cohort, only six of the eleven animals were profiled due to the high cost of metabolomics; these same six animals were sampled at all time points to maintain consistency and enable statistical comparisons without confounding. |
| Institute: | Tulane National Biomedical Research Center |
| Department: | Immunology |
| Laboratory: | Joseph Mudd |
| Last Name: | Suresh Babu |
| First Name: | Naveen |
| Address: | 18703 Three Rivers Road, Covington, Louisiana, USA, 70433. |
| Email: | nsureshbabu@tulane.edu |
| Phone: | 4126264523 |
Subject:
| Subject ID: | SU004463 |
| Subject Type: | Mammal |
| Subject Species: | Macaca mulatta |
| Taxonomy ID: | 9544 |
Factors:
Subject type: Mammal; Subject species: Macaca mulatta (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Experimental_condition |
|---|---|---|---|
| SA505450 | A6_IF12 | Plasma | Ad-Libitum |
| SA505451 | A2_KF18 | Plasma | Ad-Libitum |
| SA505452 | A1_JH80 | Plasma | Ad-Libitum |
| SA505453 | A5_JL54 | Plasma | Ad-Libitum |
| SA505454 | A4_MF56 | Plasma | Ad-Libitum |
| SA505455 | A3_JN26 | Plasma | Ad-Libitum |
| SA505456 | B4_KF18 | Plasma | Ad-Libitum + SIV |
| SA505457 | B8_IF12 | Plasma | Ad-Libitum + SIV |
| SA505458 | B6_MF56 | Plasma | Ad-Libitum + SIV |
| SA505459 | B5_JN26 | Plasma | Ad-Libitum + SIV |
| SA505460 | B7_JL54 | Plasma | Ad-Libitum + SIV |
| SA505461 | B3_JH80 | Plasma | Ad-Libitum + SIV |
| SA505462 | B3_MF56_ART | Plasma | Ad-libitum+SIV+ART |
| SA505463 | A4_HP61_ART | Plasma | Ad-libitum+SIV+ART |
| SA505464 | A3_JL60_ART | Plasma | Ad-libitum+SIV+ART |
| SA505465 | A2_IB41_ART | Plasma | Ad-libitum+SIV+ART |
| SA505466 | A1_JD37_ART | Plasma | Ad-libitum+SIV+ART |
| SA505467 | B2_KF18_ART | Plasma | Ad-libitum+SIV+ART |
| SA505468 | A5_IF12_ART | Plasma | Ad-libitum+SIV+ART |
| SA505469 | B4_JH80_ART | Plasma | Ad-libitum+SIV+ART |
| SA505470 | B5_JN26_ART | Plasma | Ad-libitum+SIV+ART |
| SA505471 | B1_JL54_ART | Plasma | Ad-libitum+SIV+ART |
| SA505472 | B2_KD65 | Plasma | CR |
| SA505473 | A7_KN43 | Plasma | CR |
| SA505474 | A9_JL97 | Plasma | CR |
| SA505475 | A10_JJ45 | Plasma | CR |
| SA505476 | B1_JN33 | Plasma | CR |
| SA505477 | A8_JT07 | Plasma | CR |
| SA505478 | C3_JN33 | Plasma | CR + SIV |
| SA505479 | C4_KD65 | Plasma | CR + SIV |
| SA505480 | C2_JJ45 | Plasma | CR + SIV |
| SA505481 | B10_JT07 | Plasma | CR + SIV |
| SA505482 | B9_KN43 | Plasma | CR + SIV |
| SA505483 | C1_JL97 | Plasma | CR + SIV |
| SA505484 | C1_JL97_ART | Plasma | CR+SIV+ART |
| SA505485 | C2_KN43_ART | Plasma | CR+SIV+ART |
| SA505486 | C3_JT07_ART | Plasma | CR+SIV+ART |
| SA505487 | C4_KD65_ART | Plasma | CR+SIV+ART |
| SA505488 | C5_JN33_ART | Plasma | CR+SIV+ART |
| SA505489 | D1_JJ45_ART | Plasma | CR+SIV+ART |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO004456 |
| Collection Summary: | This study included adult, non-obese, male and female Indian-origin rhesus macaques divided into two age-, sex-, and weight-matched cohorts, namely ad-libitum/AL cohort (fed as needed) and calorie-restricted/CR cohort (food restricted to 70% of baseline feeding habit). Following caloric restriction in the CR cohort, both the AL and CR groups were intravenously (i.v.) infected with 5,000 IU/mL of genetically barcoded SIVmac239M virus. At 28 days post-infection, all animals, regardless of their experimental status, were started on combined antiretroviral therapy (cART) composed of a regimen of three antiretroviral drugs: TDF (Tenofovir disoproxil fumarate; ~5 mg/kg), FTC (Emtricitabine; ~38 mg/kg), and DTG (Dolutegravir; ~2.5 mg/kg). LC-MS metabolomics was performed on plasma samples isolated on day 14 post-infection and 11 months post-antiretroviral therapy. All blood for the study was collected using EDTA-containing S-Monovette® tubes (Sarstedt Inc., Newton, NC). Plasma isolation was carried out via centrifugation at 900 x g for 15 minutes. Following this, plasma was frozen down in 1 mL cryovials housed in Corning cool cells and stored for later usage at -80°C. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR004472 |
| Treatment Summary: | Plasma samples were used without any treatment. |
Sample Preparation:
| Sampleprep ID: | SP004469 |
| Sampleprep Summary: | Plasma samples from ad-libitum and caloric-restriction groups were simultaneously extracted. An established protocol was followed, wherein the samples were first added to a metabolite extraction plate containing a sorbent filter for protein precipitation & phospholipid removal, followed by the addition of 99% LC-MS grade acetonitrile with 1% formic acid to the plate, at a 3:1 acetonitrile-to-sample volume ratio. The solution containing the metabolites was pushed through the sorbent filter of the plate using a positive pressure-96 processor and collected in an MS plate, while the protein and phospholipids remained trapped in the sorbent filter of the plate. The metabolite solution was then dried to 150uL, ready for acquisition. |
Chromatography:
| Chromatography ID: | CH005447 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Discovery HSF5 column (15 cm × 2.1 mm, 3 um particle size) |
| Column Temperature: | 35° C |
| Flow Gradient: | 2% B from 0 to 1 minutes, then increase from 2% to 100% B from 1 to 5.5 minutes, then hold at 100% B from 5.5 to 7 minutes. At 7 minutes, decrease from 100% to 2%B. Hold at 2% B from 7 to 9 minutes. |
| Flow Rate: | 0.7mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN007172 |
| Analysis Type: | MS |
| Chromatography ID: | CH005447 |
| Num Factors: | 6 |
| Num Metabolites: | 236 |
| Units: | Normalized intensity |
| Analysis ID: | AN007173 |
| Analysis Type: | MS |
| Chromatography ID: | CH005447 |
| Num Factors: | 6 |
| Num Metabolites: | 215 |
| Units: | Normalized intensity |
