Summary of Study ST003964

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 PR002483. The data can be accessed directly via it's Project DOI: 10.21228/M8PJ91 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 IDST003964
Study TitleImmunometabolism determinants of enhanced antileukemic activity upon rapamycin mediated mTOR inhibition in CAR-T cells of short-term responder leukemia patients receiving CD19 CAR T cell therapy
Study TypeUntargeted metabolomics
Study SummaryTo investigate role of mTOR activity on the efficacy of CAR-T cells of long-term responders, we used generated CAR-T cells from the leukaphresis products of short-term responder treated with or without mTOR inhibitor rapamycin to transiently inhibit mTOR activity. We performed metabolomics on the CAR T cells from short-term responders with or without rapamycin. We saw higher levels of glycerphospholipids, amino acids, sphioglipids and lower levels of metabolites of pentose phosphate pathway suggesting higher lipid metabolism and decreased non-oxidative pentose phosphate pathway metabolism upon rapamycin treatment which could provide insight in role of mTOR in metabolic activation and efficacy of CAR-T cell therapy.
Institute
Translational Genomics Research Institute
Last NamePirrotte
First NamePatrick
Address445 N 5TH STREET, Phoenix, Arizona
Emailkpathak@tgen.org
Phone12137931730
Submit Date2025-06-02
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-07-07
Release Version1
Patrick Pirrotte Patrick Pirrotte
https://dx.doi.org/10.21228/M8PJ91
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002483
Project DOI:doi: 10.21228/M8PJ91
Project Title:Metabolomics of CAR-T cells and their products in leukemia patients
Project Type:Untargeted metabolomics
Project Summary:Although most patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL) receiving CD19-targeted chimeric antigen receptor (CAR) T cell therapy achieve remission, loss of CAR T cell functionality and subsequent relapse remains an unmet therapeutic need. We applied an integrative approach to study the immunometabolism of pre- and post-infusion CD19-CAR T cells of patients with relapsed/refractory B-ALL. Pre-infusion CAR T cells of long-term responders (LTR) had increased oxidative phosphorylation, fatty acid oxidation, and pentose phosphate pathway activities, higher mitochondrial mass, tighter cristae, and lower mTOR expression compared to products of short-term responders. Post-infusion CAR T cells in bone marrow (BM) of LTR had high immunometabolic plasticity and mTOR-pS6 expression supported by the BM microenvironment. Transient inhibition of mTOR during manufacture induced metabolic reprogramming and enhanced anti-tumor activity of CAR T cells. Our findings provide insight into immunometabolic determinants of long-term response and suggest a therapeutic strategy to improve long-term remission.
Institute:Translational Genomics Research Institute
Last Name:Pirrotte
First Name:Patrick
Address:445 N 5TH STREET, Phoenix, Arizona
Email:ims@tgen.org
Phone:6023438454
Funding Source:NIH K12 grant no. 5K12CA001727–29, The Hyundai Hope on Wheels Young Investigator Award, NCI grant no.P30CA033572
Project Comments:Study 1 of 4
Contributors:Lior Goldberg, Eric R. Haas, Jiaqi Wu, Bryan Garcia, Ryan Urak, Vibhuti Vyas, Ruby Espinosa, Tamara Munoz, Shirley Bierkatz, Jamie R. Wagner, Jinny Paul, Mary C. Clark, Dat Ngo, Ibrahim Aldoss, Stephen J. Forman & Xiuli Wang

Subject:

Subject ID:SU004101
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 Sample source Outcome Treatment
SA452895strCT6x379WO_HILICposCAR-T cells Short term responders Not treated control
SA452896strCT8x466WO_RPposCAR-T cells Short term responders Not treated control
SA452897strCT8x466WO_RPnegCAR-T cells Short term responders Not treated control
SA452898strCT6x379WO_RPposCAR-T cells Short term responders Not treated control
SA452899strCT6x379WO_RPnegCAR-T cells Short term responders Not treated control
SA452900strCT4x293WO_RPposCAR-T cells Short term responders Not treated control
SA452901strCT4x293WO_RPnegCAR-T cells Short term responders Not treated control
SA452902strCT2x209WO_RPposCAR-T cells Short term responders Not treated control
SA452903strCT2x209WO_RPnegCAR-T cells Short term responders Not treated control
SA452904strCT12x549WO_RPposCAR-T cells Short term responders Not treated control
SA452905strCT12x549WO_RPnegCAR-T cells Short term responders Not treated control
SA452906strCT10x543WO_RPposCAR-T cells Short term responders Not treated control
SA452907strCT10x543WO_HILICposCAR-T cells Short term responders Not treated control
SA452908strCT8x466WO_HILICposCAR-T cells Short term responders Not treated control
SA452909strCT8x466WO_HILICnegCAR-T cells Short term responders Not treated control
SA452910strCT10x543WO_HILICnegCAR-T cells Short term responders Not treated control
SA452911strCT6x379WO_HILICnegCAR-T cells Short term responders Not treated control
SA452912strCT4x293WO_HILICposCAR-T cells Short term responders Not treated control
SA452913strCT12x549WO_HILICnegCAR-T cells Short term responders Not treated control
SA452914strCT12x549WO_HILICposCAR-T cells Short term responders Not treated control
SA452915strCT2x209WO_HILICposCAR-T cells Short term responders Not treated control
SA452916strCT4x293WO_HILICnegCAR-T cells Short term responders Not treated control
SA452917strCT2x209WO_HILICnegCAR-T cells Short term responders Not treated control
SA452918strCT10x543WO_RPnegCAR-T cells Short term responders Not treated control
SA452919strCT1x209W_HILICnegCAR-T cells Short term responders Rapamycin
SA452920strCT9x543W_RPposCAR-T cells Short term responders Rapamycin
SA452921strCT9x543W_RPnegCAR-T cells Short term responders Rapamycin
SA452922strCT11x549W_HILICnegCAR-T cells Short term responders Rapamycin
SA452923strCT11x549W_HILICposCAR-T cells Short term responders Rapamycin
SA452924strCT7x466W_RPposCAR-T cells Short term responders Rapamycin
SA452925strCT7x466W_RPnegCAR-T cells Short term responders Rapamycin
SA452926strCT7x466W_HILICposCAR-T cells Short term responders Rapamycin
SA452927strCT5x379W_HILICposCAR-T cells Short term responders Rapamycin
SA452928strCT5x379W_RPposCAR-T cells Short term responders Rapamycin
SA452929strCT5x379W_RPnegCAR-T cells Short term responders Rapamycin
SA452930strCT9x543W_HILICposCAR-T cells Short term responders Rapamycin
SA452931strCT9x543W_HILICnegCAR-T cells Short term responders Rapamycin
SA452932strCT3x293W_RPposCAR-T cells Short term responders Rapamycin
SA452933strCT3x293W_RPnegCAR-T cells Short term responders Rapamycin
SA452934strCT7x466W_HILICnegCAR-T cells Short term responders Rapamycin
SA452935strCT5x379W_HILICnegCAR-T cells Short term responders Rapamycin
SA452936strCT1x209W_RPposCAR-T cells Short term responders Rapamycin
SA452937strCT1x209W_RPnegCAR-T cells Short term responders Rapamycin
SA452938strCT3x293W_HILICnegCAR-T cells Short term responders Rapamycin
SA452939strCT3x293W_HILICposCAR-T cells Short term responders Rapamycin
SA452940strCT11x549W_RPposCAR-T cells Short term responders Rapamycin
SA452941strCT11x549W_RPnegCAR-T cells Short term responders Rapamycin
SA452942strCT1x209W_HILICposCAR-T cells Short term responders Rapamycin
Showing results 1 to 48 of 48

Collection:

Collection ID:CO004094
Collection Summary:De-identified clinical samples were collected from a subset of adult patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL) who received investigational CD19-specific CAR T cells in a phase 1/2 clinical trial (NCT02146924) at City of Hope. Patient or donor's Tcells were collected by leukapheresis. The leukapheresis Tcells were used for metabolomics profiling. For CAR T cells, PBMC were depleted of CD14+ monocytes and CD25+ Tregs, followed by positive selection of CD62L+ T cells. Tcm-derived CAR T cells were purified, transduced, formulated, and released. The CAR T cells treated with or without rapamycin were used for metabolomics profiling. After 28th day post CAR-T infusion bone marrow serum was collected from the patients for metabolomics profiling
Sample Type:CAR-T cells
Storage Conditions:-80℃

Treatment:

Treatment ID:TR004110
Treatment Summary:Leukapheresis products from Short-term and long-term responders were treated with rapamycin or vehicle control. These products are used for CAR T cell productions. The CAR-T cells with or without rapamycin treatment were subjected to untargeted metabolomics profiling.

Sample Preparation:

Sampleprep ID:SP004107
Sampleprep Summary:1.5 million CAR-T cells with or without rapamycin treatment were used for metabolite extraction. Metabolites were extracted using 0.4 mL of 0.4 mL of solvent mixture (water: methanol: acetonitrile, 1:2.25:0.75, v/v/v) and 3 freeze-thaw (30 seconds each) cycles. For bone marrow, 3-fold excess acetonitrile: methanol (3:1) was added for protein removal. The resultant metabolite extracts from CAR T cells were recovered by centrifuging at 13,226 xg at 4°C for 15 min. For HILIC chromatography, the extract was directly used LC-MS analysis. For reversed phase chromatography, the extract was dried under vacuum centrifugation and the dried extract was reconstituted in 20% Acetonitrile, 80% water and used used for LC-MS analysis.
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Chromatography:

Chromatography ID:CH004948
Chromatography Summary:HILIC chromatography
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:99% B for 1 min, 99–85% B for 3 min, 85–75% B for 3 min, 75–30% B for 3 min, 30% B for 1 min, 30-99%B for 1 min and 99%B for 4 min
Flow Rate:0.35 ml/min
Solvent A:95% water/5% acetonitrile; 10mM ammonium acetate; 0.1% acetic acid
Solvent B:95% acetonitrilie/5% water; 10mM ammonium acetate; 0.1% acetic acid
Chromatography Type:HILIC
  
Chromatography ID:CH004949
Chromatography Summary:Reversed phase chromatography
Instrument Name:Thermo Vanquish
Column Name:Thermo Hypersil Gold C18 (150 x 2.1mm, 1.9um)
Column Temperature:45
Flow Gradient:0% B for 1min, 0-50% B for 4 min, 50-98% B for 3 min, 98% B for 2 min, 0% B for 0.5min, 0% B for 5 min
Flow Rate:0.3 ml/min
Solvent A:100% Water; 0.1% formic acid
Solvent B:100% Acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN006515
Analysis Type:MS
Chromatography ID:CH004948
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003964_AN006515_Results.txt
Units:Peak area
  
Analysis ID:AN006516
Analysis Type:MS
Chromatography ID:CH004948
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003964_AN006516_Results.txt
Units:Peak area
  
Analysis ID:AN006517
Analysis Type:MS
Chromatography ID:CH004949
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003964_AN006517_Results.txt
Units:Peak area
  
Analysis ID:AN006518
Analysis Type:MS
Chromatography ID:CH004949
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003964_AN006518_Results.txt
Units:Peak area
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