Summary of Study ST002383
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 PR001533. The data can be accessed directly via it's Project DOI: 10.21228/M8J99C 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 | ST002383 |
| Study Title | Metabolomics of B-cell Acute Lymphoblastic Leukemia in Response to Adipocyte Conditioned Media |
| Study Type | Untargeted MS |
| Study Summary | Adipocyte conditioned media (ACM), stromal cell conditioned media (SCM) and unconditioned media (UCM) were added to B-cell Acute Lymphoblastic Leukemia cells (REH and RCH-AcV) either with or without methotrexate (MTX). The metabolomic profiles of the cells was determined by mass spectrometry. |
| Institute | Emory University |
| Department | Pediatrics |
| Laboratory | Joshua Chandler, PhD |
| Last Name | Chandler |
| First Name | Joshua |
| Address | 2015 Uppergate Drive NE, Atlanta, GA 30322 |
| joshua.chandler@emory.edu | |
| Phone | 404-727-3536 |
| Submit Date | 2022-10-07 |
| Num Groups | Two sets of two sets of three groups (MTX and no-MTX, REH and RCH-AcV, ACM vs SCM vs UCM) |
| Total Subjects | 3 replicates of each group (36 total) |
| Publications | submitted to JNCI |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-06-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001533 |
| Project DOI: | doi: 10.21228/M8J99C |
| Project Title: | The 'Omics of Obesity in B-cell Acute Lymphoblastic Leukemia |
| Project Summary: | The obesity pandemic currently affects over 70 million Americans and over 650 million individuals worldwide. In addition to increasing susceptibility to pathogenic infections (e.g., SARS-CoV-2 et al.), obesity promotes the development of many cancer subtypes and increases mortality rates in most cases. It has been demonstrated that, in the context of B-cell acute lymphoblastic leukemia (B-ALL), adipocytes promote multi-drug chemoresistance. Furthermore, it has been demonstrated that B-ALL cells exposed to the adipocyte secretome alter their metabolic states to circumvent chemotherapy-mediated cytotoxicity. To better understand how adipocytes impact the function of human B-ALL cells, we used an untargeted metabolomics mass spectroscopy approach to define adipocyte-induced changes in B-cells. These analyses revealed that the adipocyte secretome directly modulates programs in human B-ALL cells which are associated with metabolism. In all, our data increases our understanding of pathways which may promote chemoresistance in human B-ALL. |
| Institute: | Emory University |
| Department: | Pediatrics |
| Laboratory: | Joshua Chandler, PhD |
| Last Name: | Chandler |
| First Name: | Joshua |
| Address: | 2015 Uppergate Drive NE, Atlanta, GA 30322 |
| Email: | joshua.chandler@emory.edu |
| Phone: | 404-727-3536 |
| Funding Source: | This study was supported by funding for the CURE Childhood Cancer Foundation (Grant No. 001006916), Swim Across America (Grant No. 00103163), The Mark Foundation for Cancer Research (Grant No. 18-031-ASP), Emory University School of Medicine Bridge Funding (Grant No. 00098174), The American Cancer Society and Emory University Winship Cancer Institute Institutional Research Grant (Grant No. IRG-21-137-07-IRG) and the TREC Training Course (Grant No. R25CA203650) all awarded to Curtis J Henry. In additional, funding for Joshua Chandler included NIH R01 NR018666, R56 HL150658, and support from CF@LANTA, a component of Emory University and Children’s Healthcare of Atlanta. |
| Publications: | submitted to JNCI |
| Contributors: | Delaney K. Geitgey, Miyoung Lee, Kirsten A. Cottrill, Matthew B. Kilgore, Joshua D. Chandler, Curtis J. Henry |
Subject:
| Subject ID: | SU002472 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Subject Comments: | Human B-ALL cell line (REH and RCH-AcV) were a generous gift from Dr. Christopher Porter at Emory University |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Cell Type | Media | Treatment |
|---|---|---|---|---|
| SA237879 | QC-10 | n/a | n/a | n/a |
| SA237880 | Standard-1 | n/a | n/a | n/a |
| SA237881 | QC-4 | n/a | n/a | n/a |
| SA237882 | QC-2 | n/a | n/a | n/a |
| SA237883 | Blank-2 | n/a | n/a | n/a |
| SA237884 | QC-11 | n/a | n/a | n/a |
| SA237885 | QC-5 | n/a | n/a | n/a |
| SA237886 | QC-3 | n/a | n/a | n/a |
| SA237887 | SRM1950-1 | n/a | n/a | n/a |
| SA237888 | QC-1 | n/a | n/a | n/a |
| SA237889 | QC-7 | n/a | n/a | n/a |
| SA237890 | QC-6 | n/a | n/a | n/a |
| SA237891 | Blank-1 | n/a | n/a | n/a |
| SA237892 | QC-8 | n/a | n/a | n/a |
| SA237893 | Blank-3 | n/a | n/a | n/a |
| SA237894 | QC-ddMS2-1 | n/a | n/a | n/a |
| SA237895 | Blank-5 | n/a | n/a | n/a |
| SA237896 | Blank-4 | n/a | n/a | n/a |
| SA237897 | QC-9 | n/a | n/a | n/a |
| SA237843 | RCH-AcV-ACM-MTX-2 | RCH-AcV | ACM | MTX |
| SA237844 | RCH-AcV-ACM-MTX-3 | RCH-AcV | ACM | MTX |
| SA237845 | RCH-AcV-ACM-MTX-1 | RCH-AcV | ACM | MTX |
| SA237846 | RCH-AcV-ACM-1 | RCH-AcV | ACM | n/a |
| SA237847 | RCH-AcV-ACM-3 | RCH-AcV | ACM | n/a |
| SA237848 | RCH-AcV-ACM-2 | RCH-AcV | ACM | n/a |
| SA237849 | RCH-AcV-RPMI-MTX-1 | RCH-AcV | RPMI | MTX |
| SA237850 | RCH-AcV-RPMI-MTX-2 | RCH-AcV | RPMI | MTX |
| SA237851 | RCH-AcV-RPMI-MTX-3 | RCH-AcV | RPMI | MTX |
| SA237852 | RCH-AcV-RPMI-3 | RCH-AcV | RPMI | n/a |
| SA237853 | RCH-AcV-RPMI-1 | RCH-AcV | RPMI | n/a |
| SA237854 | RCH-AcV-RPMI-2 | RCH-AcV | RPMI | n/a |
| SA237855 | RCH-AcV-SCM-MTX-3 | RCH-AcV | SCM | MTX |
| SA237856 | RCH-AcV-SCM-MTX-2 | RCH-AcV | SCM | MTX |
| SA237857 | RCH-AcV-SCM-MTX-1 | RCH-AcV | SCM | MTX |
| SA237858 | RCH-AcV-SCM-3 | RCH-AcV | SCM | n/a |
| SA237859 | RCH-AcV-SCM-1 | RCH-AcV | SCM | n/a |
| SA237860 | RCH-AcV-SCM-2 | RCH-AcV | SCM | n/a |
| SA237861 | REH-ACM-MTX-3 | REH | ACM | MTX |
| SA237862 | REH-ACM-MTX-2 | REH | ACM | MTX |
| SA237863 | REH-ACM-MTX-1 | REH | ACM | MTX |
| SA237864 | REH-ACM-1 | REH | ACM | n/a |
| SA237865 | REH-ACM-3 | REH | ACM | n/a |
| SA237866 | REH-ACM-2 | REH | ACM | n/a |
| SA237867 | REH-RPMI-MTX-3 | REH | RPMI | MTX |
| SA237868 | REH-RPMI-MTX-2 | REH | RPMI | MTX |
| SA237869 | REH-RPMI-MTX-1 | REH | RPMI | MTX |
| SA237870 | REH-RPMI-3 | REH | RPMI | n/a |
| SA237871 | REH-RPMI-2 | REH | RPMI | n/a |
| SA237872 | REH-RPMI-1 | REH | RPMI | n/a |
| SA237873 | REH-SCM-MTX-1 | REH | SCM | MTX |
| SA237874 | REH-SCM-MTX-2 | REH | SCM | MTX |
| SA237875 | REH-SCM-MTX-3 | REH | SCM | MTX |
| SA237876 | REH-SCM-1 | REH | SCM | n/a |
| SA237877 | REH-SCM-2 | REH | SCM | n/a |
| SA237878 | REH-SCM-3 | REH | SCM | n/a |
| Showing results 1 to 55 of 55 |
Collection:
| Collection ID: | CO002465 |
| Collection Summary: | Human B-ALL cell lines (REH and RCH-AcV) were cultured for 24 hours in UCM, SCM, or ACM. Additionally, MTX-treated human B-ALL cells were cultured for an additional 12 hours of treatment with MTX (50nM for REH and 70 nM for RCH-AcV). This timepoint was chosen due to our prior work in this system to avoid submitting mostly apoptotic cells for analysis [18]. After the prescribed time, leukemia cells were harvested for analysis. Notably, cell viability at the time of harvest exceeded 85% in each culture (n=3 biological replicates). Cell viability was measured using cell a Bio-Rad cell counter (cat#TC20, Bio-Rad, Hercules, CA) and over 1 million viable cells were collected and washed with 1X cold PBS (pH7.4). Cell pellets were snap-frozen in dry ice and stored at -80oC until samples were submitted to our core facility. |
| Sample Type: | B cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002484 |
| Treatment Summary: | REH and RCH-AcV were maintained in RPMI1640 (cat#10-041-CV, Corning, Glendale, AZ), supplemented with 20% FBS (cat#S11550, BioTechne, Minneapolis, MN). OP-9 bone marrow stromal cells were maintained in α-MEM (cat#15-012-CV, Corning, Glendale, AZ) supplemented with 20% FBS. For adipocyte differentiation, 105 OP-9 cells were plated in 6-well plates in DMEM (cat#10-017-CV, Corning, Glendale, AZ) supplemented with 10% FBS as previously described [18, 26]. After 24 hours of culture, the media was removed and switched to differentiation media which is composed of α-MEM supplemented with 1.8mM oleate (cat#O7501, Sigma, St. Louis, MO) bound to BSA (cat#A6003, Sigma, St. Louis, MO) with molar ratio 5.5:1 along with 175nM insulin (cat#I6634, Sigma, St. Louis, MO) and 0.2% FBS. ACM was collected after 3 days of differentiation and used in the experiments describe in this study. For SCM, OP-9 cells were plated in DMEM supplemented with 10% FBS and conditioned media were collected on day 3 of culture. Human B-ALL cell lines (REH and RCH-AcV) were cultured for 24 hours in UCM, SCM, or ACM. Additionally, methotrexate (MTX)-treated human B-ALL cells were cultured for an additional 12 hours of treatment with MTX (50nM for REH and 70 nM for RCH-AcV). This timepoint was chosen due to our prior work in this system to avoid submitting mostly apoptotic cells for analysis. |
| Treatment Compound: | adipocyte- , stromal cell-, and un- conditioned media; methotrexate or not |
| Treatment Dosevolume: | methotrexate: 50-70 nM |
| Treatment Doseduration: | conditioned medias: 24 hr; methotrexate: additional 12 hr |
| Treatment Vehicle: | methotrexate: DMSO |
Sample Preparation:
| Sampleprep ID: | SP002478 |
| Sampleprep Summary: | Cell samples (1x106) were mixed with 300 µl of ice-cold 2:1 acetonitrile:water and vortexed. All samples were incubated 30 min on ice and centrifuged at 20,627 g for 10 min at 4 ˚C. The supernatant was transferred to autosampler vials (ThermoFisher) held at 4 ˚C for LC-MS acquisition. |
| Processing Storage Conditions: | On ice |
Combined analysis:
| Analysis ID | AN003882 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE |
| Units | normalized peak area |
Chromatography:
| Chromatography ID: | CH002876 |
| Chromatography Summary: | A VanquishTM Horizon Binary ultrahigh performance liquid chromatography system coupled to a Q Exactive High Field Hybrid Orbitrap mass spectrometer (ThermoFisher) was used for data collection. A SeQuant® ZIC-HILIC column (Millipore Sigma, 3.5 µm, 100 Å, 150 x 2.1 mm, PEEK) was pumped with a mixture of mobile phases of 0.1% formic acid in water (mobile phase A) or 0.1% formic acid in acetonitrile (mobile phase B) (all reagents from Millipore Sigma). The column was equilibrated with 90% B for 8.3 min at 0.25 mL/min, after which 2.5 mL of extracted sample was injected. After this, a gradient ran from 90% to 20% B over 17.5, then was held at 20% B at 0.35 mL/min for 7.5 min. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
| Flow Gradient: | he column was equilibrated with 90% B for 8.3 min at 0.25 mL/min, after which 2.5 mL of extracted sample was injected. After this, a gradient ran from 90% to 20% B over 17.5 min, then was held at 20% B at 0.35 mL/min for 7.5 min. |
| Flow Rate: | 0.25 mL/min-0.35 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003622 |
| Analysis ID: | AN003882 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Compound Discoverer 3.3 (Thermo Scientific) was used for data analysis of metabolomic experiments, including retention time alignment across runs, cubic spline normalization of areas for each metabolite in quality control pooled samples, and gap-filling based on real peak detection. The minimum peak intensity was 5x105, and metabolites were excluded if they had >50% relative standard deviation after correction or a max sample area <5-fold that of the blank. Furthermore, to be considered a high-confidence metabolite for analysis, metabolites required a) an accurate mass (5 ppm) match and either (i) retention time (±5%) matching of reference standards, and/or (ii) matching to MS2 spectra in mzCloud (mzcloud.org) (including at least one matching product ion); b) an accurate mass and retention time match to a lipid identity determined by LipidSearch (ThermoFisher, all default parameters used) based on MS2 data; and/or c) an MS2 fragment ion matching to a particular class of compounds (184.1 for phosphatidylcholine). When a chromatographic peak matched to two standards of similar retention time that were indistinguishable by MS2, we prioritized the metabolite with higher abundance in human or retained both annotations. The naming convention for the metabolites reported herein is as follows – a) if the metabolite was an accurate mass and retention time match to our curated library or to our LipidSearch library, it is listed only as the metabolite name; b) if the metabolite had an MS2 library match but no match in the aforementioned libraries, it is listed as the MS2 match and the retention time; c) if the metabolite had an MS2 compound class match, it is listed as the compound class, the chemical formula (or the molecular weight if formula was not available), and the retention time. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 275 |
| Ionization Potential: | +3.5 kV |
| Automatic Gain Control: | 1E6 |
