Summary of Study ST001476

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 PR001000. The data can be accessed directly via it's Project DOI: 10.21228/M8F982 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001476
Study TitleDesign of Experiments for Maximizing T cell endpoints
Study SummaryPurified T cells from a single healthy donor were expanded in vitro with either magnetic beads or degradable micro-scaffold (DMS) particles. Magnetic bead cultures were expanded according to manufacturer’s instructions, while DMS cultures were expanded with varying DMS particle concentration, IL2 concentration, and antigen surface density on the particles, according to a design of experiments. Media of each culture of was sampled repeatedly over the course of a 14 day period. Quantities and characteristics of activated T cells were assessed at the end of the culture period, and media was analyzed by 1H-NMR. Analysis of spectra resulted in a set of 20 features that was used in predictive modeling of T cell endpoints, along with culture parameters described above and cytokine data. A second validation experiment was performed with different values for culture parameters, using the same culture, sampling, and NMR analysis methods.
Institute
University of Georgia
DepartmentComplex Carbohydrate Research Center
LaboratoryEdison
Last NameColonna
First NameMax
Address315 Riverbend Rd
Emailmaxwellbaca@uga.edu
Phone7065420257
Submit Date2020-08-12
Num Groups2
Total Subjects1
Raw Data AvailableYes
Analysis Type DetailNMR
Release Date2020-09-10
Release Version1
Max Colonna Max Colonna
https://dx.doi.org/10.21228/M8F982
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001000
Project DOI:doi: 10.21228/M8F982
Project Title:Predicting T Cell Quality During Manufacturing Through an AI-based Integrative Multi-omics Analytical Platform
Project Summary:Large-scale, reproducible manufacturing of therapeutic cells with consistent high quality is vital for translation to clinically effective and widely accessible cell-therapies for patients. However, the biological and logistical complexity of manufacturing a living product, including challenges associated with their inherent variability as well as uncertainties of process parameters, currently make it difficult to achieve predictable cell-product quality. Using a degradable microscaffold-based T cell manufacturing process as an example, we developed an Artificial Intelligence (AI)-driven experimental-computational platform to identify a multivariate set of critical process parameters (CPPs) and critical quality attributes (CQAs) from heterogeneous, high dimensional, time-dependent multi-omics data, measurable during early stages of manufacturing and that are predictive of end-of-manufacturing product quality. Sequential, Design-of-Experiment (DOE)-based studies, coupled with a set of agnostic machine-learning framework, was used to extract multiple feature combinations from Day 4 to 6 media assessment, that were highly predictive (R2>90%) of the end-product phenotypes, specifically the total live CD4+ and CD8+ naïve and central memory T cells (CD63L+CCR7+ cells), and the CD4+/CD8+ T cell ratio. This generalizable workflow and computational platform could be broadly applied to any cell-therapy manufacturing process to identify multivariate early CQAs and CPPs that are predictable of final product quality.
Institute:University of Georgia;Georgia Institute of Technology;University of Puerto Rico Mayaguez
Last Name:Colonna
First Name:Maxwell
Address:315 Riverbend Rd, Athens, Georgia, 30602, USA
Email:maxwellbaca@uga.edu
Phone:7065420257
Funding Source:NSF EEC-1648035
Publications:Predicting T Cell Quality During Manufacturing Through an AI-based Integrative Multi-omics Analytical Platform
Contributors:Valerie Odeh-Couvertier, Nathan J. Dwarshuis, Maxwell B. Colonna, Bruce L. Levine, Arthur S. Edison, Theresa Kotanchek, Krishnendu Roy, and Wandaliz Torres-Garcia

Subject:

Subject ID:SU001550
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Biosource Or Supplier:Astarte Bio
Cell Strain Details:Cat 1017-3975JY18

Factors:

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

mb_sample_id local_sample_id method timepoint il2_conc carrier_conc abs_surface_density
SA124598batch1_92Beads 11 20 n/a n/a
SA124599batch1_67Beads 11 20 n/a n/a
SA124600batch1_103Beads 11 20 n/a n/a
SA124601batch1_32Beads 11 20 n/a n/a
SA124602batch1_72Beads 11 20 n/a n/a
SA124603batch1_118Beads 11 20 n/a n/a
SA124604batch1_20Beads 14 20 n/a n/a
SA124605batch1_78Beads 14 20 n/a n/a
SA124606batch1_11Beads 14 20 n/a n/a
SA124607batch1_2Beads 14 20 n/a n/a
SA124608batch1_36Beads 14 20 n/a n/a
SA124609batch1_26Beads 4 20 n/a n/a
SA124610batch1_39Beads 4 20 n/a n/a
SA124611batch1_119Beads 4 20 n/a n/a
SA124612batch1_63Beads 4 20 n/a n/a
SA124613batch1_101Beads 4 20 n/a n/a
SA124614batch1_28Beads 4 20 n/a n/a
SA124615batch1_116Beads 6 20 n/a n/a
SA124616batch1_31Beads 6 20 n/a n/a
SA124617batch1_117Beads 6 20 n/a n/a
SA124618batch1_45Beads 6 20 n/a n/a
SA124619batch1_51Beads 6 20 n/a n/a
SA124620batch1_65Beads 6 20 n/a n/a
SA124621batch1_62Beads 8 20 n/a n/a
SA124622batch1_108Beads 8 20 n/a n/a
SA124623batch1_123Beads 8 20 n/a n/a
SA124624batch1_59Beads 8 20 n/a n/a
SA124625batch1_18Beads 8 20 n/a n/a
SA124626batch1_9Beads 8 20 n/a n/a
SA124633batch2_108Buffer_control_last n/a n/a n/a n/a
SA124634batch1_130Buffer_control_last n/a n/a n/a n/a
SA124627batch1_48Buffer_control n/a n/a n/a n/a
SA124628batch1_96Buffer_control n/a n/a n/a n/a
SA124629batch2_1Buffer_control n/a n/a n/a n/a
SA124630batch2_96Buffer_control n/a n/a n/a n/a
SA124631batch2_48Buffer_control n/a n/a n/a n/a
SA124632batch1_1Buffer_control n/a n/a n/a n/a
SA124635batch1_128DMS 11 10 1500 80
SA124636batch1_16DMS 11 10 2500 100
SA124637batch1_89DMS 11 10 2500 60
SA124638batch1_5DMS 11 10 500 100
SA124639batch1_40DMS 11 10 500 60
SA124640batch1_70DMS 11 20 1500 100
SA124641batch1_34DMS 11 20 1500 60
SA124642batch1_6DMS 11 20 20 20
SA124643batch1_79DMS 11 20 20 20
SA124644batch1_106DMS 11 20 2500 80
SA124645batch1_37DMS 11 20 2500 80
SA124646batch1_110DMS 11 20 500 80
SA124647batch2_21DMS 11 30 1500 1282
SA124648batch2_20DMS 11 30 1500 1729
SA124649batch1_82DMS 11 30 1500 80
SA124650batch1_112DMS 11 30 1500 80
SA124651batch1_21DMS 11 30 2500 100
SA124652batch2_71DMS 11 30 2500 1282
SA124653batch2_61DMS 11 30 2500 1729
SA124654batch1_90DMS 11 30 2500 60
SA124655batch1_27DMS 11 30 500 100
SA124656batch2_103DMS 11 30 500 1282
SA124657batch2_15DMS 11 30 500 1729
SA124658batch1_33DMS 11 30 500 60
SA124659batch2_46DMS 11 35 1000 1282
SA124660batch2_7DMS 11 35 1000 1729
SA124661batch2_14DMS 11 35 2000 1282
SA124662batch2_91DMS 11 35 2000 1729
SA124663batch2_32DMS 11 35 3000 1282
SA124664batch2_72DMS 11 35 3000 1729
SA124665batch2_77DMS 11 40 1500 1282
SA124666batch2_83DMS 11 40 1500 1729
SA124667batch2_40DMS 11 40 2500 1282
SA124668batch2_4DMS 11 40 2500 1729
SA124669batch2_73DMS 11 40 3500 1282
SA124670batch2_98DMS 11 40 3500 1729
SA124671batch2_54DMS 11 40 500 1282
SA124672batch2_60DMS 11 40 500 1729
SA124673batch1_52DMS 14 10 1500 80
SA124674batch1_15DMS 14 10 2500 100
SA124675batch1_10DMS 14 10 2500 60
SA124676batch1_74DMS 14 10 500 100
SA124677batch1_107DMS 14 10 500 60
SA124678batch1_55DMS 14 20 1500 100
SA124679batch1_109DMS 14 20 1500 60
SA124680batch1_7DMS 14 20 20 20
SA124681batch1_84DMS 14 20 20 20
SA124682batch1_61DMS 14 20 2500 80
SA124683batch1_124DMS 14 20 2500 80
SA124684batch1_88DMS 14 20 500 80
SA124685batch2_50DMS 14 30 1500 1282
SA124686batch2_84DMS 14 30 1500 1729
SA124687batch1_129DMS 14 30 1500 80
SA124688batch1_43DMS 14 30 1500 80
SA124689batch1_64DMS 14 30 2500 100
SA124690batch2_59DMS 14 30 2500 1282
SA124691batch2_37DMS 14 30 2500 1729
SA124692batch1_49DMS 14 30 2500 60
SA124693batch1_120DMS 14 30 500 100
SA124694batch2_66DMS 14 30 500 1282
SA124695batch2_97DMS 14 30 500 1729
SA124696batch1_91DMS 14 30 500 60
SA124697batch2_17DMS 14 35 1000 1282
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Collection:

Collection ID:CO001545
Collection Summary:Conditioned culture media (Miltenyi Texmacs media). Was collected via pipetting as described in sample prep protocol document.
Sample Type:T-cells
Collection Method:Pipette
Volumeoramount Collected:60 uL
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001565
Treatment Summary:Cultures were prepared with varied IL2 concentration, DMS concentration, and DMS surface densities as described in study design. Culture media was replenished on days 4, 6, 8, 11 after sampling.
Cell Media:Miltenyi Texmacs (Cat. 170-076-307)

Sample Preparation:

Sampleprep ID:SP001558
Sampleprep Summary:Media samples were thawed at 4°C, then centrifuged at maximum speed for 15 minutes. 45 uL were transferred directly to NMR tube containing 5 uL of D2O with 100 uM DSS and mixed. Remaining supernatant from each sample combined for internal controls.
Sampleprep Protocol Filename:mbcolonna_20200812_100701_PR_SP_protocol.pdf
Processing Storage Conditions:4℃
Extraction Method:None

Analysis:

Analysis ID:AN002452
Laboratory Name:Edison
Analysis Type:NMR
Operator Name:Maxwell Colonna
Data Format:Bruker
Num Factors:183
Rt Units:No RT Data
Results File:ST001476_AN002452_Results.txt
Units:UNITS:AU

NMR:

NMR ID:NM000183
Analysis ID:AN002452
Instrument Name:Bruker Avance III HD
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
Field Frequency Lock:Deuterium
Spectrometer Frequency:600 MHz
NMR Probe:5mm TCI
NMR Solvent:90% H2O, 10% D2O
NMR Tube Size:1.7mm
Shimming Method:Topshim
Pulse Sequence:noesypr1d
Water Suppression:Presaturation
Pulse Width:7.45 us
Power Level:5.5584 W
Receiver Gain:203
Offset Frequency:2819.9 Hz
Presaturation Power Level:1.2333e-05 W
Chemical Shift Ref Cpd:DSS
Temperature:25
Number Of Scans:128
Dummy Scans:4
Acquisition Time:2.72 s
Relaxation Delay:4 s
Spectral Width:20 ppm
Num Data Points Acquired:65382
Line Broadening:0.3 Hz
Baseline Correction Method:Polynomial order 5
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