Summary of Study ST002235
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 PR001425. The data can be accessed directly via it's Project DOI: 10.21228/M8HX4C 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 | ST002235 |
Study Title | Application of Artificial Intelligence to Plasma Metabolomics Profiles to Predict Response to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer |
Study Summary | Summary: There is a need for biomarkers predictive of response to neoadjuvant chemotherapy (NACT) in triple-negative breast cancer (TNBC). We previously obtained evidence that a polyamine signature in the blood is associated with TNBC development and progression. In this study, we evaluated whether plasma polyamines and other metabolites may identify TNBC patients who are unlikely to respond to NACT. Pre-treatment plasma levels of acetylated polyamines were elevated in TNBC patients that had moderate to extensive tumor burden (RCB-II/III) following NACT compared to those that achieved a complete pathological response (pCR/RCB-0) or had minimal residual disease (RCB-I). We further applied artificial intelligence to comprehensive metabolic profiles to identify additional metabolites associated with treatment response. A deep learning model (DLM) consisting of two polyamines as well as nine additional metabolites was developed for improved prediction of RCB-II/III. The DLM has potential clinical value for identifying TNBC patients who are unlikely to respond to NACT and who may benefit from other treatment modalities. |
Institute | University of Texas MD Anderson Cancer Center |
Last Name | Cai |
First Name | Yining |
Address | 6767 Bertner Avenue, Houston, Texas, 77030 |
ycai4@mdanderson.org | |
Phone | 713-563-3096 |
Submit Date | 2022-05-26 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Waters) |
Analysis Type Detail | LC-MS |
Release Date | 2022-08-10 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
Analysis ID | AN003645 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Waters XEVO-G2XSQTOF |
Column | C18 |
MS Type | ESI |
MS instrument type | QTOF |
MS instrument name | Waters Xevo-G2-XS |
Ion Mode | POSITIVE |
Units | ppm |
Chromatography:
Chromatography ID: | CH002699 |
Chromatography Summary: | Instrument: XEVO-G2XSQTOF Untargeted metabolomics analysis was conducted on Waters Acquity™ UPLC system with 2D column regeneration configuration (I-class and H-class) coupled to a Xevo G2-XS quadrupole time-of-flight (qTOF) mass spectrometer as previously described.11,13-15 Chromatographic separation was performed using HILIC (Acquity™ UPLC BEH amide, 100 Å, 1.7 µm 2.1× 100mm, Waters Corporation, Milford, U.S.A) and C18 (Acquity™ UPLC HSS T3, 100 Å, 1.8 µm, 2.1×100mm, Water Corporation, Milford, U.S.A) columns at 45°C. Quaternary solvent system mobile phases were (A) 0.1% formic acid in water, (B) 0.1% formic acid in acetonitrile and (D) 100mM ammonium formate, pH 3. Samples were separated on the HILIC using the following gradient profile at 0.4 mL/min flow rate: (95% B, 5% D) linear change to (70% A, 25% B and 5% D) over 5 min; 100% A for 1 min; and 100% A for 1 min. For C18 separation, the chromatography gradient was as follows at 0.4 mL/min flow rate: 100% A with a linear change to (5% A, 95% B) over 5 min; (95% B, 5% D) for 1 min; and 1 min at (95% B, 5% D). A binary pump was used for column regeneration and equilibration. The solvent system mobile phases were (A1) 100mM ammonium formate, pH 3, (A2) 0.1% formic in 2-propanol and (B1) 0.1% formic acid in acetonitrile. The HILIC column was stripped using 90% A2 for 5 min at 0.25 mL/min flow rate, followed by a 2 min equilibration using 100% B1 at 0.3mL/min flow rate. Reverse phase C18 column regeneration was performed using 95% A1, 5% B1 for 2 min followed by column equilibration using 5% A1, 95% B1 for 5 min at 0.4mL/min flow rate. |
Instrument Name: | Waters XEVO-G2XSQTOF |
Column Name: | C18 |
Column Temperature: | 45 |
Flow Gradient: | 100% A with a linear change to (5% A, 95% B) over 5 min; (95% B, 5% D) for 1 min; and 1 min at (95% B, 5% D) |
Flow Rate: | 0.4 mL/min |
Solvent A: | 100% water; 0.1% formic acid(A), 100% acetonitrile; 0.1% formic acid(B), 100 mM ammonium formate, pH 3(D) |
Chromatography Type: | Reversed phase |