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
Email	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

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Sample Preparation:

Sampleprep ID:	SP002327
Sampleprep Summary:	Plasma metabolites were extracted from pre-aliquoted biospecimens (15µL) with 45µL of LCMS grade methanol (ThermoFisher) in a 96-well microplate (Eppendorf). Plates were heat sealed, vortexed for 5 min at 750 rpm, and centrifuged at 2000 × g for 10 minutes at room temperature. The supernatant (30µL) was transferred to a 96-well plate, leaving behind the precipitated protein. The supernatant was further diluted with 60µL of 100mM ammonium formate, pH3 (Fisher Scientific). For Hydrophilic Interaction Liquid Chromatography (HILIC) positive ion analysis, 15µL of the supernatant and ammonium formate mix were diluted with 195µL of 1:3:8:144 water (GenPure ultrapure water system, Thermofisher): LCMS grade methanol (ThermoFisher): 100mM ammonium formate, pH3 (Fisher Scientific): LCMS grade acetonitrile (ThermoFisher). For C18 analysis, 15µL of the supernatant and ammonium formate mix were diluted with 90µL water (GenPure ultrapure water system, ThermoFisher) for positive ion mode. Each sample solution was transferred to 384-well microplate (Eppendorf) for LCMS analysis.

Sampleprep ID:

SP002327

Sampleprep Summary:

Plasma metabolites were extracted from pre-aliquoted biospecimens (15µL) with 45µL of LCMS grade methanol (ThermoFisher) in a 96-well microplate (Eppendorf). Plates were heat sealed, vortexed for 5 min at 750 rpm, and centrifuged at 2000 × g for 10 minutes at room temperature. The supernatant (30µL) was transferred to a 96-well plate, leaving behind the precipitated protein. The supernatant was further diluted with 60µL of 100mM ammonium formate, pH3 (Fisher Scientific). For Hydrophilic Interaction Liquid Chromatography (HILIC) positive ion analysis, 15µL of the supernatant and ammonium formate mix were diluted with 195µL of 1:3:8:144 water (GenPure ultrapure water system, Thermofisher): LCMS grade methanol (ThermoFisher): 100mM ammonium formate, pH3 (Fisher Scientific): LCMS grade acetonitrile (ThermoFisher). For C18 analysis, 15µL of the supernatant and ammonium formate mix were diluted with 90µL water (GenPure ultrapure water system, ThermoFisher) for positive ion mode. Each sample solution was transferred to 384-well microplate (Eppendorf) for LCMS analysis.