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.

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Study IDST002235
Study TitleApplication of Artificial Intelligence to Plasma Metabolomics Profiles to Predict Response to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer
Study SummarySummary: 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 NameCai
First NameYining
Address6767 Bertner Avenue, Houston, Texas, 77030
Emailycai4@mdanderson.org
Phone713-563-3096
Submit Date2022-05-26
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2022-08-10
Release Version1
Yining Cai Yining Cai
https://dx.doi.org/10.21228/M8HX4C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001425
Project DOI:doi: 10.21228/M8HX4C
Project Title:Application of Artificial Intelligence to Plasma Metabolomics Profiles to Predict Response to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer
Project 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, TX, 77030
Email:ycai4@mdanderson.org
Phone:713-563-3096

Subject:

Subject ID:SU002321
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:50 +/-11
Gender:Female

Factors:

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

mb_sample_id local_sample_id Factor
SA212961PL244_1270702Group 1
SA212962PL244_1235250Group 1
SA212963PL244_1233887Group 1
SA212964PL244_1271325Group 1
SA212965PL244_1282931Group 1
SA212966PL244_1286838Group 1
SA212967PL244_1283937Group 1
SA212968PL244_1226561Group 1
SA212969PL244_1277158Group 1
SA212970PL127_1259011Group 1
SA212971PL076R1_1186336Group 1
SA212972PL127_1248881Group 1
SA212973PL127_1247273Group 1
SA212974PL127_1252247Group 1
SA212975PL127_1256541Group 1
SA212976PL244_1292677Group 1
SA212977PL127_1257232Group 1
SA212978PL127_1256961Group 1
SA212979PL244_1205718Group 1
SA212980PL244_1296089Group 1
SA212981PL244_1318261Group 1
SA212982PL244_1317064Group 1
SA212983PL244_1316186Group 1
SA212984PL244_1318823Group 1
SA212985PL244_1319248Group 1
SA212986PL244_1320905Group 1
SA212987PL244_1320107Group 1
SA212988PL244_1319868Group 1
SA212989PL244_1315485Group 1
SA212990PL244_1313162Group 1
SA212991PL244_1300096Group 1
SA212992PL244_1297780Group 1
SA212993PL127_1244941Group 1
SA212994PL244_1301510Group 1
SA212995PL244_1306321Group 1
SA212996PL244_1311163Group 1
SA212997PL244_1310613Group 1
SA212998PL244_1308931Group 1
SA212999PL244_1295553Group 1
SA213000PL127_1251794Group 1
SA213001PL076R1_1199905Group 1
SA213002PL094_1225423Group 1
SA213003PL094_1226981Group 1
SA213004PL076R1_1198412Group 1
SA213005PL076R1_1197283Group 1
SA213006PL094_1223999Group 1
SA213007PL094_1223685Group 1
SA213008PL076R1_1206621Group 1
SA213009PL076R1_1205171Group 1
SA213010PL076R1_1204735Group 1
SA213011PL076R1_1201708Group 1
SA213012PL076R1_1194855Group 1
SA213013PL076R1_1194858Group 1
SA213014PL127_1232134Group 1
SA213015PL076R1_1189620Group 1
SA213016PL127_1236612Group 1
SA213017PL127_1244002Group 1
SA213018PL076R1_1189743Group 1
SA213019PL127_1227136Group 1
SA213020PL076R1_1192956Group 1
SA213021PL076R1_1190029Group 1
SA213022PL076R1_1191460Group 1
SA213023PL076R1_1205402Group 2
SA213024PL244_1318419Group 2
SA213025PL076R1_1186655Group 2
SA213026PL076R1_1208534Group 2
SA213027PL244_1312729Group 2
SA213028PL244_1314974Group 2
SA213029PL094_1206035Group 2
SA213030PL127_1218367Group 2
SA213031PL127_1215709Group 2
SA213032PL094_1236361Group 2
SA213033PL127_1258803Group 2
SA213034PL127_1224847Group 2
SA213035PL127_1239706Group 2
SA213036PL127_1252243Group 2
SA213037PL127_1226721Group 2
SA213038PL094_1234137Group 2
SA213039PL094_1229043Group 2
SA213040PL076R1_1216364Group 2
SA213041PL076R1_1214978Group 2
SA213042PL076R1_1208538Group 2
SA213043PL127_1244768Group 2
SA213044PL244_1284366Group 2
SA213045PL094_1228807Group 2
SA213046PL244_1276745Group 2
SA213047PL094_1226712Group 2
SA213048PL244_1299198Group 2
Showing results 1 to 88 of 88

Collection:

Collection ID:CO002314
Collection Summary:EDTA plasma from cancer-free women (n = 167) were obtained from the MD Anderson Cancer Center (MDACC) Longitudinal High-Risk Cohort initiated September 1st, 2011, for the prospective follow-up of cancer-free highrisk women seen in the MDACC Cancer Prevention Center (IRB protocol LAB07-0086).
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002333
Treatment Summary:The specimen set consisted of pre-treatment EDTA plasma from 88 patients who received standard-of-care NACT; 62 of the 88 patients had a second plasma sample available after four cycles of AC.

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.

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

MS:

MS ID:MS003396
Analysis ID:AN003645
Instrument Name:Waters Xevo-G2-XS
Instrument Type:QTOF
MS Type:ESI
MS Comments:Data were processed using Progenesis QI (Non-linear, Waters). Peak picking and retention time alignment of LC-MS and MSe data were performed using Progenesis QI software (Non-linear, Waters)
Ion Mode:POSITIVE
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