Summary of Study ST004047
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 PR002537. The data can be accessed directly via it's Project DOI: 10.21228/M8Q839 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 | ST004047 |
| Study Title | Artificial intelligence platform for endometrial cancer risk stratification using clinical and molecular multi-omics data |
| Study Summary | Endometrial cancer (ENDOM) prevention remains challenging, creating an urgent need for better risk stratification tools. We developed a patient-centered bimodal multilevel endometrial cancer (2M-EC) predictive platform that integrates clinically accessible data with multi-biofluid multi-omics data. Our study established the MBF-ED cohort (n=531), collecting comprehensive clinical data and multi-dimensional body fluid samples. We processed these using a unique analytical pipeline: (1) simplifying clinical variables through empirical and data-driven methods, (2) extracting ENDOM-specific MS features using machine learning, and (3) developing an innovative bimodal AI architecture that fuses 2D MS omics matrices with 1D clinical vectors. The resulting patient-centered 2M-EC predictive platform provides real-time, interpretable risk stratification through an online interface. The advantages of it include overcoming single-marker limitations via multimodal integration, combining molecular depth with clinical practicality and scalable design adaptable to both resource-limited and advanced healthcare settings. This work demonstrates how AI can bridge cutting-edge molecular profiling with routine clinical practice, offering a new paradigm for patient-centered cancer risk assessment. |
| Institute | Fudan University |
| Last Name | DANDAN |
| First Name | LI |
| Address | Fudan University |
| oceanddl@sina.com | |
| Phone | 18061019632 |
| Submit Date | 2025-04-28 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-07-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002537 |
| Project DOI: | doi: 10.21228/M8Q839 |
| Project Title: | Patient-centered artificial intelligence platform for endometrial cancer risk stratification using clinical and molecular multi-omics data |
| Project Summary: | Endometrial cancer (ENDOM) prevention remains challenging, creating an urgent need for better risk stratification tools. We developed a patient-centered bimodal multilevel endometrial cancer (2M-EC) predictive platform that integrates clinically accessible data with multi-biofluid multi-omics data. Our study established the MBF-ED cohort (n=531), collecting comprehensive clinical data and multi-dimensional body fluid samples. We processed these using a unique analytical pipeline: (1) simplifying clinical variables through empirical and data-driven methods, (2) extracting ENDOM-specific MS features using machine learning, and (3) developing an innovative bimodal AI architecture that fuses 2D MS omics matrices with 1D clinical vectors. The resulting patient-centered 2M-EC predictive platform provides real-time, interpretable risk stratification through an online interface. The advantages of it include overcoming single-marker limitations via multimodal integration, combining molecular depth with clinical practicality and scalable design adaptable to both resource-limited and advanced healthcare settings. This work demonstrates how AI can bridge cutting-edge molecular profiling with routine clinical practice, offering a new paradigm for patient-centered cancer risk assessment. |
| Institute: | Fudan University |
| Department: | Chemistry department |
| Laboratory: | LiangQiao lab |
| Last Name: | DANDAN |
| First Name: | LI |
| Address: | Fudan University |
| Email: | oceanddl@sina.com |
| Phone: | 18061019632 |
Subject:
| Subject ID: | SU004193 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Sample type |
|---|---|---|---|
| SA467671 | P3-rp | blood | blood |
| SA467672 | P1 | blood | blood |
| SA467673 | P2 | blood | blood |
| SA467674 | P3 | blood | blood |
| SA467675 | P2-rp | blood | blood |
| SA467676 | P1-rp | blood | blood |
| SA467677 | C2-rp | cervix | cervix |
| SA467678 | C3-rp | cervix | cervix |
| SA467679 | C1 | cervix | cervix |
| SA467680 | C2 | cervix | cervix |
| SA467681 | C3 | cervix | cervix |
| SA467682 | C1-rp | cervix | cervix |
| SA467683 | U3 | uterine cavity | uterine cavity |
| SA467684 | U2 | uterine cavity | uterine cavity |
| SA467685 | U1 | uterine cavity | uterine cavity |
| SA467686 | U1-rp | uterine cavity | uterine cavity |
| SA467687 | U2-rp | uterine cavity | uterine cavity |
| SA467688 | U3-rp | uterine cavity | uterine cavity |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO004186 |
| Collection Summary: | Under sterile conditions in the operating room, endometrial secretions were collected using a disposable endometrial brush prior to uterine removal. The brush head was advanced 2 cm through the cervical canal and rotated three times in each uterine segment. Harvested tissue was transferred to 15 mL tubes containing 3 mL 80% methanol. Brush heads were detached with sterile forceps and co-stored. Samples were immediately flash-frozen in laparoscopic specimen liquid nitrogen containers, transported on dry ice, and stored at -80°C until metabolomic extraction. During preoperative examination, cervical secretion were collected using HPV brushes prior to bimanual palpation. Brush heads were directly immersed in 15 mL tubes with 80% methanol (Thermo Fisher Scientific, USA). Peripheral blood (8 mL) was collected preoperatively into EDTA tubes (BD Biosciences, USA). |
| Sample Type: | Uterine secretion, cervical secretion, whole blood |
Treatment:
| Treatment ID: | TR004202 |
| Treatment Summary: | no treatment |
Sample Preparation:
| Sampleprep ID: | SP004199 |
| Sampleprep Summary: | In blood metabolomics, 50 μL whole blood was mixed with 200 μL ice-cold methanol:acetonitrile (1:1, v/v; Thermo Fisher Scientific, USA). The mixture was vortexed, sonicated for 2 min, and incubated at -20°C for 30 min. Following centrifugation at 16,000×g (4°C, 20 min), 100 μL supernatant was lyophilized and reconstituted in 20 μL methanol:acetonitrile:water (1:1:2, v/v/v). Samples were thawed at 4°C and homogenized by gentle vortex mixing. After centrifugation at 12,000 rpm (4°C, 5 min), the supernatant was carefully collected and aliquoted into two replicates. The supernatant was concentrated using a vacuum centrifugal concentrator (approximately 2 h) until lyophilized powder was obtained. The dried metabolites were stored at −80°C prior to downstream analysis. After reconstitution, samples were centrifuged at 16,000×g (4°C, 30 min) and the supernatant was analyzed. For plasma processing, 100 μL plasma was mixed with 400 μL (4× volume) of ice-cold methanol/acetonitrile (1:1, v/v), vortexed for 30 s, and sonicated for 2 min. The mixture was incubated at -20°C for 30 min for protein precipitation, then centrifuged at 16,000×g (4°C, 20 min). 300 μL supernatant was collected, concentrated to dryness by centrifugation, and stored at -80°C. After reconstitution, samples were centrifuged at 16,000×g (4°C, 30 min) and the supernatant was subjected to instrumental analysis. |
Chromatography:
| Chromatography ID: | CH005082 |
| Chromatography Summary: | HILIC (LC/MS) |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um) |
| Column Temperature: | 25 |
| Flow Gradient: | Linear gradient from 5% A to 60% A over 8 minutes, followed by a return to 5% A at 9.1 minutes, with mobile phase B inversely following the same pattern. |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 100% water; 25 mM ammonium acetate; 25 mM ammonium hydroxide |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH005083 |
| Chromatography Summary: | RP (LC/MS) |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) |
| Column Temperature: | 25 |
| Flow Gradient: | Linear gradient from 99% A to 1% A over 8 minutes, followed by a return to 99% A at 9.1 minutes, with mobile phase B inversely following the same pattern. |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% water; 0.01% acetic acid |
| Solvent B: | 50% acetonitrile/50% toluene dicarboxylic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006690 |
| Analysis Type: | MS |
| Chromatography ID: | CH005082 |
| Has Mz: | 1 |
| Rt Units: | No RT data |
| Results File: | ST004047_AN006690_Results.txt |
| Units: | mg/L |
| Analysis ID: | AN006691 |
| Analysis Type: | MS |
| Chromatography ID: | CH005083 |
| Has Mz: | 1 |
| Rt Units: | No RT data |
| Results File: | ST004047_AN006691_Results.txt |
| Units: | mg/L |
