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
| 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. |
Combined analysis:
| Analysis ID | AN006690 | AN006691 |
|---|---|---|
| Chromatography ID | CH005082 | CH005083 |
| MS ID | MS006389 | MS006390 |
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um) | Phenomenex Kinetex C18 (100 x 2.1mm,2.6um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Orbitrap Exploris 480 | Thermo Orbitrap Exploris 480 |
| Ion Mode | UNSPECIFIED | UNSPECIFIED |
| Units | mg/L | mg/L |
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 |
MS:
| MS ID: | MS006389 |
| Analysis ID: | AN006690 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The electrospray ionization mass spectra were acquired in polarity switching. Data dependent acquisition (DDA) was used to collect full scan MS and MSMS information simultaneously. The ion spray voltage was set to 3,500 V for positive mode and 2,800 V for negative mode. The survey of full scan MS spectra (m/z 70-1200) was acquired in the Orbitrap with 60,000 resolutions. The normalized automatic gain control (AGC) target at 100% and the maximum injection time |
| Ion Mode: | UNSPECIFIED |
| MS ID: | MS006390 |
| Analysis ID: | AN006691 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The electrospray ionization mass spectra were acquired in polarity switching. Data dependent acquisition (DDA) was used to collect full scan MS and MSMS information simultaneously. The ion spray voltage was set to 3,500 V for positive mode and 2,800 V for negative mode. The survey of full scan MS spectra (m/z 70-1200) was acquired in the Orbitrap with 60,000 resolutions. The normalized automatic gain control (AGC) target at 100% and the maximum injection time |
| Ion Mode: | UNSPECIFIED |
