Summary of Study ST004167
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 PR002627. The data can be accessed directly via it's Project DOI: 10.21228/M8326S This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004167 |
| Study Title | Targeted Lipidomic Profiling of STBD1 Knockdown in Clear Cell Renal Carcinoma Cells |
| Study Summary | To investigate the role of STBD1 in lipid metabolism of ccRCC, we performed targeted lipidomics comparing STBD1-knockdown and control cells. A total of 21 lipid classes showed reduced abundance upon STBD1 depletion, including monoglycerides and diglycerides, the precursors for triacylglycerol synthesis. This indicates that STBD1 knockdown diminishes lipid substrates required for lipid droplet biogenesis. Conversely, STBD1-deficient cells exhibited an accumulation of polyunsaturated fatty acid (PUFA)-containing phospholipids, such as phosphatidylcholine, whereas PUFA-containing triacylglycerols were decreased. Together, these findings suggest that STBD1 regulates lipid droplet dynamics by coordinating autophagy and lipid metabolic pathways. |
| Institute | The Affiliated Cancer Hospital of Zhengzhou University |
| Department | Medical laboratory |
| Laboratory | Department of Laboratory Medicine |
| Last Name | Wang |
| First Name | Hao |
| Address | 127 Dongming Road, Jinshui District, Zhengzhou, Henan, China, Zhengzhou, Henan Province, 450003, China |
| wanghao123@tmu.edu.cn | |
| Phone | +8613642140283 |
| Submit Date | 2025-08-28 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-09-25 |
| Release Version | 1 |
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Project:
| Project ID: | PR002627 |
| Project DOI: | doi: 10.21228/M8326S |
| Project Title: | Targeted Lipidomic Profiling of STBD1 Knockdown in Clear Cell Renal Carcinoma Cells |
| Project Summary: | Clear cell renal cell carcinoma (ccRCC) is characterized by profound metabolic reprogramming, with marked accumulation of glycogen and lipid droplets (LDs). However, the molecular mechanisms linking glycogen metabolism to LD biogenesis remain poorly understood. In this project, we aimed to elucidate the role of the glycogen-binding protein and selective glycophagy receptor STBD1 in coordinating glycogen and lipid droplet metabolism in ccRCC. Using proximity labeling combined with affinity purification mass spectrometry, we identified STBD1 as a novel LD-associated protein. Mechanistic studies demonstrated that STBD1 is targeted to LDs through N-terminal myristoylation, thereby mediating glycogen–LD colocalization and promoting LD biogenesis. Knockdown of STBD1 suppressed LD formation, highlighting a direct metabolic crosstalk between glycogen and lipid metabolism in ccRCC. To further investigate the functional impact of STBD1 loss, we performed proteomic analysis, which revealed significant alterations in proteins related to autophagy and lipid metabolism. Complementary targeted lipidomics analysis quantified 1,684 lipid species across 40 lipid classes. STBD1 knockdown cells exhibited reduced levels of multiple lipid classes, including monoglycerides (MG) and diglycerides (DG), precursors for triglyceride (TG) synthesis. In contrast, phospholipids enriched in polyunsaturated fatty acids (PUFAs) were increased, suggesting a remodeling of lipid composition that may elevate lipid peroxidation potential. In summary, this study uncovers a novel role of STBD1 in bridging glycogen and lipid droplet metabolism, regulating LD biogenesis, and potentially modulating ferroptosis resistance in ccRCC. These findings provide new mechanistic insights into metabolic vulnerabilities of renal cancer and highlight STBD1-related pathways as potential biomarkers and therapeutic targets. |
| Institute: | The Affiliated Cancer Hospital of Zhengzhou University |
| Department: | Medical laboratory |
| Laboratory: | Department of Laboratory Medicine |
| Last Name: | Wang |
| First Name: | Hao |
| Address: | 127 Dongming Road, Jinshui District, Zhengzhou, Henan, China, Zhengzhou, Henan Province, 450003, China |
| Email: | wanghao123@tmu.edu.cn |
| Phone: | +8613642140283 |
Subject:
| Subject ID: | SU004318 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor Value[Group] | Sample source |
|---|---|---|---|
| SA481345 | Blank_4_Pos | Control | Renal cancer cells (RCC4) |
| SA481346 | Blank_1_Pos | Control | Renal cancer cells (RCC4) |
| SA481347 | Blank_5_Pos | Control | Renal cancer cells (RCC4) |
| SA481348 | Blank_5_Neg | Control | Renal cancer cells (RCC4) |
| SA481349 | Blank_1_Neg | Control | Renal cancer cells (RCC4) |
| SA481350 | Blank_4_Neg | Control | Renal cancer cells (RCC4) |
| SA481351 | Blank_3_Neg | Control | Renal cancer cells (RCC4) |
| SA481352 | Blank_2_Pos | Control | Renal cancer cells (RCC4) |
| SA481353 | Blank_2_Neg | Control | Renal cancer cells (RCC4) |
| SA481354 | Blank_3_Pos | Control | Renal cancer cells (RCC4) |
| SA481355 | QC_3_Pos | QC | Renal cancer cells (RCC4) |
| SA481356 | QC_3_Neg | QC | Renal cancer cells (RCC4) |
| SA481357 | QC_2_Pos | QC | Renal cancer cells (RCC4) |
| SA481358 | QC_2_Neg | QC | Renal cancer cells (RCC4) |
| SA481359 | QC_1_Pos | QC | Renal cancer cells (RCC4) |
| SA481360 | QC_1_Neg | QC | Renal cancer cells (RCC4) |
| SA481361 | Target_5_Pos | shSTBD1 | Renal cancer cells (RCC4) |
| SA481362 | Target_4_Neg | shSTBD1 | Renal cancer cells (RCC4) |
| SA481363 | Target_5_Neg | shSTBD1 | Renal cancer cells (RCC4) |
| SA481364 | Target_4_Pos | shSTBD1 | Renal cancer cells (RCC4) |
| SA481365 | Target_3_Pos | shSTBD1 | Renal cancer cells (RCC4) |
| SA481366 | Target_3_Neg | shSTBD1 | Renal cancer cells (RCC4) |
| SA481367 | Target_2_Neg | shSTBD1 | Renal cancer cells (RCC4) |
| SA481368 | Target_1_Pos | shSTBD1 | Renal cancer cells (RCC4) |
| SA481369 | Target_1_Neg | shSTBD1 | Renal cancer cells (RCC4) |
| SA481370 | Target_2_Pos | shSTBD1 | Renal cancer cells (RCC4) |
| Showing results 1 to 26 of 26 |
Collection:
| Collection ID: | CO004311 |
| Collection Summary: | Stable STBD1-knockdown (shSTBD1) and control (shNC) renal cancer cells (RCC4) were cultured under standard conditions (DMEM supplemented with 10% fetal bovine serum, 5% CO₂, 37°C). At 70–80% confluence, cells were harvested, washed twice with ice-cold PBS to remove medium components, pelleted by centrifugation, and immediately snap-frozen in liquid nitrogen. Cell pellets were aliquoted into cryovials to avoid repeated freeze–thaw cycles and stored at −80°C until metabolite extraction. |
| Sample Type: | Renal cancer cells (RCC4) |
Treatment:
| Treatment ID: | TR004327 |
| Treatment Summary: | Control group (Blank) cells were transfected with control shRNA, while the experimental group (Target) cells were transfected with STBD1-specific shRNA to achieve gene knockdown. |
Sample Preparation:
| Sampleprep ID: | SP004324 |
| Sampleprep Summary: | RCC4 cells from control (shNC) and STBD1-knockdown (shSTBD1) groups were cultured in 10 cm dishes. After washing three times with PBS, cells were scraped and pelleted by centrifugation at 500 g for 5 min. Lipids were extracted from the pellets using a methanol–chloroform method, followed by phase separation. The organic phase was collected, dried under nitrogen, and reconstituted in 50% isopropanol/acetonitrile for LC–MS analysis. |
Combined analysis:
| Analysis ID | AN006917 | AN006918 |
|---|---|---|
| Chromatography ID | CH005254 | CH005254 |
| MS ID | MS006614 | MS006615 |
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity |
| Column | Waters ACQUITY UPLC CSH C18 (150 x 2.1 mm, 1.7 μm) | Waters ACQUITY UPLC CSH C18 (150 x 2.1 mm, 1.7 μm) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | ng/10^7 cells | ng/10^7 cells |
Chromatography:
| Chromatography ID: | CH005254 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC CSH C18 (150 x 2.1 mm, 1.7 μm) |
| Column Temperature: | 45°C |
| Flow Gradient: | 30% of B and was held for 2 min, which was then increased to 100% of B over 23 min, the gradient was returned to 30% B over 1 min, and was finally equilibrated for 9 min. |
| Flow Rate: | 300 μL/min |
| Solvent A: | 60% Acetonitrile/40% Water |
| Solvent B: | 10% Acetonitrile/90% Isopropanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS006614 |
| Analysis ID: | AN006917 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data-dependent acquisition methods were used for MS/MS analyses of lipidome. 10 MS2 scans were collected after each MS1 full scan. The resolution of MS1 is 70000 at m/z 200 and resolution of MS2 is 17500 at m/z 200. The ESI conditions were set at follows: Heater Temp 300°C, Sheath Gas Flow rate 45 arb, Aux Gas Flow Rate15 arb, Sweep Gas Flow Rate 1arb, spray voltage 3.0KV, Capillary Temp 350°C, S-Lens RF Level 50%, MS1 scan ranges: 200-1800. |
| Ion Mode: | POSITIVE |
| MS ID: | MS006615 |
| Analysis ID: | AN006918 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data-dependent acquisition methods were used for MS/MS analyses of lipidome. 10 MS2 scans were collected after each MS1 full scan. The resolution of MS1 is 70000 at m/z 200 and resolution of MS2 is 17500 at m/z 200. The ESI conditions were set at follows: Heater Temp 300°C, Sheath Gas Flow rate 45 arb, Aux Gas Flow Rate15 arb, Sweep Gas Flow Rate 1arb, spray voltage 3.0KV, Capillary Temp 350°C, S-Lens RF Level 50%, MS1 scan ranges: 200-1800. |
| Ion Mode: | NEGATIVE |
