Summary of Study ST003153
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 PR001959. The data can be accessed directly via it's Project DOI: 10.21228/M8H72Q 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 | ST003153 |
| Study Title | Untargeted metabolomic profile in control and YEATS4 knockdown MCF-7 cells |
| Study Summary | The integration between epigenetic regulation and metabolism is critical to maintain cellular homeostasis. As an epigenetic mark mainly linked to gene activation, histone crotonylation (Kcr) uses the donor of crotonyl-CoA, a metabolite generated primarily from fatty acid oxidation. Whether there is an intrinsic crosstalk between histone Kcr and fatty acid metabolism remains to be explored. We report here that YEATS family protein YEATS4 is a reader of histone Kcr preferentially towards H3K14cr. YEATS4 is amplified and overexpressed in breast cancer cells, mainly in the ER+ subtype. Integrative epigenomic and transcriptomic analyses reveals extensively overlapped chromatin distribution of YEATS4 with H3K14cr, leading to activation of multiple genes involved in fatty-acid trafficking and metabolism, such as CD36, CPT1/2, and ACOX1. Depletion of YEATS4 in breast cancer cells led to compromised fatty acid uptake and -oxidation. Interestingly, YEATS4 is upregulated in ALDH+ breast cancer stem cells, leading to boosted fatty acid metabolism, enhanced self-renewal, and accelerated tumor growth. Clinicalpathological evidence indicates that elevated YEATS4 expression is correlated with poor prognosis and worse overall survival of ER+ breast cancer patients. Together, our study uncovers a feedforward epigenetic-metabolic loop implicated in breast carcinogenesis, supporting the pursuit of YEATS4 as a potential therapeutic target for breast cancer intervention. |
| Institute | Peking University |
| Last Name | Peng |
| First Name | Zijun |
| Address | Xueyuan Road No.38, Beijing, Bejing, 100191, China |
| zj_peng@126.com | |
| Phone | +86 17317790671 |
| Submit Date | 2024-03-31 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-09-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001959 |
| Project DOI: | doi: 10.21228/M8H72Q |
| Project Title: | YEATS4 Links Histone Crotonylation to Fatty-acid Uptake/Metabolism and Breast Cancer Stemness |
| Project Summary: | The integration between epigenetic regulation and metabolism is critical to maintaining cellular homeostasis. As an epigenetic mark mainly linked to gene activation, histone crotonylation (Kcr) uses the donor of crotonyl-CoA, a metabolite generated primarily from fatty acid oxidation. Whether there is an intrinsic crosstalk between histone Kcr and fatty acid metabolism remains to be explored. We report here that the YEATS family protein YEATS4 is a reader of histone Kcr preferentially towards H3K14cr. YEATS4 is amplified and overexpressed in breast cancer cells, mainly in the ER+ subtype. Integrative epigenomic and transcriptomic analyses reveal extensively overlapped chromatin distribution of YEATS4 with H3K14cr, leading to activation of multiple genes involved in fatty acid trafficking and metabolism, such as CD36, CPT1/2, and ACOX1. Depletion of YEATS4 in breast cancer cells led to compromised fatty acid uptake and β-oxidation. Interestingly, YEATS4 is upregulated in ALDH+ breast cancer stem cells, leading to boosted fatty acid metabolism, enhanced self-renewal, and accelerated tumor growth. Clinical pathological evidence indicates that elevated YEATS4 expression is correlated with a poor prognosis and worse overall survival in ER+ breast cancer patients. Together, our study uncovers a feedforward epigenetic-metabolic loop implicated in breast carcinogenesis, supporting the pursuit of YEATS4 as a potential therapeutic target for breast cancer intervention. |
| Institute: | Peking University |
| Last Name: | Peng |
| First Name: | Zijun |
| Address: | Xueyuan Road No.38, Beijing, Bejing, 100191, China |
| Email: | zj_peng@126.com |
| Phone: | +8617317790671 |
Subject:
| Subject ID: | SU003270 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA341011 | QC_3 | quality control |
| SA341012 | QC_1 | quality control |
| SA341013 | QC_2 | quality control |
| SA340999 | shNC_6 | Wild-type |
| SA341000 | shNC_1 | Wild-type |
| SA341001 | shNC_5 | Wild-type |
| SA341002 | shNC_4 | Wild-type |
| SA341003 | shNC_3 | Wild-type |
| SA341004 | shNC_2 | Wild-type |
| SA341005 | shYEATS4_1 | YEATS4 knockdown |
| SA341006 | shYEATS4_2 | YEATS5 knockdown |
| SA341007 | shYEATS4_3 | YEATS6 knockdown |
| SA341008 | shYEATS4_4 | YEATS7 knockdown |
| SA341009 | shYEATS4_5 | YEATS8 knockdown |
| SA341010 | shYEATS4_6 | YEATS9 knockdown |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO003263 |
| Collection Summary: | Cells were counted, washed with cold PBS and then flash-frozen in liguid N2. Then for each sample, 1000 μL extract solution (acetonitrile: methanol: water = 2: 2: 1) containing the isotopically-labeled internal standard mixture was added. After 30 seconds of vortex, the samples were homogenized at 35 Hz for 4 min and sonicated for 5 min in an ice-water bath. The homogenization and sonication cycle was repeated 2 times. The samples were sonicated for 5 min in an ice-water bath incubated at -40 ℃ for 1 h and centrifuged at 12000 rpm for 15 min at 4°C. 800 μL of supernatant was transferred to a fresh tube and dried in a vacuum concentrator at 37 ℃. Then, the dried samples were reconstituted in 200 μL of 50% acetonitrile by sonication on ice for 10 min. The constitution was then centrifuged at 13000 rpm for 15 min at 4 ℃, and 75 μL of supernatant was transferred to a fresh glass vial for LC/MS analysis. The quality control (QC) sample was prepared by mixing an equal aliquot of the supernatants from all of the samples. |
| Sample Type: | Breast cancer cells |
Treatment:
| Treatment ID: | TR003279 |
| Treatment Summary: | no treatment |
Sample Preparation:
| Sampleprep ID: | SP003277 |
| Sampleprep Summary: | For each sample, 1000 μL extract solution (acetonitrile: methanol: water = 2: 2: 1) containing the isotopically-labeled internal standard mixture was added. After 30 seconds of vortex, the samples were homogenized at 35 Hz for 4 min and sonicated for 5 min in an ice-water bath. The homogenization and sonication cycle was repeated 2 times. The samples were sonicated for 5 min in an ice-water bath incubated at -40 ℃ for 1 h and centrifuged at 12000 rpm for 15 min at 4 ℃. 800 μL of supernatant was transferred to a fresh tube and dried in a vacuum concentrator at 37 ℃. Then, the dried samples were reconstituted in 200 μL of 50% acetonitrile by sonication on ice for 10 min. The constitution was then centrifuged at 13000 rpm for 15 min at 4 ℃, and 75 μL of supernatant was transferred to a fresh glass vial for LC/MS analysis. The quality control (QC) sample was prepared by mixing an equal aliquot of the supernatants from all of the samples. |
Chromatography:
| Chromatography ID: | CH003913 |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um) |
| Column Temperature: | 25 |
| Flow Gradient: | 0-0.5 min, 95%B; 0.5-7.0 min, 95%-65% B; 7.0-8.0 min, 65%-40% B; 8.0-9.0 min, 40% B; 9.0-9.1 min, 40%-95% B; 9.1-12.0 min, 95% B |
| Flow Rate: | 2 μl/min |
| Solvent A: | 100% water; 25 mmol/L ammonium acetate; 25 mmol/L ammonium hydroxide (pH = 9.75） |
| Solvent B: | 100% acetonitrile;25 mmol/L ammonium acetate; 25 mmol/L ammonia hydroxide |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN005173 |
| Analysis Type: | MS |
| Chromatography ID: | CH003913 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Seconds |
| Results File: | ST003153_AN005173_Results.txt |
| Units: | Peak area |
