Summary of Study ST003193
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 PR001989. The data can be accessed directly via it's Project DOI: 10.21228/M8MT61 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 | ST003193 |
| Study Title | Metabolomics study on frozen tissue derived from the tumor and adjacent non-malignant liver tissue (NML) of patient afflicted with fibrolamellar carinoma (FLC) |
| Study Type | LC-MS quantitative analysis |
| Study Summary | Fibrolamellar carcinoma (FLC) is a rare, early-onset liver cancer. The five-year survival rate is low, and there is a critical need for new therapeutics. The primary driver in FLC is the fusion oncoprotein, DNAJ-PKAc, which remains challenging to target therapeutically. It is critical, therefore, to expand understanding of the FLC molecular landscape to identify druggable pathways/targets. To date, only one study has attempted to characterize the FLC proteome and metabolome, but with modest sample size (proteomics—n = 16 patient samples; metabolomics—n = 10 patient samples) and protein detection (n = 4620 proteins). We have performed the most comprehensive characterization of FLC in both proteomics (n = 23 patient samples; n = 8485 proteins) and metabolomics (n = 26 patient samples; n = 135 metabolites). Targeted metabolomics on central carbon metabolism (polar metabolite extraction) was performed followed by extensive quantitative and qualitative assessment of its relationship with the proteome of FLC to gain insight on how the metabolic network is constructed in this cancer. Frozen patient tissue was derived from both primary and metastatic tumors as well as adjacent non-malignant liver tissue (NML). Primary and metastatic tumors served as our FLC cohort while NMLs served as our control cohort. |
| Institute | Cornell University |
| Department | Biomedical Sciences |
| Laboratory | Praveen Sethupathy |
| Last Name | Long Jr. |
| First Name | Donald |
| Address | 618 Tower Road, Ithaca, New York, 14853, USA |
| dl964@cornell.edu | |
| Phone | 4355312013 |
| Submit Date | 2024-05-06 |
| Num Groups | 2 |
| Total Subjects | 26 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-05-29 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001989 |
| Project DOI: | doi: 10.21228/M8MT61 |
| Project Title: | Proteo-metabolomics and patient tumor slice functional studies point to the centrality of amino acids for re-wired mitochondria in fibrolamellar carcinoma |
| Project Type: | LC-MS quantitative analysis |
| Project Summary: | Fibrolamellar carcinoma (FLC) is a rare, early-onset liver cancer. The five-year survival rate is low, and there is a critical need for new therapeutics. The primary driver in FLC is the fusion oncoprotein, DNAJ-PKAc, which remains challenging to target therapeutically. It is critical, therefore, to expand understanding of the FLC molecular landscape to identify druggable pathways/targets. To date, only one study has attempted to characterize the FLC proteome and metabolome, but with modest sample size (proteomics—n = 16 patient samples; metabolomics—n = 10 patient samples) and protein detection (n = 4620 proteins). We have performed the most comprehensive characterization of FLC in both proteomics (n = 23 patient samples; n = 8485 proteins) and metabolomics (n = 26 patient samples; n = 135 metabolites). Additionally, we have conducted respirometry analyses as well as RNAi- and small molecule inhibitor-mediated loss of function assays in FLC tumors and non-malignant liver tissue from patients. We propose a model of cellular energetics in FLC that centers on amino acids. Our model points to proline anabolism that is very likely mediated by ornithine aminotransferase hyperactivity and ornithine transcarbamylase hypoactivity with serine and glutamine catabolism providing the starting substrate. The metabolic rewiring in FLC proposed by our model, with a particular emphasis on mitochondria, can be exploited for therapeutic vulnerabilities. |
| Institute: | Cornell University |
| Department: | Biomedical Sciences |
| Laboratory: | Praveen Sethupathy |
| Last Name: | Long Jr. |
| First Name: | Donald |
| Address: | 618 Tower Road, Ithaca, New York, 14853, USA |
| Email: | dl964@cornell.edu |
| Phone: | 4355312013 |
| Funding Source: | Fibrolamellar Carcinoma Foundation |
| Contributors: | Guoan Zhang (Weill Cornell) |
Subject:
| Subject ID: | SU003312 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 15-54 |
| Gender: | Male and female |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Cohort | Tissue Classification (via Physician) |
|---|---|---|---|---|
| SA347909 | FLC06_DZIS | Liver | FLC | Met |
| SA347910 | FLC15_AWTJ | Liver | FLC | Met |
| SA347911 | FLC11_WHAY | Liver | FLC | Pri |
| SA347912 | FLC07_LFOC | Liver | FLC | Pri |
| SA347913 | FCF58_T | Liver | FLC | Pri |
| SA347914 | FCF82_T | Liver | FLC | Pri |
| SA347915 | FCF56_T | Liver | FLC | Pri |
| SA347916 | FCF83_T | Liver | FLC | Pri |
| SA347917 | FLC24_DJZW | Liver | FLC | Pri |
| SA347918 | FLC26_YJEE | Liver | FLC | Pri |
| SA347919 | FLC18_MKZC | Liver | FLC | Pri |
| SA347920 | FCF83_N | Liver | NML | NML |
| SA347921 | FCF82_N | Liver | NML | NML |
| SA347922 | FCF84_N | Liver | NML | NML |
| SA347923 | FLC34_PMVV | Liver | NML | NML |
| SA347924 | FLC27_BWSX | Liver | NML | NML |
| SA347925 | FLC26_ICBQ | Liver | NML | NML |
| SA347926 | FLC33_NYTS | Lung | FLC | Met |
| SA347927 | FLC29_QLXW | Lung | FLC | Met |
| SA347928 | FLC20_ZDNV | Lymph Node | FLC | Met |
| SA347929 | FLC25_UYHR | Lymph Node | FLC | Met |
| SA347930 | FLC28_RKXK | Lymph Node | FLC | Met |
| SA347931 | FLC27_XDGP | Lymph Node | FLC | Met |
| SA347932 | FLC31_OTOK | Lymph Node | FLC | Met |
| SA347933 | FLC30_KPKS | Peritoneal | FLC | Met |
| SA347934 | FLC14_EQPR | Spinal | FLC | Met |
| Showing results 1 to 26 of 26 |
Collection:
| Collection ID: | CO003305 |
| Collection Summary: | Informed consent was obtained from all individuals and studies were performed in accordance with the protection of human subjects guidelines (U.S. Common Rule). FLC tumors (metastatic and primary) and NML samples were obtained from various biobanks around the US in accordance with IRB protocols 1802007780, 1811008421 (Cornell University, Ithaca, NY) and 33970/1 (FCF). Both male and female subjects were included, and all samples were deidentified. Frozen samples were stored at -80 degrees C when received. |
| Sample Type: | Liver; Lymph node; Lung; Spinal; Peritoneal |
Treatment:
| Treatment ID: | TR003321 |
| Treatment Summary: | No experimental treatments were performed on the patients or to their donated tissues. |
Sample Preparation:
| Sampleprep ID: | SP003319 |
| Sampleprep Summary: | Metabolites were extracted from cells (derived from tissue homogenate of samples) using pre-chilled 80% methanol (-80 °C). The extract was dried completely with a Speedvac and redissolved in HPLC grade water prior to application on hydrophilic interaction chromatography LC-MS. |
Combined analysis:
| Analysis ID | AN005241 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | normalized-BatchCorrected-Imputed-log2transformed Intensity |
Chromatography:
| Chromatography ID: | CH003968 |
| Chromatography Summary: | Metabolites were measured on a Q Exactive Orbitrap mass spectrometer (Thermo Scientific), which was coupled to a Vanquish UPLC system (Thermo Scientific) via an Ion Max ion source with a HESI II probe (Thermo Scientific). A Sequant ZIC-pHILIC column (2.1 mm i.d. × 150 mm, particle size of 5 µm, Millipore Sigma) was used for separation of metabolites. A 2.1 × 20 mm guard column with the same packing material was used for protection of the analytical column. Flow rate was set at 150 μL/min. Buffers consisted of 100% acetonitrile for mobile phase A, and 0.1% NH 4 OH/20 mM CH 3 COONH 4 in water for mobile phase B. The chromatographic gradient ran from 85% to 30% A in 20 min followed by a wash with 30% A and re-equilibration at 85% A. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | SeQuant ZIC- pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | - |
| Flow Gradient: | 85% to 30% A in 20 minutes |
| Flow Rate: | 150uL/min |
| Solvent A: | 100% acetonitrile |
| Solvent B: | 100% water; 0.1% ammonium hydroxide; 20mM ammonium acetate |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004974 |
| Analysis ID: | AN005241 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The Q Exactive was operated in full scan, polarity-switching mode with the following parameters: the spray voltage 3.0 kV, the heated capillary temperature 300 °C, the HESI probe temperature 350 °C, the sheath gas flow 40 units, the auxiliary gas flow 15 units. MS data acquisition was performed in the m/z range of 70–1,000, with 70,000 resolution (at 200 m/z). The AGC target was 1e6 and the maximum injection time was 250 milliseconds. The MS data was processed using Xcalibur 4.1 (Thermo Scientific) to obtain the metabolite signal intensity for relative quantitation. Metabolites were identified using an in-house library established using chemical standards. Identification required exact mass (within 5ppm) and standard retention times. |
| Ion Mode: | UNSPECIFIED |
