Summary of Study ST002536

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 PR001632. The data can be accessed directly via it's Project DOI: 10.21228/M8RB05 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	ST002536
Study Title	Effectors enabling adaptation to mitochondrial complex I loss in Hürthle cell carcinoma
Study Type	comparison of tumor versus normal tissue
Study Summary	With the goal of performing RNA-seq and metabolomic profiling, a cohort of fresh frozen oncocytic (Hürthle cell) thyroid carcinoma (HCC) samples was established with confirmation of mtDNA mutation status and chromosomal copy number. This cohort contained 24 oncocytic (Hürthle cell) tumors with 18 cases having matched normal thyroid tissue. Tumor samples included 21 primary tumors comprised of 19 HCC (8 widely invasive, 11 minimally invasive) and 2 oncocytic (Hürthle cell) adenomas as well as 2 locoregional recurrences (LR) and 1 distant metastasis (DM). HCC samples were collected and stored as part of the Mass General Brigham Institutional Review Board (protocol number 2008P001466). Frozen tissue was accessed to create the cohort used in the study.
Institute	Broad Institute of MIT and Harvard
Department	Metabolomics Platform
Last Name	Clish
First Name	Clary
Address	415 Main Street, Cambridge, MA, 02142, USA
Email	clary@broadinstitute.org
Phone	617-714-7654
Submit Date	2023-03-30
Num Groups	2
Total Subjects	tumors from 24 subjects and matched normal tissue from a subset of 18 subjects
Num Males	N/A
Num Females	N/A
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2023-04-17
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001632
Project DOI:	doi: 10.21228/M8RB05
Project Title:	Effectors enabling adaptation to mitochondrial complex I loss in Hürthle cell carcinoma
Project Summary:	Oncocytic (Hürthle cell) carcinoma of the thyroid (HCC) is genetically characterized by complex I mitochondrial DNA mutations and widespread chromosomal losses. In this project, RNA-seq and metabolomics were used to identify candidate molecular effectors activated by these genetic drivers.
Institute:	Broad Institute of MIT and Harvard
Department:	Metabolomics Platform
Last Name:	Clish
First Name:	Clary
Address:	415 Main Street, Cambridge, MA, 02142, USA
Email:	clary@broadinstitute.org
Phone:	617-714-7654
Funding Source:	Inflammatory Bowel Disease Grant DK043351, Boston Area Diabetes and Endocrinology Research Center (BADERC) Award DK057521, the Bertarelli Rare Cancers Fund, the Elizabeth and Michael Ruane family, 2T32DK007028-46, NIH K00CA212468, NIH K12CA087723, and the Howard Hughes Medical Institute
Publications:	submitted
Contributors:	Raj K. Gopal, Venkata R. Vantaku, Apekshya Panda, Bryn Reimer, Sneha Rath, Tsz-Leung To, Adam S. Fisch, Murat Cetinbas, Maia Livneh, Michael J. Calcaterra, Benjamin J. Gigliotti, Kerry Pierce, Clary B. Clish, Dora Dias-Santagata, Peter M. Sadow, Lori J. Wirth, Gilbert H. Daniels, Ruslan I. Sadreyev, Sarah E. Calvo, Sareh Parangi, Vamsi K. Mootha

Subject:

Subject ID:	SU002636
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Tissue type
SA254994	HC011_N	normal
SA254995	HC010_N	normal
SA254996	HC008_N	normal
SA254997	HC012_N	normal
SA254998	HC009_N	normal
SA254999	HC015_N	normal
SA255000	HC022_N	normal
SA255001	HC021_N	normal
SA255002	HC016_N	normal
SA255003	HC007_N	normal
SA255004	HC014_N	normal
SA255005	HC013_N	normal
SA255006	HC004_N	normal
SA255007	HC002_N	normal
SA255008	HC001_N	normal
SA255009	HC005_N	normal
SA255010	HC003_N	normal
SA255011	HC006_N	normal
SA255012	PREFA3	pooled homogenate QC
SA255013	PREFA2	pooled homogenate QC
SA255014	PREFB1	pooled homogenate QC
SA255015	PREFA1	pooled homogenate QC
SA255016	PREFB2	pooled homogenate QC
SA255017	PREFB3	pooled homogenate QC
SA255018	HC021_T	tumor
SA255019	HC020_T	tumor
SA255020	HC008_T	tumor
SA255021	HC002_T	tumor
SA255022	HC023_T	tumor
SA255023	HC019_T	tumor
SA255024	HC006_T	tumor
SA255025	HC024_T	tumor
SA255026	HC022_T	tumor
SA255027	HC018_T	tumor
SA255028	HC012_T	tumor
SA255029	HC001_T	tumor
SA255030	HC004_T	tumor
SA255031	HC011_T	tumor
SA255032	HC010_T	tumor
SA255033	HC009_T	tumor
SA255034	HC013_T	tumor
SA255035	HC014_T	tumor
SA255036	HC016_T	tumor
SA255037	HC017_T	tumor
SA255038	HC007_T	tumor
SA255039	HC015_T	tumor
SA255040	HC003_T	tumor
SA255041	HC005_T	tumor

Showing results 1 to 48 of 48

Showing results 1 to 48 of 48

Collection:

Collection ID:	CO002629
Collection Summary:	HCC and normal samples were collected surgically and stored as part of the Mass General Brigham Institutional Review Board (protocol number 2008P001466). Frozen tissue was accessed to create the cohort used in this study.
Collection Protocol ID:	MGB IRB 2008P001466
Sample Type:	Oncocytic (Hürthle cell) thyroid carcinoma (HCC) tumors and normal thyroid tissue
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002648
Treatment Summary:	no treatment was used in the study

Sample Preparation:

Sampleprep ID:	SP002642
Sampleprep Summary:	Frozen tissues were weighed and homogenized in 4 volumes of water (4 µL of water/mg tissue, 4°C) using a bead beater (TissueLyser II, QIAGEN; Germantown, MD). Tissue homogenates were aliquoted to prepare extracts for four different LC-MS methods: HILIC-pos: 10 µL of each tissue homogenate was extracted using 90 µL of acetonitrile/methanol/formic acid (74.9:24.9:0.2 v/v/v) containing stable isotope-labeled internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. HILIC-neg: 30 µL of each tissue homogenate was extracted using 120 µL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. C8-pos: 10 µL of each tissue homogenate was extracted using 190 µL of isopropanol containing 1,2-didodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids; Alabaster, AL). The samples were centrifuged (10 min, 9,000 x g, ambient temperature), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. C18-neg: 30 µL of each tissue homogenate was extracted using 90 µL of methanol containing 15R-15-methyl PGA2, 15S-15-methyl PGD2, 15S-15-methyl PGE1, 15S-15-methyl PGE2, and 15R-15-methyl PGF2alpha as an internal standards (Cayman Chemical Co.; Ann Arbor, MI). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts.

Sampleprep ID:

SP002642

Sampleprep Summary:

Frozen tissues were weighed and homogenized in 4 volumes of water (4 µL of water/mg tissue, 4°C) using a bead beater (TissueLyser II, QIAGEN; Germantown, MD). Tissue homogenates were aliquoted to prepare extracts for four different LC-MS methods: HILIC-pos: 10 µL of each tissue homogenate was extracted using 90 µL of acetonitrile/methanol/formic acid (74.9:24.9:0.2 v/v/v) containing stable isotope-labeled internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. HILIC-neg: 30 µL of each tissue homogenate was extracted using 120 µL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. C8-pos: 10 µL of each tissue homogenate was extracted using 190 µL of isopropanol containing 1,2-didodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids; Alabaster, AL). The samples were centrifuged (10 min, 9,000 x g, ambient temperature), and the supernatants were transferred to autosampler vials containing deactivated glass inserts. C18-neg: 30 µL of each tissue homogenate was extracted using 90 µL of methanol containing 15R-15-methyl PGA2, 15S-15-methyl PGD2, 15S-15-methyl PGE1, 15S-15-methyl PGE2, and 15R-15-methyl PGF2alpha as an internal standards (Cayman Chemical Co.; Ann Arbor, MI). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were transferred to autosampler vials containing deactivated glass inserts.

Combined analysis:

Analysis ID	AN004171	AN004172	AN004173	AN004174
Analysis type	MS	MS	MS	MS
Chromatography type	HILIC	HILIC	Reversed phase	Reversed phase
Chromatography system	Shimadzu Nexera X2	Shimadzu Nexera X2	Shimadzu Nexera X2	Shimadzu Nexera X2
Column	Waters Atlantis HILIC (150 x 2.1mm,3um,100Å	Phenomenex Luna NH2 (150 x 2 mm,5um;100Å)	Waters ACQUITY UPLC BEH C8 Column (2.1 mm X 100 mm,1.7 µm,130Å)	Waters ACQUITY UPLC BEH C18 Column (2.1 mm X 150 mm,1.7 µm,130Å)
MS Type	ESI	ESI	ESI	ESI
MS instrument type	Orbitrap	Orbitrap	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Plus Orbitrap	Thermo Exactive Plus Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE	POSITIVE	NEGATIVE
Units	peak area	peak area	peak area	peak area

Chromatography:

Chromatography ID:	CH003089
Chromatography Summary:	HILIC-pos: Hydrophilic interaction liquid chromatography (HILIC) analysis of water soluble metabolites in the positive ionization mode
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters Atlantis HILIC (150 x 2.1mm,3um,100Å
Column Temperature:	30
Flow Gradient:	0-0.5 min, isocratic 95% B; 0.5-10.5 min, gradient to 40% B; 10.5-15 min, isocratic 40% B; 15-17 min, gradient to 95% B
Flow Rate:	250 uL/min
Solvent A:	100% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	HILIC

Chromatography ID:	CH003090
Chromatography Summary:	HILIC-neg: Hydrophilic interaction liquid chromatography (HILIC) analysis of water soluble metabolites in the negative ionization mode
Instrument Name:	Shimadzu Nexera X2
Column Name:	Phenomenex Luna NH2 (150 x 2 mm,5um;100Å)
Column Temperature:	30
Flow Gradient:	0-10 min, gradient from 90% B to 0% B; 10-12 min, isocratic 0% B; 12-14 min, gradient from 0% B to 90% B
Flow Rate:	400 uL/min
Solvent A:	100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide
Solvent B:	75% methanol/25% acetonitrile; 10 mM ammonium hydroxide
Chromatography Type:	HILIC

Chromatography ID:	CH003091
Chromatography Summary:	C8-pos: Reversed-phase C8 chromatography analysis of polar and nonpolar lipids in the positive ionization mode
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters ACQUITY UPLC BEH C8 Column (2.1 mm X 100 mm,1.7 µm,130Å)
Column Temperature:	40
Flow Gradient:	0-1 min, isocratic 20% B; 1-3 min, gradient to 80% B; 3-10 min, gradient to 100% B; 10-13 min, isocratic 100% B; 13-14 min, gradient to 20% B
Flow Rate:	450 uL/min
Solvent A:	95% water/5% methanol; 0.1% formic acid; 10 mM ammonium acetate
Solvent B:	100% methanol; 0.1% formic acid
Chromatography Type:	Reversed phase

Chromatography ID:	CH003092
Chromatography Summary:	C18-neg: Reversed-phase C18 chromatography analysis of compounds of intermediate polarity in the negative ionization mode
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters ACQUITY UPLC BEH C18 Column (2.1 mm X 150 mm,1.7 µm,130Å)
Column Temperature:	45
Flow Gradient:	0-3 min, isocratic 20% B; 3-15 min, gradient to 100% B; 15-18 min, isocratic 100% B; 18-19 min, gradient to 20% B
Flow Rate:	450 uL/min
Solvent A:	100% water; 0.01% formic acid
Solvent B:	100% acetonitrile; 0.01% acetic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003918
Analysis ID:	AN004171
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS analyses were carried out using electrospray ionization in the positive ion mode using full scan analysis over 70-800 m/z at 70,000 resolution and 3 Hz data acquisition rate. Other MS settings were: sheath gas 40, sweep gas 2, spray voltage 3.5 kV, capillary temperature 350°C, S-lens RF 40, heater temperature 300°C, microscans 1, automatic gain control target 1e6, and maximum ion time 250 ms. Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards.
Ion Mode:	POSITIVE

MS ID:	MS003919
Analysis ID:	AN004172
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS analyses were carried out using electrospray ionization in the negative ion mode using full scan analysis over m/z 70-750 at 70,000 resolution and 3 Hz data acquisition rate. Additional MS settings were: ion spray voltage, -3.0 kV; capillary temperature, 350°C; probe heater temperature, 325 °C; sheath gas, 55; auxiliary gas, 10; and S-lens RF level 50. Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards.
Ion Mode:	NEGATIVE

MS ID:	MS003920
Analysis ID:	AN004173
Instrument Name:	Thermo Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS analyses were carried out using electrospray ionization in the positive ion mode using full scan analysis over 200–1100 m/z at 70,000 resolution and 3 Hz data acquisition rate. Other MS settings were: sheath gas 50, in source CID 5 eV, sweep gas 5, spray voltage 3 kV, capillary temperature 300°C, S-lens RF 60, heater temperature 300°C, microscans 1, automatic gain control target 1e6, and maximum ion time 100 ms. Representative standards from each lipid class were used to identify lipids based on RT and m/z patterns, and characteristic product ion spectra. Lipid identities were denoted by total acyl carbon number and total number of double bond number.
Ion Mode:	POSITIVE

MS ID:	MS003921
Analysis ID:	AN004174
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	MS analyses were carried out using electrospray ionization in the negative ion mode using full scan analysis over m/z 70-850 at 70,000 resolution and 3 Hz data acquisition rate. Additional MS settings were: ion spray voltage, -3.5 kV; capillary temperature, 320°C; probe heater temperature, 300 °C; sheath gas, 45; auxiliary gas, 10; and S-lens RF level 60. Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards.
Ion Mode:	NEGATIVE