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. Author manuscript; available in PMC: 2022 Sep 16.
Published in final edited form as: Mol Cell. 2021 Jul 20;81(18):3833–3847.e11. doi: 10.1016/j.molcel.2021.06.027

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
DYKDDDDK Tag Antibody Cell Signaling Technology Cat#2368S;
Clone# N/A;
RRID:AB_2217020
Mouse monoclonal ANTI-FLAG M2 antibody Sigma-Aldrich Cat# F3165;
Clone# M2;
RRID: AB_259529
Phospho-Tyrosine Mouse mAb (P-Tyr-100) antibody Cell Signaling Technology Cat# 9411S;
Clone# N/A;
RRID:AB_331228
IDH2 Santa Cruz Biotechnology Cat# sc-374476;
Clone# B-6;
RRID: AB_10986415
IDH2 Cell Signaling Technology Cat# 56439S;
Clone# D8E3B;
RRID: AB_2799511
ac-IDH2K413 GeneTel Laboratories Cat# AC0004;
Clone# N/A;
RRID: N/A
ACAT1 Novus Biologicals Cat#NB400–141;
Clone# N/A;
RRID: AB_10001588
p-ACAT1 Y407 Cell Signaling Technology(Fan et al., 2016) Cat# N/A;
Clone# N/A;
RRID: N/A
p-IDH2 Y107 Shanghai HuiOu Biotechnology Com.LTD Cat# N/A;
Clone# N/A;
RRID: N/A
p-SIRT3 Y226 Shanghai HuiOu Biotechnology Com.LTD Cat# N/A;
Clone# N/A;
RRID: N/A
ACAT1 Antibody Cell Signaling Technology Cat# 44276;
Clone# N/A;
RRID: AB_2799262
p-IDH1 Y42 SHANGHAI GENOMICS,INC.(Chen et al., 2019) Cat# N/A;
Clone# N/A;
RRID: N/A
p-IDH1 Y391 SHANGHAI GENOMICS,INC.(Chen et al., 2019) Cat# N/A;
Clone# N/A;
RRID: N/A
Human Isocitrate Dehydrogenase1/IDH1 Antibody R&D SYSTEMS Cat# MAB7049;
Clone# 843219;
RRID: AB_2811299
Acetylated-Lysine Antibody Cell Signaling Technology Cat# 9441;
Clone# N/A;
RRID: AB_331805
ACAT2 (E1L8V) Rabbit mAb Cell Signaling Technology Cat# 13294;
Clone# E1L8V;
RRID: AB_2798172
ChIPAb+ Trimethyl-Histone H3 (Lys4) antibody Millipore Cat# 17–614;
Clone# N/A;
RRID: AB_1587135
Di-Methyl-Histone H3 (Lys9) Antibody Cell Signaling Technology Cat# 9753S;
Clone# N/A;
RRID: AB_659848
Rabbit Anti-Histone H3, trimethyl (Lys9) ChIP Grade Polyclonal Antibody, Unconjugated Abcam Cat# ab8898;
Clone# N/A;
RRID: AB_306848
Histone H3 (D1H2) XP Rabbit mAb antibody Cell Signaling Technology Cat# 4499S;
Clone# N/A;
RRID: AB_10544537
PDC-E2 (H-160) antibody (DLAT) Santa Cruz Biotechnology Cat#sc-32925;
Clone# H-160;
RRID:AB_2091782
SirT3 (C73E3) Rabbit mAb Cell Signaling Technology Cat#2627S;
Clone# N/A;
RRID: AB_2188622
SIRT4 Abcam Cat#ab90485;
Clone# N/A;
RRID: AB_2286004
APC anti-human CD45 Antibody Biolegend Cat# 368512
Clone# Clone 2D1;
RRID: AB_2566372
PE anti-mouse CD45.2 Antibody Biolegend Cat# 109808
Clone# Clone 104;
RRID: AB_313445
SIRT5 Abcam Cat# ab13697
Clone# N/A;
RRID: AB_300574
5-Hydroxymethylcytosine (5-hmC) antibody (pAb) ACTIVE MOTIF Cat# 39069
Clone# N/A;
RRID: N/A
Mouse monoclonal Anti-beta-Actin antibody Sigma-Aldrich Cat# A1978;
Clone# AC-15;
RRID: AB_476692
Goat anti-Mouse IgG (H+L) Secondary Antibody, HRP Thermo Fisher Scientific Cat# 31430;
Clone# N/A;
RRID: AB_228307
Goat anti-Rabbit IgG (H+L) Secondary Antibody, HRP Thermo Fisher Scientific Cat# 31460;
Clone# N/A;
RRID: AB_ 228341
Bacterial and Virus Strains
BL21(DE3) Chemically Competent Cells Sigma-Aldrich Cat# CMC0014
Biological Samples
PDX (FLT3 ITD|IDH2 R140Q) Dana Farber Cat#DFAM-10360-V1
Patient samples Memorial Sloan-Kettering Cancer Center, # 55653
# 45588
# 87794
Patient samples Emory University # UPN1284
Patient samples Ohio State University # U-18–3562
# U-19–0875
# U-19–0877
Chemicals, Peptides, and Recombinant Proteins
Myelin Basic Protein bovine Sigma-Aldrich Cat# M1891
Coomassie Brilliant Blue R-250 Staining Solution Bio-rad Cat# 1610436
DL-Isocitric acid trisodium salt hydrate Sigma-Aldrich Cat# I1252
CAS: 1637–73-6
β-Nicotinamide adenine dinucleotide phosphate hydrate Sigma-Aldrich Cat# N5755
CAS: 53–59-8
β-Nicotinamide adenine dinucleotide 2′-phosphate reduced tetrasodium salt hydrate Sigma-Aldrich Cat# N1630
CAS: 2646–71-1
α-Ketoglutaric acid sodium salt Sigma-Aldrich Cat# K2010
CAS: 22202–68-2
Diaphorase from Clostridium kluyveri Sigma-Aldrich Cat# D5540
CAS: 9001–18-7
Resazurin sodium salt Sigma-Aldrich Cat# R7017
CAS: 62758–13-8
Ketoglutaric Acid, Sodium Salt, α-[1-14C]-, 50µCi (1.85MBq) PerkinElmer Cat# NEC597050UC
Trichostatin A Sigma-Aldrich Cat# T1952
Blue Sepharose CL-6B Amersham Biosciences Cat# 17–0830-01
Nicotinamide Sigma-Aldrich Cat# N0636
TFMB-R-2-HG Cayman Cat# 20461
CAS: 1445700–01-5
1-(Methoxymethyl)-3-(trifluoromethyl)benzene Combi-Blocks Cat# OT-0769–1g
CAS: 380633–51-2
Arecoline hydrobromide Sigma-Aldrich Cat# 10980
CAS: 300–08-3
Quizartinib (AC220) Selleckchem Cat# S1526
CAS: 950769–58-1
acetyl CoA Sigma-Aldrich Cat# S7008
CAS: 102029–73-2
Recombinant IDH2 (R140Q) proteins ACTIVE MOTIF Cat# 31617
FLT3 Recombinant Human Protein Thermo Fisher Cat# PV3182
FLT3 [ITD] Recombinant Human Protein Thermo Fisher Cat# PV6190
Recombinant Human GM-CSF Protein, CF R&D SYSTEMS 215GM050
Adenosine 5′-triphosphate (ATP) disodium salt hydrate Sigma-Aldrich Cat# A7699
CAS: 34369–07-8
Hygromycin B Gibco Cat# 10687010
CAS: 31282–04-9
Puromycin dihydrochloride from Streptomyces alboniger Sigma-Aldrich Cat# P8833
CAS: 58–58-2
ANTI-FLAG® M2 Affinity Gel Sigma-Aldrich Cat# A2220
FLAG® Peptide Sigma-Aldrich Cat# F3290
Protein G Sepharose® 4 Fast Flow Sigma-Aldrich Cat# GE17–0618-01
Critical Commercial Assays
TransIT®-LT1 Transfection Reagent Mirus Cat# MIR 2305
Wizard™ Genomic DNA Purification Kits Promega Cat# A1125
Deposited Data
RNA-seq Data This study GEO: GSE173531
Original western blot images have been deposited at Mendeley and are publicly available as of the date of publication: This study https://data.mendeley.com/datasets/wrt34nw5z9/draft?a=0c0cc371-dfd3–441d-a8f8-c6577c8e4caf
Experimental Models: Cell Lines
Human: HEK293T cells ATCC Cat# CRL-3216;
RRID: CVCL_0063
Human:TF-1 cells ATCC Cat# CRL-2003;
RRID:CVCL_0559
Human: EL-1 cells ATCC Cat# CRL-9854;
RRID: N/A
Human: MOLM-14 (Fan et al., 2016) Cat# N/A;
RRID: N/A
Experimental Models: Organisms/Strains
Mouse: NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ The Jackson Laboratory Stock# 005557
RRID: IMSR_JAX:005557
Oligonucleotides
shRNA targeting IDH2 sequence:
5’-TGCAAGAACTATGACGGAGAT −3’
BROAD Institute/Open Biosystems N/A
Primers: IDH2 K48R mutation, Forward:
5’-aggatcaaggtggcgaggcccgtggtggagatg’
This paper N/A
Primers: IDH2 K48R mutation, Reverse:
5’-catctccaccacgggcctcgccaccttgatcct-3’
This paper N/A
Primers: IDH2 K67R mutation, Forward:
5’-atctggcagttcatcagggagaagctcatcctg-3’
This paper N/A
Primers: IDH2 K67R mutation, Reverse:
5’- caggatgagcttctccctgatgaactgccagat −3’
This paper N/A
Primers: IDH2 K69R mutation, Forward:
5’-cagttcatcaaggagaggctcatcctgccccac −3’
This paper N/A
Primers: IDH2 K69R mutation, Reverse:
5’-gtggggcaggatgagcctctccttgatgaactg-3’
This paper N/A
Primers: IDH2 K80R mutation, Forward:
5’-gtggacatccagctaaggtattttgacctcggg’
This paper N/A
Primers: IDH2 K80R mutation, Reverse:
5’-cccgaggtcaaaataccttagctggatgtccac-3’
This paper N/A
Primers: IDH2 K106R mutation, Forward:
5’-gcactggccacccagaggtacagtgtggctgtc-3’
This paper N/A
Primers: IDH2 K106R mutation, Reverse:
5’-gacagccacactgtacctctgggtggccagtgc-3’
This paper N/A
Primers: IDH2 K127R mutation, Forward:
5’-cgtgtggaagagttcaggctgaagaagatgtgg-3’
This paper N/A
Primers: IDH2 K127R mutation, Reverse:
5’- ccacatcttcttcagcctgaactcttccacacg −3’
This paper N/A
Primers: IDH2 K133R mutation, Forward:
5’-ctgaagaagatgtggagaagtcccaatggaact-3’
This paper N/A
Primers: IDH2 K133R mutation, Reverse:
5’-agttccattgggacttctccacatcttcttcag-3’
This paper N/A
Primers: IDH2 K155R mutation, Reverse:
5’- gagcccatcatctgcagaaacatcccacgccta −3’
This paper N/A
Primers: IDH2 K155R mutation, Forward:
5’-taggcgtgggatgtttctgcagatgatgggctc-3’
This paper N/A
Primers: IDH2 K166R mutation, Forward:
5’-gtccctggctggaccaggcccatcaccattggc-3’
This paper N/A
Primers: IDH2 K166R mutation, Reverse:
5’- gccaatggtgatgggcctggtccagccagggac-3’
This paper N/A
Primers: IDH2 K180R mutation, Forward:
5’-catggcgaccagtacagggccacagactttgtg’
This paper N/A
Primers: IDH2 K180R mutation, Reverse:
5’-cacaaagtctgtggccctgtactggtcgccatg-3’
This paper N/A
Primers: IDH2 K242R mutation, Forward:
5’-cagtatgccatccagaggaaatggccgctgtac-3’
This paper N/A
Primers: IDH2 K242R mutation, Reverse:
5’-gtacagcggccatttcctctggatggcatactg −3’
This paper N/A
Primers: IDH2 K256R mutation, Forward:
5’-aagaacaccatactgagagcctacgatgggcgt-3’
This paper N/A
Primers: IDH2 K256R mutation, Reverse:
5’-acgcccatcgtaggctctcagtatggtgttctt-3’
This paper N/A
Primers: IDH2 K263R mutation, Forward:
5’-tacgatgggcgtttcagggacatcttccaggag-3’
This paper N/A
Primers: IDH2 K263R mutation, Reverse:
5’-ctcctggaagatgtccctgaaacgcccatcgta-3’
This paper N/A
Primers: IDH2 K272R mutation, Forward:
5’-caggagatctttgacaggcactataagaccgac-3’
This paper N/A
Primers: IDH2 K272R mutation, Reverse:
5’gtcggtcttatagtgcctgtcaaagatctcctg-3’
This paper N/A
Primers: IDH2 K275R mutation, Forward:
5’-tttgacaagcactataggaccgacttcgacaag-3’
This paper N/A
Primers: IDH2 K275R mutation, Reverse:
5’-cttgtcgaagtcggtcctatagtgcttgtcaaa-3’
This paper N/A
Primers: IDH2 K280R mutation, Forward:
5’-aagaccgacttcgacaggaataagatctggtat-3’
This paper N/A
Primers: IDH2 K280R mutation, Reverse:
5’-ataccagatcttattcctgtcgaagtcggtctt-3’
This paper N/A
Primers: IDH2 K282R mutation, Forward:
5’-gacttcgacaagaataggatctggtatgagcac-3’
This paper N/A
Primers: IDH2 K282R mutation, Reverse:
5’gtgctcataccagatcctattcttgtcgaagtc-3’
This paper N/A
Primers: IDH2 K384R mutation, Forward:
5’-ctggagcaccgggggaggctggatgggaaccaa-3’
This paper N/A
Primers: IDH2 K384R mutation, Reverse:
5’-ttggttcccatccagcctcccccggtgctccag-3’
This paper N/A
Primers: IDH2 K442R mutation, Forward:
5’-ttcctcgacaccatcaggagcaacctggacaga-3’
This paper N/A
Primers: IDH2 K442R mutation, Reverse:
5’ -tctgtccaggttgctcctgatggtgtcgaggaa-3’
This paper N/A
Primers: IDH2 K413R mutation, Forward:
5’-agtggagccatgaccagggacctggcgggctgcatt-3’
This paper N/A
Primers: IDH2 K413R mutation, Reverse:
5’-aatgcagcccgccaggtccctggtcatggctccact-3’
This paper N/A
Primers: IDH2 K413Q mutation, Forward:
5’-agtggagccatgaccCaggacctggcgggctgcatt-3’
This paper N/A
Primers: IDH2 K413Q mutation, Reverse:
5’ -aatgcagcccgccaggtcctGggtcatggctccact-3’
This paper N/A
Primers: IDH2 Y81F mutation, Forward:
5’-atccagctaaagttttttgacctcgggct-3’
This paper N/A
Primers: IDH2 Y81F mutation, Reverse:
5’-gtccacgtggggcaggatgagcttctcctt-3’
This paper N/A
Primers: IDH2 Y107F mutation, Forward:
5’-ctggccacccagaagttcagtgtggctgtcaag-3’
This paper N/A
Primers: IDH2 Y107F mutation, Reverse:
5’-tgcagagtcaatggtgacctggtcatcagtctg-3’
This paper N/A
Primers: IDH2 Y210F mutation, Forward:
5’-atccagctaaagttttttgacctcgggct-3’
This paper N/A
Primers: IDH2 Y210F mutation, Reverse:
5’-gacaccactgccatcttttggggtgaagac-3’
This paper N/A
Primers: IDH2 Y238F mutation, Forward:
5’-cacagctgcttccagtttgccatccagaagaaa-3’
This paper N/A
Primers: IDH2 Y238F mutation, Reverse:
5’-cgcaaaacctgagatggactcgtcggtgttgtacat-3’
This paper N/A
Primers: SIRT3 Y165F mutation, Forward:
5’-ggagtggcctgttcagcaacctccagcag-3’
This paper N/A
Primers: SIRT3 Y165F mutation, Reverse:
5’-ctgctggaggttgctgtacaggccactcc-3’
This paper N/A
Primers: SIRT3 Y171F mutation, Forward:
5’-agcaacctccagcagttcgatctcccgtac-3’
This paper N/A
Primers: SIRT3 Y171F mutation, Reverse:
5’ -agcaacctccagcagttcgatctcccgtac3’
This paper N/A
Primers: SIRT3 Y175F mutation, Forward:
5’-cagtacgatctcccgttccccgaggccattttt-3’
This paper N/A
Primers: SIRT3 Y175 mutation, Reverse:
5’-aaaaatggcctcggggaacgggagatcgtactg-3’
This paper N/A
Primers: SIRT3 Y200F mutation, Forward:
5’-tggccaaggagctgttccctggaaactacaag-3’
This paper N/A
Primers: SIRT3 Y200F mutation, Reverse:
5’-cttgtagtttccagggaacagctccttggcca-3’
This paper N/A
Primers:SIRT3 Y204F mutation, Forward:
5’-ctgtaccctggaaacttcaagcccaacgtcact-3’
This paper N/A
Primers: SIRT3 Y204F mutation, Reverse:
5’-agtgacgttgggcttgaagtttccagggtacag-3’
This paper N/A
Primers: SIRT3 Y211F mutation, Forward:
5’-cccaacgtcactcacttctttctccggctgctt-3’
This paper N/A
Primers:SIRT3 Y211F mutation, Reverse:
5’-aagcagccggagaaagaagtgagtgacgttggg-3’
This paper N/A
Primers: SIRT3 Y226F mutation, Forward:
5’-ctgcttctgcggctcttcacgcagaacatcgat-3’
This paper N/A
Primers: SIRT3 Y226F mutation, Reverse:
5’-atcgatgttctgcgtgaagagccgcagaagcag-3’
This paper N/A
Recombinant DNA
pLVX-IDH2-FLAG This paper N/A
pLVX -IDH2-FLAG K413R This paper N/A
pLVX -IDH2-FLAG K413Q This paper N/A
pLVX-IDH2-FLAG R140Q This paper N/A
pLVX -IDH2-FLAG R140Q/K413R This paper N/A
pLVX -IDH2-FLAG R140Q/K413Q This paper N/A
pcDNA3.0-IDH2 From Ross Levine Lab(Memorial Sloan Kettering Cancer Center) N/A
pcDNA3.0-IDH2 R140Q From Ross Levine Lab (Memorial Sloan Kettering Cancer Center) N/A
pcDNA3.0-IDH2 R172K From Ross Levine Lab (Memorial Sloan Kettering Cancer Center) N/A
pET53-DEST-FLAG-SIRT3 (Fan et al., 2016) N/A
pET53-DEST-FLAG-ACAT1 (Fan et al., 2016) N/A
pET53-DEST-FLAG-ACAT1 Y407F (Shan et al., 2014) N/A
pLHCX-FLAG-ACAT1 (Fan et al., 2016) N/A
pLHCX-FLAG-ACAT1 Y407F (Fan et al., 2016) N/A
pET53-DEST-FLAG-ACAT2 (Shan et al., 2014) N/A
pET53-DEST-FLAG-DLAT (Shan et al., 2014) N/A
pET53-DEST-FLAG-CobB (Shan et al., 2014) N/A
pET53-DEST-IDH2-FLAGK48R This paper N/A
pET53-DEST -IDH2-FLAGK67R This paper N/A
pET53-DEST -IDH2-FLAGK69R This paper N/A
pET53-DEST -IDH2-FLAGK80R This paper N/A
pET53-DEST -IDH2-FLAG K106R This paper N/A
pET53-DEST -IDH2-FLAG K127R This paper N/A
pET53-DEST -IDH2-FLAG K133R This paper N/A
pET53-DEST -IDH2-FLAG K155R This paper N/A
pET53-DEST -IDH2-FLAG K166R This paper N/A
pET53-DEST -IDH2-FLAG K180R This paper N/A
pET53-DEST -IDH2-FLAG K242R This paper N/A
pET53-DEST -IDH2-FLAG K256R This paper N/A
pET53-DEST -IDH2-FLAG K263R This paper N/A
pET53-DEST -IDH2-FLAG K272R This paper N/A
pET53-DEST -IDH2-FLAG K275R This paper N/A
pET53-DEST -IDH2-FLAG K280R This paper N/A
pET53-DEST -IDH2-FLAG K282R This paper N/A
pET53-DEST -IDH2-FLAG K384R This paper N/A
pET53-DEST -IDH2-FLAG K442R This paper N/A
pET53-DEST -IDH2-FLAG K413R This paper N/A
pET53-DEST -IDH2-FLAG K413Q This paper N/A
pET53-DEST -IDH2-FLAG This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K48R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K67R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K69R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K80R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K106R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K127R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K133R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K155R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K166R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K180R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K242R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K256R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K263R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K272R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K275R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K280R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K282R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K384R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K442R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K413R This paper N/A
pET53-DEST -IDH2-FLAG R140Q/K413Q This paper N/A
pET53-DEST -IDH2-FLAGR140Q This paper N/A
pET53-DEST -IDH2-FLAG Y81F This paper N/A
pET53-DEST -IDH2-FLAG Y107F This paper N/A
pET53-DEST -IDH2-FLAG Y210F This paper N/A
pET53-DEST -IDH2-FLAG Y238F This paper N/A
pET53-DEST -SIRT3 (Shan et al., 2014) N/A
pET53-DEST -SIRT3 Y165F This paper N/A
pET53-DEST -SIRT3 Y171F This paper N/A
pET53-DEST -SIRT3 Y175F This paper N/A
pET53-DEST -SIRT3 Y200F This paper N/A
pET53-DEST -SIRT3 Y204F This paper N/A
pET53-DEST -SIRT3 Y211F This paper N/A
pET53-DEST -SIRT3 Y226F This paper N/A
Software and Algorithms
GraphPad Prism 7 software GraphPad Software https://www.graphpad.com/
Other
N/A