Reprogramming of Amino Acid Transporters to Support Aspartate and Glutamate Dependency Sustains Endocrine Resistance in Breast Cancer

. 2019 Jul 2;28(1):104–118.e8. doi: 10.1016/j.celrep.2019.06.010

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

Mouse monoclonal anti-tubulin	Sigma	Cat# T5168; RRID: AB_477579
Rabbit polyclonal anti-GATA2	Cell signaling	Cat# 4595; RRID: AB_2108579
Mouse monoclonal anti-SLC1A2	Santa Cruz Biotechnology	Cat# 365634; RRID: AB_10844832
Rabbit polyclonal anti-SLC6A14	Abcam	Cat# ab99102; RRID: AB_10696963
Rabbit polyclonal anti-beclin1	Thermo Fisher Scientific	Cat# PA1-16857; RRID:AB_568459
Rabbit polyclonal anti-LC3	Thermo Fisher Scientific	Cat# PA1-16930; RRID: AB_2281384
Mouse monoclonal anti-ubiquitin-K63	Thermo Fischer Scientific	Cat# 14-6077-80; RRID:AB_1257214
Mouse monoclonal anti-APG7	Santa Cruz Biotechnology	Cat# sc-376212 RRID:AB_10988418
Mouse monoclonal anti-beclin1	Santa Cruz Biotechnology	Cat# sc-48341 RRID:AB_626745
Goat anti-Rabbit IgG (H+L) Secondary Antibody, Alexa Fluor 488 conjugate	Thermo Fisher Scientific	Cat# A-11034; RRID:AB_2576217
Goat Anti-Rabbit IgG (H+L) Highly Cross-adsorbed Antibody, Alexa Fluor 633 conjugate	Thermo Fisher Scientific	Cat# A-21071; RRID:AB_141419

Biological Samples

Patient-derived xenografts HBCx34	Prof. Elisabetta Marangoni	Cottu et al., 2014

Chemicals, Peptides, and Recombinant Proteins

Methanol	Sigma	Cat# 900688-1
Acetonitrile	Sigma	Cat# 34851
4-N,N-dimethylaminoazobenzene-4’-sulfonyl chloride	Supelco	Cat# 502219
KH₂PO₄	Sigma	Cat# P3786
Amino acids standards	Sigma	Cat# A9781
Chloroform	Sigma	Cat# 34854-1
Water	Merck	Cat# 102699-1000
Norvaline	Sigma	Cat# 53721
Methoxyamine hydrochloride	Sigma	Cat# 226904
Pyridine	Thermo Fisher Scientific	Cat# 25104
N-Methyl-N-(trimethylsilyl)trifluoroacetamide with 1% trimethylchlorosilane	Sigma	Cat# 69478
Chloroquine diphosphate	Sigma	Cat# C6628
Glutamine	Sigma	Cat# G7513
RPMI 1640 medium	GIBCO	Cat# 11835-063
DMEM 1X	GIBCO	Cat# A14430-01
¹⁴C-Glutamic acid	Perkin Elmer	Cat# NEC290E050UC
¹⁴C-Aspartic acid	Perkin Elmer	Cat# NEC268E050UC
¹⁴C-Amino Acid Mixture	Perkin Elmer	Cat# NEC850E050UC
¹³C-Glutamic acid	Sigma	Cat# 604860
¹³C-Aspartic acid	Cambridge Isotope Laboratories	Cat# CNLM-544-H-0.25
D-Glutamic acid	Sigma	Cat# G1001
L-Aspartic acid	Sigma	Cat# A9256
Z-4-hydroxytamoxifen	Sigma	Cat# H7904
17-β-estradiol	Sigma	Cat# E2758
Fulvestrant	Sigma	Cat# I4409
Lipofectamine RNAiMAX	Thermo Fisher Scientific	Cat# 13778-150
Opti-MEM	GIBCO	Cat# 31985062
Fetal Bovine Serum	Euroclone	Cat# ECS0180L
Charcoal/Dextran Treated FBS (DCC)	Hyclone	Cat# SH30068.03
Protease inhibitor cocktail	Sigma	Cat# P8340
Matrigel Matrix	BD Biosciences	Cat# 356234
Protein A/G-PLUS Agarose beads	Santa Cruz Biotechnology	Cat# sc-2003
DiffQuick solution	BD Biosciences	Cat# 726443
Laemmli Sample Buffer	Bio-Rad	Cat# 161-0737
Clarity Western ECL Substrate	Bio-Rad	Cat# 170-5061
XFe Seahorse RPMI medium	Agilent Technologies	Cat# 103336-100

Critical Commercial Assays

TaqMan Universal Mastermix no UNG	Applied Biosystems	Cat# 4440040
QuantiTect Reverse Transcription Kit	QIAGEN	Cat# 205311
TaqMan MicroRNA Reverse Transcription Kit	Applied Biosystems	Cat# 43665967
miRNeasy Mini Kit	QIAGEN	Cat# 217004
SosAdvanced Universal Sybr Green Supermix	Bio-Rad	Cat# 1725270
Cayman Chemicals Protein Synthesis Assay	Cayman Chemical	Cat# 601100
Seahorse XF Cell Mito Stress Kit	Agilent Technologies	Cat# 103015-100
Human genome microarray	Agilent Technologies	Cat# G4851A
Human miRNA microarray v16	Agilent Technologies	Cat# G4870A

Deposited Data

mRNA and miRNA microarray data	This paper	GEO: GSE120931
Gene expression data	Rème et al., 2013	ArrayExpress: E-MTAB-365
The Cancer Genome Atlas (TGCA)	https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga	RRID:SCR_003193
Gene expression data	Loi et al., 2007	GEO: GSE6532
Gene expression data	Dedeurwaerder et al., 2011	GEO: GSE20711
Gene expression data	Desmedt et al., 2007	GEO: GSE7390
Gene expression data	Sabatier et al., 2011	GEO: GSE21653
Gene expression data	Wang et al., 2005	GEO: GSE2034
Gene expression data	Sotiriou et al., 2006	GEO: GSE2990
Gene expression data	Symmans et al., 2010	GEO: GSE17705
Gene expression data	Zhang et al., 2009	GEO: GSE12093
Gene expression data	Loi et al., 2008	GEO: GSE9195
Gene expression data	Miller et al., 2005	GEO: GSE3494
Gene expression data	Karn et al., 2010	GEO: GSE4611
Gene expression data	Nagalla et al., 2013	GEO: GSE45255
Gene expression data	Minn et al., 2005	GEO: GSE2603
Gene expression data	Desmedt et al., 2009	GEO: GSE16391
Gene expression data	Clarke et al., 2013	GEO: GSE42568
Gene expression data	Filipits et al., 2011	GEO: GSE26971
Gene expression data	Li et al., 2010	GEO: GSE19615
Gene expression data	Miller et al., 2007	GEO: GSE5462
Gene expression data	Massarweh et al., 2011	GEO: GSE33658
Gene expression data	Pereira et al., 2016	METABRIC

Experimental Models: Cell Lines

MCF7	ATCC	Cat# HTB-22
ZR75.1	ATCC	Cat# CRL-1500
HCC1428	ATCC	Cat# CRL-2327
LTED Cells	Bacci et al., 2016	N/A
MCF7-TAMR	This paper	N/A
MCF7-FULVR	This paper	N/A

Experimental Models: Organisms/Strains

BALB/c mice	Charles River Laboratories	Cat# 236CB17SCID
NSG mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ)	Simões et al., 2015	N/A

Oligonucleotides

anti-miR-23b-3p	Ambion	Cat# MH10711
siSLC1A2	Sigma	Cat# Hs01_00109453
siCTR	Sigma	Cat# SIC001
anti-miR-negative control (anti-miR-CTR)	Ambion	Cat# AM17011
siGATA2	Sigma	Cat# Hs01_00106117
siATG7_71	Sigma	Cat# Hs02_00341471
siATG7_49	Sigma	Cat# Hs01_00077649
siATG7_48	Sigma	Cat# Hs01_00077648
SLC6A14 (Hs00924564_m1)	Applied Biosystems	Cat# 4448892
SLC1A2 (Hs01102423_m1)	Applied Biosystems	Cat# 4448892
GATA2 (Hs00231119_m1)	Applied Biosystems	Cat# 4453320
GAPDH (Hs02786624_g1)	Applied Biosystems	Cat# 4331182
ACTB (Id:Hs99999903_m1)	Applied Biosystems	Cat# 4331182
miR-23b-3-p (000400)	Applied Biosystems	Cat# 4427975
RNU48 (001006)	Applied Biosystems	Cat# 4427975
U6 (001973)	Applied Biosystems	Cat# 4427975
TNFAIP3 precast primer (HsaCID0012648)	Bio-Rad	Cat# 10025636
Beclin-1 precast primer (HsaCID0016032)	Bio-Rad	Cat# 10025636
GAPDH precast primer (HsaCED0038674)	Bio-Rad	Cat# 10025636

Software and Algorithms

Masshunter Quantitative Analysis Software	Agilent Technologies	RRID: SCR_015040
Masshunter Qualitative Analysis	Agilent Technologies	RRID:SCR_016657
Fihen Metabolomics RTL library	Agilent Technologies	Cat# G1676AA
7500 Real-Time PCR Software	Applied Biosystems	RRID:SCR_014596
Thermo XCalibur Quan Browser software	Thermo Fisher Scientific	RRID: SCR_014593
FiJi	https://fiji.sc	N/A
GraphPad Prism v8.0c	https://www.graphpad.com/	N/A
KM plotter	Györffy et al., 2010, Lánczky et al., 2016	http://kmplot.com/analysis/
cBioPortal	https://www.cbioportal.org/	RRID:SCR_014555
Firebrowse	http://firebrowse.org/	N/A
Seahorse Wave software	Agilent Technologies	RRID:SCR_014526
GeneSpring GX v.14.8 software	Agilent Technologies	RRID:SCR_010972
R Statistical Software	https://www.r-project.org/	N/A