Metabolic classification suggests the GLUT1/ALDOB/G6PD axis as a therapeutic target in chemotherapy-resistant pancreatic cancer

. 2023 Aug 18;4(9):101162. doi: 10.1016/j.xcrm.2023.101162

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

GLUT1	abcam	Cat#ab115730; RRID:AB_10903230
ALDOA	proteintech	Cat#11217-1-AP; RRID:AB_2224626
ALDOB	proteintech	Cat#18065-1-AP; RRID:AB_2273968
ALDOC	proteintech	Cat#14884-1-AP; RRID:AB_2226691
G6PD	abcam	Cat#ab993; RRID:AB_296714
α-tubulin	proteintech	Cat#11224-1-AP; RRID:AB_2210206
actin	abmart	Cat#M20011; RRID:AB_2936240

Biological samples

Human tissue samples for sequencing analyses	This study	N/A
Human blood samples for sequence analyses	This study	N/A

Chemicals, peptides, and recombinant proteins

Advanced DMEM/F12	Gibco	Cat#12634010
HEPES	Gibco	Cat#15630080
GlutMAX	Gibco	Cat#35050061
Penicillin-Streptomycin	Gibco	Cat#15140122
Primocin	InvivoGen	Cat#ant-pm-2
B27 supplement	Gibco	Cat#17504044
Wnt3A conditioned medium	Gao lab	N/A
R-spondin conditioned medium	Gao lab	N/A
Noggin conditioned medium	Gao lab	N/A
Nicotinamide	SIGMA	Cat#N0636-100G
EGF	Invitrogen	Cat#PHG0313
FGF10	PEPRO TECH	Cat#K2717
N-acetyl-L-cysteine	SIGMA	Cat#A9165-100G
A83-01	TOCRIS	Cat#2939
Y-27632	Selleck chemicals	Cat#S1049
Forskolin	Selleck chemicals	Cat#S2449
TrypLE™ Express	Gibco	Cat#12605028
Collagenase Type II	Gibco	Cat#17101015
Matrigel Matrix (For organoid culture)	CORNING	Cat#356231
Matrigel Matrix (For xenograft)	CORNING	Cat#354234
Gemcitabine	TargetMol	Cat#T0251
Paclitaxel	Selleck chemicals	Cat#S1150
5-fluorouracil	SIGMA	Cat#F6627
Oxaliplatin	Selleck chemicals	Cat#S1124
Irinotecan	Selleck chemicals	Cat#S1198
BAY-876	Selleck chemicals	Cat#S8452
6AN	Selleck chemicals	Cat#S9783
MLN8054	TargetMol	Cat#T6315
Alisertib	Selleck chemicals	Cat#S1133
Uridine	Sigma	Cat#U3003
Cytidine	Sigma	Cat#C4654
Thymidine	Sigma	Cat#T1895
Guanosine	Sigma	Cat#G6264
adenosine	Sigma	Cat#A4036
R5P	MCE	Cat#207671-46-3
CellTiter-Glo Luminescent	Promega	Cat#G7573
DMSO	Innoche	Cat#D3850-500ML
TRIzol reagent	Ambion	Cat#15596018
PrimeScriptTM RT Master Mix	TaKaRa	Cat#RR036A
Power SYBR Green PCR Master Mix	Qiagen	Cat#208054
Glucose-6-phosphate	Sigma	G7879-500mg
DMEM	Gibco	11966–025
[U-¹³C₆] glucose	CIL	CLM-1396-1
Nonlabeled glucose	Sigma	G7021

Critical commercial assays

Widely targeted metabolomics assay	Wuhan Metware Biotechnology Co., Ltd	LC-ESI-MS/MS system analysis
Widely targeted lipidomics assay	Wuhan Metware Biotechnology Co., Ltd	LC-ESI-MS/MS system analysis
Metabolon-based energy metabolism detection	Applied Protein Technology, Shanghai, China	LC-MS/MS analysis

Deposited data

Widely targeted metabolomics	This study	OMIX: OMIX003772
Widely targeted lipidomics assay	This study	OMIX: OMIX004117
Metabolon-based energy metabolism in PDAC organoids	This study	OMIX: OMIX004545
RNA expression data of PDAC organoids	This study	OMIX: OMIX003773
ATAC-seq peaks of PDAC organoids	This study	OMIX: OMIX003774
Coding mutations in PDAC organoids	This study	OMIX: OMIX003813

Experimental models: Cell lines

HEK-293T	ATCC	Cat#CRL-1573

Experimental models: Organisms/strains

Human PDAC organoids	This study	N/A
DH5α	AlpaLifeBio	KTSM101L

Oligonucleotides

shRNA hairpins	This study	Table S6
qRT-PCR primers	This study	Table S6

Software and algorithms

R version 4.0.3	The R Foundation for Statistical Computing	N/A
“CancerSubtypes” Bioconductor package for R	Xu et al.⁷¹	https://bioconductor.org/packages/release/bioc/html/CancerSubtypes.html
MBROLE 2.0	López-Ibáñez et al.⁷²	https://csbg.cnb.csic.es/mbrole2/
“GSVA” Bioconductor package for R	Hänzelmann et al.⁷³	https://www.bioconductor.org/packages/release/bioc/html/GSVA.html
“limma” Bioconductor package for R	Ritchie et al.⁷⁴	https://bioconductor.org/packages/release/bioc/html/limma.html
Nearest Template Prediction (NTP)	Hoshida.⁷⁵	https://github.com/genepattern/NearestTemplatePrediction/blob/master/src/NTPez.R
“clusterProfiler” Bioconductor package for R	Wu et al.⁷⁶	https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
Bowtie v2.3.1	Langmead and Salzberg.⁷⁷	https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Sambamba v0.6.6	Tarasov et al.⁷⁸	https://lomereiter.github.io/sambamba/
Samtools v1.4	Li et al.⁷⁹	https://samtools.sourceforge.net/
MACS2 v2.1.1	Zhang et al.⁸⁰	https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html
deepTools	Ramírez et al.⁸¹	https://deeptools.readthedocs.io/en/develop/
“DiffBind” Bioconductor package for R	Ross-Innes et al.⁸²	https://bioconductor.org/packages/release/bioc/html/DiffBind.html