Stabilized epithelial phenotype of cancer cells in primary tumors leads to increased colonization of liver metastasis in pancreatic cancer

. Author manuscript; available in PMC: 2021 Apr 27.

Published in final edited form as: Cell Rep. 2021 Apr 13;35(2):108990. doi: 10.1016/j.celrep.2021.108990

KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit monoclonal anti-Slug	Cell Signaling Technology	Cat# 9585; RRID:AB_2239535
Rabbit polyclonal anti-FSP1	Agilent (originally DAKO)	Cat#A5114; RRID:AB_2335679
Rabbit polyclonal anti-Zeb1	Novus	Cat# NBP1-05987; RRID:AB_2273178
Rat monoclonal anti-cytokeratin 8	DSHB	Cat# TROMA-I; RRID:AB_531826
Chicken polyclonal anti-GFP	Aves	Cat# GFP-1020; RRID:AB_10000240
Mouse monoclonal anti-Twist1	Novus	Cat# NBP2–37364; RRID:AB_2801339
Rabbit monoclonal anti-Vimentin	Cell Signaling Technology	Cat# 5741; RRID:AB_10695459
Rabbit polyclonal anti-Snail + Slug	Abeam	Cat# ab180714; RRID:AB_2728773
Mouse monoclonal anti-aSMA	Agilent (originally DAKO)	Cat# M0851; RRID:AB_2223500
Rabbit monoclonal anti-Ecadherin	Cell Signaling Technology	Cat# 3195; RRID:AB_2291471
Rabbit monoclonal anti-Ki-67	Thermo Scientific	Cat# RM-9106-S; RRID:AB_149707
Rabbit on Rodent HRP Polymer	Biocare Medical	Cat# RMR622
Mouse-on-Mouse HRP-Polymer	Biocare Medical	Cat# MM620
Polink-1 HRP Rat-NM for DAB Bulk Kit	GBI labs	Cat# D35–110
Polink-2 Plus HRP Chicken IgY for DAB Kit	GBI labs	Cat# D84–60
Goat polyclonal anti-Rabbit Alexa Fluor 488	Invitrogen	Cat# A-11008; RRID: AB_143165
Goat polyclonal anti-Chicken Alexa Fluor 594	Invitrogen	Cat# A-11042; RRID: AB_2534099
Goat polyclonal anti-Rat Alexa Fluor 647	Invitrogen	Cat# A-21247; RRID: AB_141778
Goat polyclonal anti-Rabbit, Biotinylated	Vector Laboratories	Cat# BA-1000; RRID:AB_2313606
Bacterial and virus strains
Ad-CMV-iCre	Vector Biolabs	Cat#1045
Biological samples
mouse model pancreatic tumor and mixed organ FFPE blocks	This paper	N/A
Critical commercial assays
Opal 7 color IHC Kit	Akoya Biosciences	NEL811001KT
TSA Coumarin System	Akoya Biosciences	NEL703001KT
VECTASTAIN Elite® ABC System	Vector Labs	PK-6100
Power SYBR Green PCR Master Mix	Thermo Fisher	4367659
Fluoroshield mounting media	Sigma Aldrich	F618
Vectashield Mounting Media	Vector Laboratories	H1000
Deposited data
Raw and analyzed microarray data	This paper	GEO:GSE164612
Raw and analyzed scRNA-seq data	This paper	GEO:GSE165534
GDC TCGA Pancreatic Cancer (PAAD)	TCGA	https://xenabrowser.net/datapages/
Patient scRNA-seq data	Peng et al., 2019	N/A
Source Data	N/A	Mendeley Data: https://dx.doi.org/10.17632/sxc5zk4m9w.1
Experimental models: Cell lines
Control Line 978U; Pdx1-Cre; Kras^G12D; p53^R172H/+; Rosa26-LSL-EYFP^F/F; Female	This paper	N/A
Control Line H444; Pdx1-Cre; Kras^G12D; p53^R172H/+; Rosa26-LSL-EYFP^F/+;Female	This paper	N/A
Control Line 0739; Pdx1-Cre; Kras^G12D; p53^R172H/+; Rosa26-LSL-EYFP^F/+; Male	This paper	N/A
KPC-ST Line 309P; Pdx1-Cre; Kras^G12D; p53^R172H/+; Snai1^F/F; Twist1^F/F ; Rosa26-LSL-EYFP^F/+; αSMA-RFP; Female	This paper	N/A
KPC-ST Line 404P; Pdx1-Cre; Kras^G12D; p53^R172H/+; Snai1^F/F; Twist1^F/F ; Rosa26-LSL-EYFP^F/+; αSMA-RFP; Female	This paper	N/A
KPC-ST Line 407P; Pdx1-Cre; Kras^G12D; p53^R172H/+; Snai1^F/F; Twist1^F/F; Rosa26-LSL-EYFP^F/F; αSMA-RFP; Female	This paper	N/A
KPC Ecad KO Line 28B; Adenoviral-Cre; Kras^G12D; p53^R172H/+; Cdh1^F/F; Rosa26-LSL-EYFP^F/F; Female	This paper	N/A
Experimental models: Organisms/strains
KPC; Pdx1-Cre; Kras^G12D; p53^R172H/+ (may contain Rosa26-LSL-EYFP or αSMA-RFP)	This paper	N/A
KPC;ST; Pdx1-Cre; Kras^G12D; p53^R172H/+; Snai1^F/F; Twist1^F/F (may contain Rosa26-LSL-EYFP or αSMA-RFP)	This paper	N/A
KPPC; P48-Cre; Kras^G12D; p53^F/F (may contain Rosa26-LSL-EYFP)	This paper; Dr. Rhim	N/A
KPPC;Z^F+; P48-Cre; Kras^G12D; p53^F/F; Zeb1^F/+ (may contain Rosa26-LSL-EYFP)	This paper; Dr. Rhim	N/A
KPPC;Z^{cKO +}; P48-Cre; Kras^G12D; p53^F/F; Zeb1^F/F (may contain Rosa26-LSL-EYFP)	This paper; Dr. Rhim	N/A
KP;E^FF-AdCre ⁺; Adenoviral-Cre; Kras^G12D; p53^R172H/+; Cdh1^F/F (may contain Rosa26-LSL-EYFP or αSMA-RFP)	This paper	N/A
Oligonucleotides
mouse Snai1 Forward; CACACGCTGCCTTGTGTCT	Lovisa et al., 2015	N/A
mouse Snai1 Reverse; GGTCAGCAAAAGCACGGTT	Lovisa et al., 2015	N/A
mouse Twist1 Forward; CTGCCCTCGGACAAGCTGAG	Lovisa et al., 2015	N/A
mouse Twist Reverse; CTAGTGGGACGCGGACATGG	Lovisa et al., 2015	N/A
mouse Zeb1 Forward; GCTGGCAAGACAACGTGAAAG	Harvard Primer Bank	N/A
mouse Zeb1 Reverse; GCCTCAGGATAAATGACGGC	Harvard Primer Bank	N/A
mouse Cdh1 Forward; GTCAACACCTACAACGCTGCC	Lovisa et al., 2015	N/A
mouse Cdh1 Reverse; GTTGTGCTCAAGCCTTCAC	Lovisa et al., 2015	N/A
mouse Vim Forward; CTTGAACGGAAAGTGGA ATCCT	Lovisa et al., 2015	N/A
mouse Vim Reverse; GTCAGGCTTGGAAAC GTCC	Lovisa et al., 2015	N/A
mouse Col1a1 Forward; CTCCTCTTAGGGGCCACT	Lovisa et al., 2015	N/A
mouse Col1a1 Reverse; CCACGTCTCACCATTGGGG	Lovisa et al., 2015	N/A
mouse 18s Forward; GTAACCCGTTGAACCCCATT	Lovisa et al., 2015	N/A
mouse 18s Reverse; CCATCCAATCGGTAGTAGCG	Lovisa et al., 2015	N/A
mouse Rhoa Forward; AGCTTGTGGTAAGACAT GCTTG	Harvard Primer Bank	N/A
mouse Rhoa Reverse; GTGTCCCATAAAGCCAACT CTAC	Harvard Primer Bank	N/A
mouse Rock1 Forward; GACTGGGGACAGTTTTGAGAC	Harvard Primer Bank	N/A
mouse Rock1Reverse; GGGCATCCAATCCATCCAGC	Harvard Primer Bank	N/A
mouse Rac1 Forward; GAGACGGAGCTGTTGGTAAAA	Harvard Primer Bank	N/A
mouse Rac1Reverse; ATAGGCCCAGATTCACTGGTT	Harvard Primer Bank	N/A
mouse Sdc1 Forward; GAGACGGAGCTGTTGGTAAAA	Harvard Primer Bank	N/A
mouse Sdc1 Reverse; AACGGGCCTCAACAGTCAG	Harvard Primer Bank	N/A
mouse Ctsb Forward; TCCTTGATCCTTCTTTCTTGCC	Harvard Primer Bank	N/A
mouse Ctsb Reverse; ACAGTGCCACACAGCTTCTTC	Harvard Primer Bank	N/A
mouse Lamp1 Forward; CAGCACTCTTTGAGGTGAAAAAC	Harvard Primer Bank	N/A
mouse Lamp1 Reverse; ACGATCTGAGAACCATTCGCA	Harvard Primer Bank	N/A
mouse Max Forward; ACCATAATGCACTGGAACGAAA	Harvard Primer Bank	N/A
mouse Max Reverse; GTCCCGCAAACTGTGAAAGC	Harvard Primer Bank	N/A
mouse Jun Forward; CCTTCTACGACGATGCCCTC	Harvard Primer Bank	N/A
mouse Jun Reverse; GGTTCAAGGTCATGCTCTGTTT	Harvard Primer Bank	N/A
mouse Sec24b Forward; GGTCCAGCACAGAGTCCAATG	Harvard Primer Bank	N/A
mouse Sec24b Reverse; GGAGTCCCCGAATTTTGTGTT	Harvard Primer Bank	N/A
mouse Ndufb11 Forward; CCTCCAGGGCTGTAATCGC	Harvard Primer Bank	N/A
mouse Ndufb11 Reverse; GGTTCTTCGCGTAGACGTTTTC	Harvard Primer Bank	N/A
mouse Apoe Forward; CTGACAGGATGCCTAGCCG	Harvard Primer Bank	N/A
mouse Apoe Reverse; CGCAGGTAATCCCAGAAGC	Harvard Primer Bank	N/A
Software and algorithms
Prism 8	GraphPad	N/A
InForm v2.4.6	Akoya Biosciences	N/A
Vis 6.2019	Visiopharm	N/A
UCSC Xena browser	Goldman et al., 2020	N/A
Seurat (version 3.6.1)	Butler et al., 2018; Stuart et al., 2019	N/A
library Matrix and library Rmagic	van Dijk et al., 2018	N/A
Monocle 3	Haghverdi et al., 2018	N/A
L-Function	Carstens et al., 2017	N/A
FIJI with Phantast plugin	NIH; Jaccard et al., 2014	N/A
QuPath	Bankhead et al., 2017	N/A
SPSS Statistics	IBM	N/A