Human APOBEC3B promotes tumor development in vivo including signature mutations and metastases

. 2023 Oct 4;4(10):101211. doi: 10.1016/j.xcrm.2023.101211

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

Rabbit monoclonal anti-CD3	Abcam	Cat# ab16669 RRID: AB_443425
Rabbit monoclonal anti-A3B	Brown et al.¹⁷	5210-87-13; RRID: AB_2721202
Rat monoclonal anti-B220	BD Pharmogen	Cat# 550286 RRID: AB_393581
Rabbit monoclonal anti-γ-H2AX	Cell Signaling	Cat# 9718 RRID: AB_2118009
Mouse monoclonal anti-tubulin	Sigma-Aldrich	Cat# T5168 RRID: AB_477579
Rabbit anti-actin	Sigma-Aldrich	Cat# A2066 RRID: AB_476693
Goat anti-rabbit HRP	Cell Signaling	Cat# 7074P2 RRID: AB_2099233
Goat anti-mouse IRdye 800CW	LI-COR	Cat# 926-32210 RRID: AB_621842

Biological samples

Human Head and Neck FFPE sections	Argyris et al.⁶¹	Table S2

Chemicals, peptides, and recombinant proteins

Cytoseal	Thermo Fisher Scientific	Cat# 23-244257
CitriSolv	Decon Labs	Cat# 1601
Dulbecco’s Modified Eagle Medium (DMEM)	Gibco	Cat# 11965-084
Fetal Bovine Serum (FBS)	Gibco	Cat# A52567-01
Reveal decloaker	Biocare	Cat# RV1000M
Background sniper	Biocare	Cat# BS966
TransIT-LT1 Transfection Reagent	Mirus	Cat# MIR2304
Penicillin-Streptomycin	Gibco	Cat# 15140122
MEM, GlutaMAX™ Supplement	Gibco	Cat# 41090036
MEM Non-Essential Amino Acids Solution	Gibco	Cat# 11140050
2-Mercaptoethanol	Gibco	Cat# 21985023
Novolink Max Polymer detection system	Leica Biosystems	Cat# RE7280-CE
Mayer’s Hematoxylin	Electron Microscopy Sciences	Cat# 26043-06
Permount	Thermo Fisher Scientific	Cat# SP15-100
cOmplete protease inhibitor	Sigma-Aldrich	Cat# 11697498001
RNase A	Qiagen	Cat# 19101
Poly-Prep chromatography columns	Bio-Rad	Cat# 7311550
Ni-NTA Superflow	Qiagen	Cat# 30410
Doxycycline rodent diet (625 mg/kg)	Harlan-Teklad	Cat# TD.01306
Uracil-DNA glycosylase	New England Biolabs	Cat# M0280L
Eosin Y disodium salt	Sigma-Aldrich	Cat# E6003-25G
Nigrosin	Sigma-Aldrich	Cat# 198285-25G
Human chorionic gonadotropin	Sigma-Aldrich	Cat# CG10
CARD MEDIUM set (includes FERTIUP)	CosmoBioUSA	Cat# KYD-005-EX
CARD HyperOva	CosmoBioUSA	Cat# KYD-010-EX-X5
Mineral oil	Sigma-Aldrich	Cat# M5310
BSA (Fraction V, fatty acid-free) embryo tested lot	Sigma-Aldrich	Cat# A3311
Sodium lactate (60% w/w)	Sigma-Aldrich	Cat# L7900
Glucose (D+)	Sigma-Aldrich	Cat# P4562
Penicillin G	Sigma-Aldrich	Cat# P7794
Streptomycin	Sigma-Aldrich	Cat# S1277
MluI-HF	New England Biolabs	Cat# R3198S
Phusion high fidelity DNA polymerase	New England Biolabs	Cat# M0530S
APOBEC3A-MycHis	Stenglein et al.⁶²	N/A

Critical commercial assays

RNeasy Mini Kit	Qiagen	Cat# 74104
Qiashredder	Qiagen	Cat# 79654
DNeasy Blood & Tissue Kit	Qiagen	Cat# 69506
Bradford Protein Assay	Bio-Rad	Cat# 5000001

Deposited data

WGS data	This paper	Sequence Read Archive # PRJNA927047
RNA-seq data	This paper	Sequence Read Archive # PRJNA927047

Experimental models: Cell lines

293T	American Type Culture Collection	Cat# CRL-3216 RRID: CVCL_0063
KH2 ES cells	Gifted by Dr. Sagrario Ortega	Beard et al.⁶³

Experimental models: Organisms/strains

Mouse: B6.C-Tg(CMV-cre)1Cgn/J	The Jackson Laboratory	Strain# 006054 RRID: IMSR_JAX:006054
Mouse: B6.Tg(MMTV-cre)4Mam/J	The Jackson Laboratory	Strain# 003553 RRID: IMSR_JAX:003553
Mouse: B6.Rosa26::LSL-A3Bi	Boumelha et al.¹⁵	N/A
Mouse: B6.Rosa26::CAG-LSL-A3Bi	This paper	Donated to Jackson Laboratory: Strain# 038176
Mouse: B6.Rosa26::CAG-LSL-A3Bi-E255A	This paper	Donated to Jackson Laboratory: Strain# 038177
Mouse: B6.Cg-Gt(ROSA)26Sor^{tm1(rtTA∗M2)Jae}/J	The Jackson Laboratory	Strain# 006965 RRIS: IMSR_JAX:006965
Mouse: B6.Col1a1::TetO-A3B-tGFP	This paper and de la Vega et al.²⁰	N/A

Oligonucleotides

Table S3	Integrated DNA Technologies	N/A

Recombinant DNA

Col1a1::TetO-A3B-tGFP	This paper and de la Vega et al.²⁰	N/A
R26::CAG-LSL-A3Bi	This study	N/A
R26::LSL-A3Bi	Boumelha et al.¹⁵	N/A
R26::CAG-LSL-A3Bi-E255A	This paper	N/A
pcDNA3.1-A3Ai-Myc-His	Stenglein et al.⁶²	N/A
pAi38	Addgene	RRID: Addgene_34883
pEGFP-N3-A3Bi-E255A	This paper	N/A

Software and algorithms

SAS v9.4	SAS Institute	https://www.sas.com/en_us/software/stat.html
GraphPad Prism v9.4	GraphPad software	http://www.graphpad.com
QuPath v0.4.2	Bankhead et al.⁶⁴	https://qupath.github.io
NIS Elements v4.11.0	NIS-Elements Viewer software	https://www.microscope.healthcare.nikon.com/products/software/nis-elements/viewer
STAR/2.7.10a	Dobin et al.⁶⁵	https://github.com/alexdobin/STAR/releases
Picard tools v2.18.16	Broad Institute	https://broadinstitute.github.io/picard/
TRUST4 v1.0.8	Song et al.⁶⁶	https://github.com/liulab-dfci/TRUST4
HISAT2	Kim et al.⁶⁷	https://github.com/DaehwanKimLab/hisat2
Cufflinks	Trapnell et al.⁶⁸	https://github.com/cole-trapnell-lab/cufflinks
deconstructSigs v1.8.0	Rosenthal et al.⁶⁹	https://github.com/raerose01/deconstructSigs
Trimmomatic v0.33	Bolger et al.⁷⁰	https://github.com/timflutre/trimmomatic
SpeedSeq v0.1.2	Chiang et al.⁷¹	https://github.com/hall-lab/speedseq
GATK3 v3.6.0	Broad Institute	https://gatk.broadinstitute.org/hc/en-us
MutationalPatterns v3.17	Blokzijl et al.⁷²	https://github.com/ToolsVanBox/MutationalPatterns
SigProfilerTopography v.1.0.70	SigProfiler Bioinformatic Tools	https://github.com/AlexandrovLab/SigProfilerTopography
lsa v0.73.3	CRAN R Project for Statistical Computing	https://CRAN.R-project.org/package=lsa
Pyclone-VI v0.1.1	Gillis et al.³⁵	https://github.com/Roth-Lab/pyclone-vi
CNVKit v0.9.10	Talevich et al.⁷³	https://github.com/etal/cnvkit
Manta v1.6.0	Chen et al.⁷⁴	https://github.com/Illumina/manta

Other

Typhoon FLA-7000 Image Reader	GE Life Sciences	N/A
Odyssey Fc	Li-COR	N/A
Odyssey Classic	Li-COR	N/A
NovaSeq 6000	Illumina	N/A
Aperio AT2	Aperio	N/A
Reichert-Jung BioCut 2030 Rotary Microtome	Leica	N/A
Huron TissueScope LE	Huron Digital Pathology	N/A
C2 DS-Ri1	Nikon	N/A
MC170 HD	Leica	N/A
DM IRE2	Leica	N/A
Branson 450 Analog Sonifier	Branson	N/A