| Antibodies |
| CD172a (SIRPa)-FITC, human |
Miltenyi Biotec Inc |
130-099-896 |
| REA Control-FITC |
Miltenyi Biotec Inc |
130-113-449 |
| Anti-SIRPα antibody |
Abcam |
ab8120 |
| hFAB Rhodamine anti-GAPDH Primary Antibody |
Bio-Rad Laboratories |
12004168 |
| hFAB™ Rhodamine anti-Actin Primary Antibody |
Bio-Rad Laboratories |
12004163 |
| Brilliant Violet 510™ anti-mouse CD172a (SIRPα) |
Biolegend |
144032; RRID: AB_2810411 |
| Brilliant Violet 510™ Rat IgG1, κ Isotype Ctrl Antibody |
Biolegend |
400435 |
| InVivoPlus rat IgG2b isotype control, anti-keyhole limpet hemocyanin |
Biolegend |
BP0090; RRID: AB_1107780 |
| InVivoPlus anti-mouse PD-L1 (B7-H1) |
Bioxcell |
BP0101; RRID: AB_10949073 |
| InVivoPlus anti-mouse/human/rat CD47 (IAP) |
Bioxcell |
MIAP410; RRID: AB_2687806 |
| InVivoMAb mouse IgG1 isotype control, |
Bioxcell |
MOPC-21;RRID: AB_1107784 |
| Anti-CD47 mIAP430 |
Absolute Antibdody |
AB00738-7.1 |
| Bacterial and virus strains |
| Endura™ Chemically Competent Cells |
Lucigen |
60240-2 |
| Chemicals, peptides, or recombinant proteins |
| jetPRIME® Versatile DNA/siRNA transfection reagent(0.75ml) |
Polyplus |
114-07 |
| A 33 mm diameter sterile syringe filter with a 0.45 μm pore size hydrophilic PVDF membrane |
EMD Millipore Corp |
SLHV033RS |
| Recombinant Mouse IL-2 Protein |
R&D System,lnc |
402-ML |
| RIPA Lysis and Extraction Buffer |
Thermo Fisher |
89901 |
| Western Lightning® Plus-ECL, Enhanced Chemiluminescence Substrate |
PerkinElmer Inc. |
NEL103001EA |
| Pierce BCA Protein Assay Kit |
Thermo Fisher |
23227 |
| RPMI 1640 |
Fisher Scientific |
MT10040CV |
| DMEM with L-Glutamine, 4.5g/L Glucose and Sodium Pyruvate |
Fisher Scientific |
10013CV |
| Penicillin-Streptomycin (10,000U/mL) |
Thermo Fisher |
15140122 |
| Trypsin-EDTA (0.05%), phenol red |
Thermo Fisher |
25300120 |
| InVivoPure pH 7.0 Dilution Buffer |
Bioxcell |
IP0070 |
| InVivoPure pH 6.5 Dilution Buffer |
Bioxcell |
IP0065 |
| GP100(25-33) |
ANASPEC |
AS-62589 |
| Critical commercial assays |
| EasySep™ Mouse CD8+ T Cell Isolation Kit |
Stemcell |
19853 |
| CountBright Absolute Counting Beads, for flow cytometry |
Thermo Fisher |
C36950 |
| Dynabeads™ Mouse T-Activator CD3/CD28 for T-Cell Expansion and Activation |
Thermo Fisher |
11456D |
| Deposited data |
| Immuno-oncology targets (Figure 1A) |
Immuno-Oncology Landscape, Cancer Research Institute (online published on Sep 18, 2020) |
https://www.cancerresearch.org/scientists/immuno-oncology-landscape
|
| Bulk proteomics data from anti-PD-1-treatment-responding and non-responding melanoma patients (Figure 1A–C, E) |
Harel et al., 2019
|
https://www.sciencedirect.com/science/article/pii/S0092867419309006
|
| Bulk RNA-seq data from anti-PD-1-treatment-responding and non-responding melanoma patients (Figure 1A–D; Figure 2I; Figure S6A) |
Hugo et al., 2016
|
GEO: GSE78220
|
| Bulk RNA-seq data from anti-PD-1-treatment-responding and non-responding melanoma patients (Figure 1A–D) |
Gide et al., 2019
|
ENA: PRJEB23709 |
| Bulk RNA-seq data from anti-PD-1-treatment-responding and non-responding melanoma patients (Figure 1A–D) |
Riaz et al., 2017
|
GEO: GSE91061
|
| Bulk RNA-seq data from anti-PD-1-treatment-responding and non-responding melanoma patients (Figure 1A–D) |
Liu et al., 2019
|
dbGaP: phs000452.v3.p1 |
| Bulk RNA-seq data from BRAFi-treatment-responding and non-responding melanoma patients (Figure S1A, B) |
Rizos et al., 2014 |
GEO: GSE50509
|
| Bulk RNA-seq data from BRAFi-treatment-responding and non-responding melanoma patients (Figure S1A, B) |
Kakavand et al., 2017 |
GEO: GSE99898
|
| Tumor mutation burden in melanoma patients (Figure S1C) |
Wang et al., 2019 |
https://elifesciences.org/articles/49020
|
| Survival data in TCGA melanoma patients (Figure S1D) |
The Cancer Genome Atlas (TCGA) |
https://gdc.cancer.gov/about-data/publications/pancanatlas
|
| Single-cell RNA-seq data from pre- and post-anti-PD-1-treatment melanoma patients (Figure 2A–C, J) |
Jerby-Arnon et al., 2018
|
GEO: GSE115978
|
| Single-cell RNA-seq data from treatment-naïve melanoma patients (Figure 2I; Figure 4B) |
Tirosh et al., 2016
|
GEO: GSE70630
|
| Single-cell RNA-seq data from metastatic melanoma patients (Figure 2D–F) |
Smalley et al., 2021
|
GEO: GSE174401
|
| Single-cell proteomics data from human melanoma and monocyte cell lines (Figure 2G, H) |
Leduc et al., 2022
|
https://scp.slavovlab.net/Leduc_et_al_2022
|
| Single-cell RNA-seq data from anti-PD-1-treatment-responding and -non-responding melanoma patients (Figure 2K) |
Sade-Feldman et al., 2018
|
GEO: GSE120575
|
| CCLE quantitative mass spectrometry data (Figure S2A; Figure 3E) |
Nusinow et al., 2020 |
https://www.sciencedirect.com/science/article/pii/S0092867419313856
|
| CCLE gene expression data (Figure S2B; Figure 3C) |
Cancer Cell Line Encyclopedia |
https://portals.broadinstitute.org/ccle
|
| SIRPα RPPA data in melanoma cell lines (Figure 3D) |
This study |
https://tcpaportal.org
|
| Bulk RNA-seq data of patient-derived melanoma cell lines (Figure 3A–C) |
Tsoi et al., 2018
|
GEO: GSE80829
|
| Bulk RNA-seq data of in vitro differentiating melanocytes derived from ESC/iPSC (Figure 3F, G) |
Mica et al., 2013
|
GEO: GSE45227
|
| Single-cell RNA-seq data from human normal skin samples of different developmental stages (Figure 3H–J; Figure S3C) |
Belote et al., 2020 |
GEO: GSE151091
|
| Single-cell RNA-seq data from stepwise-edited melanoma cell lines (Figure S3A, B) |
Hodis et al., 2022
|
Single Cell Portal: SCP1334 |
| Spatial transcriptomics data from treatment-naïve melanoma patients (Figure 4A) |
Thrane et al., 2018
|
http://www.spatialomics.org/SpatialDB/download.php
|
| DICE immune cell type gene expression data (Figure S4A, B) |
Schmiedel et al., 2018 |
https://dice-database.org
|
| Bulk proteomics data from human hematopoietic cell populations sorted from peripheral blood (Figure S4C, D) |
Rieckmann et al., 2017 |
http://www.immprot.org
|
| Bulk RNA-seq data of B16F10 cells with SIRPA perturbations |
This study |
GEO: GSE211226
|
| SIRPα RPPA data in TCGA-SKCM samples (Figure 6A–C; Figure S6B) |
This study |
https://tcpaportal.org
|
| TCGA-SKCM RNA-seq data (bam files; Figure 3K; Figure 6D–F; Figure S6B) |
The Cancer Genome Atlas (TCGA) |
https://tcga-data.nci.nih.gov/docs/publications/tcga
|
| Processed TCGA SCNA data (Figure 6A, B) |
The Cancer Genome Atlas (TCGA) |
Synapse: syn5049520.1 |
| Processed TCGA DNA methylation, mutation, and miRNA expression data (Figure 6A, C–G) |
The Cancer Genome Atlas (TCGA) |
https://gdc.cancer.gov/about-data/publications/pancanatlas
|
| Whole-exome sequencing data from anti-PD-1-treatment-responding and non-responding melanoma patients (Figure S6A) |
Hugo et al., 2016
|
SRA: SRP090294 and SRP067938 |
| Experimental models: Cell lines |
| HEK293T |
MD Anderson Characterized Cell Line Core Facility |
HEK293T |
| A375 |
MD Anderson Characterized Cell Line Core Facility |
A375M |
| A375-dCas9-SAM |
This study |
N/A |
| B16F10 |
ATCC |
CRL-6475 |
| Experimental models: Organisms/strains |
| Mouse:B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J |
The Jackson Laboratory |
JAX:005023; RRID:IMSR_JAX:005023 |
| Mouse:C57BL/6J |
The Jackson Laboratory |
JAX:000664; RRID:IMSR_JAX:005023 |
| Oligonucleotides |
| Scramble gRNA-F: 5’-CACCGGTATTACTGATATTGGTGGG-3’ |
This study |
N/A |
| Scrambel gRNA-R: 5’-AAACCCCACCAATATCAGTAATACC-3’ |
This study |
N/A |
|
SIRPAP1-1-F: 5’-CACCGGTAGGGTCGCGAGACGGATG -3’ |
This study |
N/A |
|
SIRPAP1-1-R: 5’-AAACCATCCGTCTCGCGACCCTACC-3’ |
This study |
N/A |
| Recombinant DNA |
| pCMV-VSV-G |
Addgene |
8454; RRID:Addgene_8454 |
| pCMV-dR8.2 dvpr |
Addgene |
8455; RRID:Addgene_8455 |
| lenti sgRNA(MS2)_zeo backbone |
Addgene |
61427; RRID:Addgene_61427 |
| lenti dCAS-VP64_Blast |
Addgene |
61425; RRID:Addgene_61425 |
| lentiMPH v2 |
Addgene |
89308; RRID:Addgene_89308 |
| plenti-CMV-Puro-Dest |
Addgene |
17452; RRID:Addgene_17452 |
| pDONR221-Human SIRPAP1 |
Epoch Life Science |
GS65919 |
| pDONR221-Mouse SIRPA |
Epoch Life Science |
GS68006 |
| plenti-CMV-Puro-Human SIRPAP1 |
This study |
N/A |
| plenti-CMV-Puro-Mouse SIRPA |
This study |
N/A |
| MISSION® pLKO.1-puro Non-Target shRNA Control Plasmid DNA |
Sigma-Aldrich |
SHC016-1EA |
| SHCLNG MISSION shRNA-1 |
Sigma-Aldrich |
TRCN0000029914 |
| SHCLNG MISSION shRNA-2 |
Sigma-Aldrich |
TRCN0000055053 |
| SHCLNG MISSION shRNA-3 |
Sigma-Aldrich |
TRCN0000029915 |
| SHCLNG MISSION shRNA-4 |
Sigma-Aldrich |
TRCN0000029916 |
| SHCLNG MISSION shRNA-5 |
Sigma-Aldrich |
TRCN0000029917 |
| Software and Algorithms |
| FlowJo10.0.7 |
FlowJo LLC |
https://www.flowjo.com; RRID:SCR_008520 |
| Salmon v1.4.0 |
Patro et al., 2017 |
https://combine-lab.github.io/salmon/
|
| Subread v2.0.1 |
Liao et al., 2014 |
http://subread.sourceforge.net/; RRID:SCR_009803 |
| CIBERSORTx |
Newman et al., 2019
|
https://cibersortx.stanford.edu/index.php
|
| GSVA |
Hanzelmann et al., 2013 |
https://pypi.org/project/GSVA/; RRID:SCR_021058 |
| RNAhybrid |
Krüger et al., 2006 |
https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid; RRID:SCR_003252 |
| miRDB |
Chen et al., 2020 |
http://www.mirdb.org/; RRID:SCR_010848 |
| TarPmiR |
Ding et al., 2016
|
http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/
|
| CellPhoneDB |
Efremova et al., 2020
|
https://www.cellphonedb.org/; RRID:SCR_017054 |
| Scanpy |
Wolf et al., 2018
|
https://scanpy.readthedocs.io/en/stable/; RRID:SCR_018139 |
| tSNE |
van der Maaten and Hinton, 2008 |
https://github.com/DmitryUlyanov/Multicore-TSNE
|
| Python v3.6 |
Python, 2015 |
https://python.org; RRID:SCR_008394 |
| R v3.6 |
The R Foundation |
https://www.r-project.org; RRID:SCR_001905 |
| Prism 6 |
GraphPad |
https://www.graphpad.com/scientific-software/prism/; RRID:SCR_002798 |
| BioRender |
BioRender |
https://app.biorender.com/; RRID:SCR_018361 |
