| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Antibodies used for mass cytometry | ||
| AKT (C67E7) - purified | Cell Signaling Technologies | Cat# 4691; RRID:AB_915783 |
| Anti-rabbit IgG (polyclonal) - purified | Vector Labs | Cat# AI-1000; RRID:AB_2336193 |
| AR (D6F11) - purified | Cell Signaling Technologies | Cat# 5153; RRID:AB_10692774 |
| BCL-2 (100) - purified | Biolegend | Cat# 658702; RRID:AB_2562959 |
| c-MET (D1C2) - purified | Cell Signaling Technologies | Cat# 8198; RRID:AB_10860590 |
| c-MYC (D84C12) - purified | Cell Signaling Technologies | Cat# 5605; RRID:AB_1903938 |
| CA9 (polyclonal) - purified | R&D Systems | Cat# AF2188; RRID:AB_416562 |
| CD11b (M1/70) - purified | Biolegend | Cat# 101202; RRID:AB_312785 |
| CD11c (Bu15) - purified | Biolegend | Cat# 337221; RRID:AB_2562834 |
| CD123 (6H6) - purified | Biolegend | Cat# 306002; RRID:AB_314576 |
| CD14 (RMO52) - purified | Beckman Coulter | Cat# A22331; RRID:AB_10639528 |
| CD15 (HI98) - purified | Biolegend | Cat# 301902; RRID:AB_314194 |
| CD16 (3G8) - purified | Biolegend | Cat# 302002; RRID:AB_314202 |
| CD163 (GHI/61) - purified | Biolegend | Cat# 333602; RRID:AB_1088991 |
| CD169 (7-239) - purified | Biolegend | Cat# 346002; RRID:AB_2189031 |
| CD192/CCR2 (K036C2) - purified | Biolegend | Cat# 357202; RRID:AB_2561851 |
| CD197/CCR7 (G043H7) - purified | Biolegend | Cat# 353202; RRID:AB_10945157 |
| CD20 (H1(FB1)) - purified | BD Biosciences | Cat# 555677; RRID:AB_396030 |
| CD204 (351615) - purified | R&D Systems | Cat# MAB2708; RRID:AB_2235696 |
| CD206 (15-2) - purified | Biolegend | Cat# 321112; RRID:AB_571921 |
| CD24 (ML5) - purified | BD Biosciences | Cat# 555426; RRID:AB_395820 |
| CD25 (M-A251) - purified | Biolegend | Cat# 356102; RRID:AB_2561752 |
| CD274/PD-L1 (E1L3N) - purified | Cell Signaling Technologies | Cat# 13684; RRID:AB_2687655 |
| CD278/ICOS (C398.4A) - purified | Biolegend | Cat# 313502; RRID:AB_416326 |
| CD279/PD-1 (EH12.2H7) - purified | Biolegend | Cat# 329902; RRID:AB_940488 |
| CD3 (UCHT1) - purified | Biolegend | Cat# 300402; RRID:AB_314056 |
| CD31 (HC1/6) - purified | EMD Millipore | Cat# CBL468-K; RRID:AB_1586934 |
| CD32 (FUN-2) - purified | Biolegend | Cat# 303202; RRID:AB_314334 |
| CD36 (5-271) - purified | Biolegend | Cat# 336215; RRID:AB_2563745 |
| CD38 (HIT2) - purified | Biolegend | Cat# 303502; RRID:AB_314354 |
| CD4 (RPA-T4) - purified | Biolegend | Cat# 300516; RRID:AB_314084 |
| CD44 (IM7) - purified | BD Biosciences | Cat# 550538; RRID:AB_393732 |
| CD45 (HI30) - purified | Biolegend | Cat# 304002; RRID:AB_314390 |
| CD45RA (HI100) - purified | Biolegend | Cat# 304102; RRID:AB_314406 |
| CD49f (GoH3) - purified | Biolegend | Cat# 313614; RRID:AB_893371 |
| CD64 (10.1) - purified | Biolegend | Cat# 305002; RRID:AB_314486 |
| CD68 (KP1) - purified | Biolegend | Cat# 916104; RRID:AB_2616797 |
| CD68 (Y1/82A) - purified | Biolegend | Cat# 333802; RRID:AB_1089058 |
| CD7 (M-T701) - purified | BD Biosciences | Cat# 555359; RRID:AB_395762 |
| CD86 (233(FUN-1)) - purified | BD Biosciences | Cat# 555655; RRID:AB_396010 |
| CD8a (RPA-T8) - purified | Biolegend | Cat# 301002; RRID:AB_314120 |
| CD93 (R139) - purified | eBioscience | Cat# 14-0939-82; RRID:AB_891508 |
| Cleaved CASPASE-3 (C92-605) - purified | BD Biosciences | Cat# 559565; RRID:AB_397274 |
| Cleaved PARP-1 (F21-852) - purified | BD Biosciences | Cat# 552596; RRID:AB_394437 |
| CTLA-4 (L3D10) - purified | Biolegend | Cat# 349902; RRID:AB_10642827 |
| Cyclin B1 (GNS-11) - purified | BD Biosciences | Cat# 554179; RRID:AB_395290 |
| E-CADHERIN (24E10) - purified | Cell Signaling Technologies | Cat# 3195; RRID:AB_10694492 |
| E-CADHERIN (67A4) - purified | Biolegend | Cat# 324102; RRID:AB_756064 |
| EGFR (EP38Y) - purified | Abcam | Cat# ab52894; RRID:AB_869579 |
| EpCAM (9C4) - purified | Biolegend | Cat# 324202; RRID:AB_756076 |
| ERα (EP1) - purified | Epitomics | Cat# AC-0015; RRID:AB_10704040 |
| EZH2 (D2C9) - purified | Cell Signaling Technologies | Cat# 5246; RRID:AB_10694683 |
| FAP (polyclonal) - purified | R&D Systems | Cat# AF3715; RRID:AB_2102369 |
| FOXP3 (236A/E7) - purified | ThermoFisher | Cat# 14-4777-82; RRID:AB_467556 |
| H3K27me3 (C36B11) - purified | Cell Signaling Technologies | Cat# 9733; RRID:AB_2616029 |
| HER2 (3B5) - purified | BD Biosciences | Cat# 554299; RRID:AB_395352 |
| HLA-DR (L243) - purified | Biolegend | Cat# 307602; RRID:AB_314680 |
| K14 (polyclonal) - purified | ThermoFisher | Cat# PA5-16722; RRID:AB_10980222 |
| K5 (EP1601Y) - purified | Abcam | Cat# ab52635; RRID:AB_869890 |
| K7 (RCK105) - purified | BD Biosciences | Cat# 550507; RRID:AB_2134456 |
| K8/18 (C51) - purified | Cell Signaling Technologies | Cat# 4546; RRID:AB_2134843 |
| Ki-67 (8D5) - purified | Cell Signaling Technologies | Cat# 9449; RRID:AB_2715512 |
| P53 (EPR17343) - purified | Abcam | Cat# ab179477; RRID:AB_2737134 |
| Pan Keratin (AE1) - purified | EMD Millipore | Cat# MAB1612; RRID:AB_2132794 |
| Pan Keratin (AE3) - purified | EMD Millipore | Cat# MAB1611; RRID:AB_2134409 |
| PRB (YR85) - purified | Abcam | Cat# ab32085; RRID:AB_777452 |
| PTEN (138G6) - purified | Cell Signaling Technologies | Cat# 9559; RRID:AB_390810 |
| SLAMF7 (162.1) - purified | Biolegend | Cat# 331802; RRID:AB_961330 |
| SMA (1A4) - purified | Abcam | Cat# ab8207; RRID:AB_306356 |
| SURVIVIN (71G4B7) - purified | Cell Signaling Technologies | Cat# 2808; RRID:AB_10691694 |
| TIM-3 (F38-2E2) - purified | Biolegend | Cat# 345035; RRID:AB_2566086 |
| VIMENTIN (EPR3776) - purified | Abcam | Cat# ab92547; RRID:AB_10562134 |
| Antibodies used for immunofluorescence | ||
| CD3e (LN10) | Leica | Cat# NCL-L-CD3-565; RRID:AB_563541 |
| CD68 (KP1) | eBioscience/ThermoFisher | Cat# 14-0688-82; RRID:AB_11151139 |
| CTLA-4 (BSB-88) | BIOSB | Cat# BSB2884; RRID:AB_2762365 |
| PD-1 (D4W2J) | Cell Signaling Technologies | Cat# 86163S; RRID:AB_2728833 |
| PD-L1 (E1L3N) | Cell Signaling Technologies | Cat# 13684S; RRID:AB_2687655 |
| Pan Keratin (h-240) | Santa Cruz | Cat# sc-15367; RRID:AB_2134438 |
| EpCAM (EPR20532-225) | Abcam | Cat# ab223582; RRID:AB_2762366 |
| Anti-mouse IgG (min X reactivity), HRP-conjugated (polyclonal) | JacksonImmunoReseach | Cat# 715-035-151; RRID:AB_2340771 |
| Anti-rabbit IgG (min X reactivity), HRP-conjugated (polyclonal) | JacksonImmunoReseach | Cat# 711-035-152; RRID:AB_10015282 |
| Anti-goat IgG (min X reactivity), HRP-conjugated (polyclonal) | JacksonImmunoReseach | Cat# 705-035-147; RRID:AB_2313587 |
| Biological Samples | ||
| Breast cancer and adjacent non-tumor tissue samples | University Hospital Basel, University Hospital Zurich, Patient’s Tumor Bank of Hope (PATH), St. Johannes Hospital Dortmund and Institute of Pathology at Josefshaus, University Hospital Giessen and Marburg, Marburg site | |
| Reduction mammoplasty samples | University Hospital Zurich | |
| Peripheral blood mononuclear cells (PBMCs) | Zurich Blood Transfusion Service | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 4′,6 diamidine-2-phenylindole (DAPI) | ThermoFischer | Cat# D1306 |
| Antibody Stabilizer PBS | Candor Bioscience | Cat# 131 050 |
| Bis(2,2′-bipyridine)-4′-methyl-4-carboxybipyridine-ruthenium-N-succidimyl ester-bis(hexafluorophosphate) (96Ru, 98-102Ru, 104Ru) | Sigma Aldrich | Cat# 96631 |
| Bismuth trichloride (209Bi) | Sigma Aldrich | Cat# 450723 |
| Bromoacetamidobenzyl-EDTA (BABE) | Dojindo Laboratories | Cat# B437-10 |
| Cisplatin | Fluidigm | Cat# 201064 |
| DMSO | Sigma Aldrich | Cat# D2438 |
| EDTA | StemCell Technologies, Inc. | Cat# EDS-100G |
| EQ™ Four Element Calibration Beads | Fluidigm | Cat# 201078 |
| FcR Blocking Reagent, human | Miltenyi Biotech | Cat# 130-059-901 |
| Indium (113In, 115In) | Fluidigm | N/A |
| Iridium (191Ir, 193Ir) | Fluidigm | Cat# 201192A |
| Lanthanide (III) metal isotopes as chloride salts | Fluidigm | N/A |
| MACS Tissue Storage Solution | Miltenyi Biotech | Cat# 130-100-008 |
| Magne Protein A Beads | Promega | Cat# G8781 |
| Magne Protein G Beads | Promega | Cat# G7471 |
| Maleimido-mono-amide-DOTA (mDOTA) | Macrocyclics | Cat# B-272 |
| Palladium (105Pd, 106Pd, 108Pd, 110Pd) | Fluidigm | N/A |
| Paraformaldehyde | Electron Microscopy Sciences | Cat# 15710 |
| ProLong® Diamond Antifade Mountant | Thermo Fisher | Cat# P36961 |
| Rhodium trichloride (103Rh) | Sigma Aldrich | Cat# 450286 |
| Saponin | Sigma Aldrich | Cat# S7900 |
| Trilogy 20x Concentrate | CellMarque | Cat# 920P-06 |
| Yttrium (89Y) | Sigma Aldrich | N/A |
| Critical Commercial Assays | ||
| Opal 7-Color IHC Kit | PerkinElmer | Cat# NEL821001KT |
| Tumor Dissociation Kit, human | Miltenyi Biotech | Cat# 130-095-929 |
| Maxpar X8 Multimetal Labeling Kit | Fluidigm | Cat# 201300 |
| Deposited Data | ||
| Mass cytometry data | This paper | Mendeley Data https://doi.org/10.17632/gb83sywsjc.1 |
| Immunofluorescence images | This paper | Mendeley Data https://doi.org/10.17632/gb83sywsjc.1 |
| Experimental Models: Cell Lines | ||
| MCF-10A | American Type Culture Collection (ATCC) | Cat# CRL-10317 |
| MDA-MB-134-VI | American Type Culture Collection (ATCC) | Cat# HTB-23 |
| MDA-MB-231 | American Type Culture Collection (ATCC) | Cat# HTB-26 |
| MDA-MB-453 | American Type Culture Collection (ATCC) | Cat# HTB-131 |
| SK-BR-3 | American Type Culture Collection (ATCC) | Cat# HTB-30 |
| ZR-75-1 | American Type Culture Collection (ATCC) | Cat# CRL-1500 |
| Fibroblasts | Gift from the laboratory of Prof. Silvio Hemmi at the University of Zurich | |
| Software and Algorithms | ||
| CATALYST | Chevrier et al., 2018 | http://bioconductor.org/packages/release/bioc/html/CATALYST.html |
| circlize (R package) version 0.4.4 | Gu et al., 2014 | https://github.com/jokergoo/circlize |
| Concatenation tool | Cytobank, Inc | https://support.cytobank.org/hc/en-us/articles/206336147-FCS-file-concatenation-tool |
| Cytobank | Kotecha et al., 2010 | https://www.cytobank.org/ |
| Fiji | Schindelin et al., 2012 | https://imagej.net/Welcome |
| InForm Cell Analysis | PerkinElmer | http://www.perkinelmer.com |
| MATLAB R2018a Neural Network Toolbox | MathWorks, Inc., 2018 | https://www.mathworks.com/ |
| Normalizer | Finck et al., 2013 | https://github.com/nolanlab/bead-normalization/releases |
| PhenoGraph | Levine et al., 2015 | https://github.com/jacoblevine/PhenoGraph |
| Python | Python Software | https://www.python.org/ |
| R 3.4.1 | R Core Team, 2016 | https://www.R-project.org |
| t-SNE | Van Der Maaten and Hinton, 2008 | https://github.com/jkrijthe/Rtsne |
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