Recombinant:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
Magnetic Beads:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
Protease Inhibitor:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
Cell Isolation:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
RNA sequencing:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
cDNA Synthesis:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
Quantitative RT-PCR:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
Polymerase Chain Reaction:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
Flow Cytometry:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
Purification:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
Chromatin Immunoprecipitation:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER MCF7 ATCC Cat#HTB-22 MDAMB231 ATCC Cat#HTB-26 BT474 ATCC Cat#HTB-20 SKBR3 ATCC Cat#HTB-30 BT20 ATCC Cat#HTB-19 HCC70 ATCC Cat#CRL-2315 HEK293T In house stock N/A Oligonucleotides Oligonucleotides used for RT-qPCR have been added as a supplemenrtal document and can be found in Data S1 N/A N/A Recombinant DNA pCMV-HA-hRB-wt Narasimha et al. 61 obtained via Addgene Plasmid #58905 pCMV-HA-hRb-deltaCDK Narasimha et al. 61 obtained via Addgene Plasmid #58906 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000010419 MISSION pLKO.1-puro shRNA against human RB1Plasmid Sigma-Aldrich ID:TRCN0000040163 MISSION® pLKO.1-puro Non-Mammalian shRNA Control Plasmid DNA Sigma-Aldrich ID:SHC002 Software and algorithms DeepLC Bouwmeester et al. 103 https://compomics.github.io/ projects/DeepLC BamQuery Ruiz Cuevas et al. 41 https://github.com/lemieux-lab/BamQuery BD FACSDiva TM software (v.8.0.2) BD Biosciences https://www.bdbiosciences.com COMET version 2020.01 Eng et al. 103 https://uwpr.github.io/Comet/ DeepHLApan Wu et al. 56 https://github.com/jiujiezz/deephlapan DeepImmuno Li et al. 57 https://deepimmuno.research.cchmc.org/ Deeptools (v3.5.1) Ramirez et al. 104 https://github.com/deeptools/deepTools DESeq2 package Love et al. 105 https://bioconductor.org/packages/ devel/bioc/html/DESeq2.html AID EliSpot v8.0 software AID GmbH Germany https://www.aid-diagnostika.com/ Fgsea Korotkevich et al. 106 https://github.com/alserglab/fgsea FlowJo (v10) BD Biosciences https://www.flowjo.com/ Freebayes (v1.0.2) Garrison et al. 107 https://github.com/freebayes/freebayes ggplot2 Wickham et al. 108 https://ggplot2.tidyverse.org/ ggpubr Kassambara et al. 109 https://github.com/kassambara/ggpubr GSEA (v4.2.3) Mootha et al. 110 https://www.gsea-msigdb. org/gsea/index.jsp ImageLab software (v6.1.0) Bio-Rad https://www.bio-rad.com/ Inkscape (v.1.3.2) Inkscape https://inkscape.org Jellyfish (v2.2.377) Març ais et al. 111 https://github.com/gmarcais/Jellyfish Jupyterlab notebook (v4.2.5) Project Jupyter https://jupyter.org/install Kallisto (v0.43.0) Bray et al. 112 https://github.com/pachterlab/kallisto MAPDP Courcelles et al. 113 https://gitlab.com/iric-proteo/mapdp Matplotlib (v3.9.2) Hunter et al. 114 https://matplotlib.org/ Msigdbr Dolgalev et al. 115 https://igordot.github.io/msigdbr/ NEKTAR Audemard et al. 116 https://github.com/iric-soft/nektar NetMHCpan-4.1b Reynisson et al. 117 https://services.healthtech. dtu.dk/NetMHCpan-4.1/ (Continued on next page) 22 Cell Reports 44, 116676, December 23, 2025
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