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 CatCLHLA-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
Control: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 CatCLHLA-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
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 CatCLHLA-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
Modification: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 CatCLHLA-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
Western Blot: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 CatCLHLA-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
Membrane: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 CatCLHLA-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
Enzyme-linked Immunospot: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 CatCLHLA-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
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