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KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.

Cancer cell | 2018

Members of the KDM5 histone H3 lysine 4 demethylase family are associated with therapeutic resistance, including endocrine resistance in breast cancer, but the underlying mechanism is poorly defined. Here we show that genetic deletion of KDM5A/B or inhibition of KDM5 activity increases sensitivity to anti-estrogens by modulating estrogen receptor (ER) signaling and by decreasing cellular transcriptomic heterogeneity. Higher KDM5B expression levels are associated with higher transcriptomic heterogeneity and poor prognosis in ER+ breast tumors. Single-cell RNA sequencing, cellular barcoding, and mathematical modeling demonstrate that endocrine resistance is due to selection for pre-existing genetically distinct cells, while KDM5 inhibitor resistance is acquired. Our findings highlight the importance of cellular phenotypic heterogeneity in therapeutic resistance and identify KDM5A/B as key regulators of this process.

Pubmed ID: 30472020 RIS Download

Research resources used in this publication

Additional research tools detected in this publication

Antibodies used in this publication

Associated grants

  • Agency: NCI NIH HHS, United States
    Id: R35 CA197623
  • Agency: NCI NIH HHS, United States
    Id: P01 CA080111
  • Agency: NCI NIH HHS, United States
    Id: R01 CA202634
  • Agency: NHGRI NIH HHS, United States
    Id: U54 HG008097
  • Agency: NCI NIH HHS, United States
    Id: U54 CA193461

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This is a list of tools and resources that we have found mentioned in this publication.


ATCC (tool)

RRID:SCR_001672

Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.

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Genentech (tool)

RRID:SCR_003997

A biotechnology corporation that uses human genetic information to discover, develop, manufacture and commercialize medicines to treat patients with serious or life-threatening medical conditions.

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Picard (tool)

RRID:SCR_006525

Java toolset for working with next generation sequencing data in the BAM format.

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H3K27ac-human (antibody)

RRID:AB_2118291

This polyclonal targets H3K27ac

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Cdk4 (antibody)

RRID:AB_397299

This monoclonal targets Cdk4

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H3-celegans (antibody)

RRID:AB_302613

This polyclonal targets H3

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c-erbB-2 (antibody)

RRID:AB_395352

This monoclonal targets c-erbB-2

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Cyclin A (antibody)

RRID:AB_395286

This monoclonal targets Cyclin A

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H3K27me2-dmelanogaster (antibody)

RRID:AB_448222

This polyclonal targets H3K27me2

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p63 antibody [EPR5701] (antibody)

RRID:AB_10971840

This monoclonal targets p63 antibody [EPR5701]

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Purified anti-Cdc2 (p34) (antibody)

RRID:AB_2074779

This monoclonal targets cdc2 p34

View all literature mentions

Anti-KDM5B antibody produced in rabbit (antibody)

RRID:AB_1851987

This polyclonal targets KDM5B antibody produced in rabbit

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Anti-Histone H3 (tri methyl K4) antibody - ChIP Grade (antibody)

RRID:AB_306649

This polyclonal targets Histone H3 (tri methyl K4)

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Androgen Receptor (D6F11) XP Rabbit mAb (antibody)

RRID:AB_10691711

This monoclonal targets Androgen Receptor (D6F11) XP Rabbit mAb

View all literature mentions

EGF Receptor (D38B1) XP Rabbit mAb (antibody)

RRID:AB_2246311

This monoclonal targets EGF Receptor

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Histone H3 (di methyl K36) antibody - ChIP Grade (antibody)

RRID:AB_1280939

This polyclonal targets Histone H3 (di methyl K36) antibody - ChIP Grade

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Histone H3 (phospho S10) antibody - Mitosis Marker (antibody)

RRID:AB_304763

This polyclonal targets Histone H3 (phospho S10) antibody - Mitosis Marker

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Phospho-S6 Ribosomal Protein (Ser235/236) (D57.2.2E) XP Rabbit mAb (antibody)

RRID:AB_916156

This monoclonal targets Phospho-S6 Ribosomal Protein (Ser235/236) (D57.2.2E) XP Rabbit mAb

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Phospho-Stat3 (Tyr705) (D3A7) XP Rabbit mAb (antibody)

RRID:AB_2491009

This monoclonal targets Phospho-Stat3 (Tyr705)

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JARID1B Antibody (antibody)

RRID:AB_10004656

This unknown targets JARID1B

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CDK6 (D4S8S) Rabbit mAb (antibody)

RRID:AB_2721897

This monoclonal targets CDK6

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CD10 (antibody)

RRID:AB_395775

This monoclonal targets CD10

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SUZ12-human (antibody)

RRID:AB_2196850

This monoclonal targets SUZ12

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Estrogen Receptor α (D6R2W) Rabbit mAb #13258 (antibody)

RRID:AB_2632959

This monoclonal targets Estrogen Receptor alpha

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Keratin 8/18 (C51) Mouse mAb (antibody)

RRID:AB_2134843

This monoclonal targets Keratin 8/18

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Cyclin D3 antibody [DCS22] (antibody)

RRID:AB_2070798

This monoclonal targets CCND3

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Phospho-Estrogen Receptor alpha (Ser118) (16J4) Mouse mAb (antibody)

RRID:AB_331289

This monoclonal targets Phospho-Estrogen Receptor alpha (Ser118) (16J4) Mouse mAb

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H3K79me2-human (antibody)

RRID:AB_303937

This polyclonal targets H3K79me2

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Purified anti-human CD24 (antibody)

RRID:AB_314851

This monoclonal targets CD24

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Phospho-Akt (Ser473) (D9E) XP® Rabbit mAb (antibody)

RRID:AB_2315049

This monoclonal targets Phospho-Akt (Ser473)

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Histone H3 (tri methyl K4) antibody [mAbcam1012] - ChIP Grade (antibody)

RRID:AB_442796

This monoclonal targets Histone H3 (tri methyl K4) antibody [mAbcam1012] - ChIP Grade

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Histone H3 (tri methyl K27) antibody [mAbcam 6002] - ChIP Grade (antibody)

RRID:AB_305237

This monoclonal targets Histone H3 (tri methyl K27) antibody [mAbcam 6002] - ChIP Grade

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Vimentin (D21H3) XP Rabbit mAb (antibody)

RRID:AB_10695459

This monoclonal targets Vimentin

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E-Cadherin (24E10) Rabbit mAb (antibody)

RRID:AB_2291471

This monoclonal targets E-Cadherin (24E10) Rabbit mAb

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Cleaved Caspase-3 (Asp175) Antibody (antibody)

RRID:AB_2341188

This polyclonal targets Cleaved Caspase-3 (Asp175)

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Phospho-Smad2 (Ser465/467)/Smad3 (Ser423/425) (D27F4) Rabbit mAb (antibody)

RRID:AB_2631089

This monoclonal targets Phospho-Smad2 (Ser465/467)/Smad3 (Ser423/425)

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BT-474 (cell line)

RRID:CVCL_0179

Cell line BT-474 is a Cancer cell line with a species of origin Homo sapiens (Human)

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MDA-MB-231 (cell line)

RRID:CVCL_0062

Cell line MDA-MB-231 is a Cancer cell line with a species of origin Homo sapiens (Human)

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HCC2157 (cell line)

RRID:CVCL_1261

Cell line HCC2157 is a Cancer cell line with a species of origin Homo sapiens (Human)

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HCC1937 (cell line)

RRID:CVCL_0290

Cell line HCC1937 is a Cancer cell line with a species of origin Homo sapiens (Human)

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T-47D (cell line)

RRID:CVCL_0553

Cell line T-47D is a Cancer cell line with a species of origin Homo sapiens (Human)

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BT-549 (cell line)

RRID:CVCL_1092

Cell line BT-549 is a Cancer cell line with a species of origin Homo sapiens (Human)

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ZR-75-1 (cell line)

RRID:CVCL_0588

Cell line ZR-75-1 is a Cancer cell line with a species of origin Homo sapiens (Human)

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HCC2157 (cell line)

RRID:CVCL_1261

Cell line HCC2157 is a Cancer cell line with a species of origin Homo sapiens (Human)

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ZR-75-1 (cell line)

RRID:CVCL_0588

Cell line ZR-75-1 is a Cancer cell line with a species of origin Homo sapiens (Human)

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HCC1937 (cell line)

RRID:CVCL_0290

Cell line HCC1937 is a Cancer cell line with a species of origin Homo sapiens (Human)

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T-47D (cell line)

RRID:CVCL_0553

Cell line T-47D is a Cancer cell line with a species of origin Homo sapiens (Human)

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BT-549 (cell line)

RRID:CVCL_1092

Cell line BT-549 is a Cancer cell line with a species of origin Homo sapiens (Human)

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MDA-MB-231 (cell line)

RRID:CVCL_0062

Cell line MDA-MB-231 is a Cancer cell line with a species of origin Homo sapiens (Human)

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BT-474 (cell line)

RRID:CVCL_0179

Cell line BT-474 is a Cancer cell line with a species of origin Homo sapiens (Human)

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Histone H3 (tri methyl K4) antibody [mAbcam1012] - ChIP Grade (antibody)

RRID:AB_442796

This monoclonal targets Histone H3 (tri methyl K4) antibody [mAbcam1012] - ChIP Grade

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Anti-KDM5B antibody produced in rabbit (antibody)

RRID:AB_1851987

This polyclonal targets KDM5B antibody produced in rabbit

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JARID1B Antibody (antibody)

RRID:AB_10004656

This unknown targets JARID1B

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SUZ12-human (antibody)

RRID:AB_2196850

This monoclonal targets SUZ12

View all literature mentions

Histone H3 (tri methyl K27) antibody [mAbcam 6002] - ChIP Grade (antibody)

RRID:AB_305237

This monoclonal targets Histone H3 (tri methyl K27) antibody [mAbcam 6002] - ChIP Grade

View all literature mentions

Histone H3 (di methyl K36) antibody - ChIP Grade (antibody)

RRID:AB_1280939

This polyclonal targets Histone H3 (di methyl K36) antibody - ChIP Grade

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H3K79me2-human (antibody)

RRID:AB_303937

This polyclonal targets H3K79me2

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H3K27ac-human (antibody)

RRID:AB_2118291

This polyclonal targets H3K27ac

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H3-celegans (antibody)

RRID:AB_302613

This polyclonal targets H3

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Histone H3 (phospho S10) antibody - Mitosis Marker (antibody)

RRID:AB_304763

This polyclonal targets Histone H3 (phospho S10) antibody - Mitosis Marker

View all literature mentions

Phospho-Estrogen Receptor alpha (Ser118) (16J4) Mouse mAb (antibody)

RRID:AB_331289

This monoclonal targets Phospho-Estrogen Receptor alpha (Ser118) (16J4) Mouse mAb

View all literature mentions

Cleaved Caspase-3 (Asp175) Antibody (antibody)

RRID:AB_2341188

This polyclonal targets Cleaved Caspase-3 (Asp175)

View all literature mentions

Anti-Histone H3 (tri methyl K4) antibody - ChIP Grade (antibody)

RRID:AB_306649

This polyclonal targets Histone H3 (tri methyl K4)

View all literature mentions

H3K27me2-dmelanogaster (antibody)

RRID:AB_448222

This polyclonal targets H3K27me2

View all literature mentions

c-erbB-2 (antibody)

RRID:AB_395352

This monoclonal targets c-erbB-2

View all literature mentions

CD10 (antibody)

RRID:AB_395775

This monoclonal targets CD10

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Cyclin D3 antibody [DCS22] (antibody)

RRID:AB_2070798

This monoclonal targets CCND3

View all literature mentions

CDK6 (D4S8S) Rabbit mAb (antibody)

RRID:AB_2721897

This monoclonal targets CDK6

View all literature mentions

Purified anti-Cdc2 (p34) (antibody)

RRID:AB_2074779

This monoclonal targets cdc2 p34

View all literature mentions

Cdk4 (antibody)

RRID:AB_397299

This monoclonal targets Cdk4

View all literature mentions

E-Cadherin (24E10) Rabbit mAb (antibody)

RRID:AB_2291471

This monoclonal targets E-Cadherin (24E10) Rabbit mAb

View all literature mentions

Keratin 8/18 (C51) Mouse mAb (antibody)

RRID:AB_2134843

This monoclonal targets Keratin 8/18

View all literature mentions

Phospho-S6 Ribosomal Protein (Ser235/236) (D57.2.2E) XP Rabbit mAb (antibody)

RRID:AB_916156

This monoclonal targets Phospho-S6 Ribosomal Protein (Ser235/236) (D57.2.2E) XP Rabbit mAb

View all literature mentions

Vimentin (D21H3) XP Rabbit mAb (antibody)

RRID:AB_10695459

This monoclonal targets Vimentin

View all literature mentions

Purified anti-human CD24 (antibody)

RRID:AB_314851

This monoclonal targets CD24

View all literature mentions

EGF Receptor (D38B1) XP Rabbit mAb (antibody)

RRID:AB_2246311

This monoclonal targets EGF Receptor

View all literature mentions

Phospho-Stat3 (Tyr705) (D3A7) XP Rabbit mAb (antibody)

RRID:AB_2491009

This monoclonal targets Phospho-Stat3 (Tyr705)

View all literature mentions

Phospho-Akt (Ser473) (D9E) XP® Rabbit mAb (antibody)

RRID:AB_2315049

This monoclonal targets Phospho-Akt (Ser473)

View all literature mentions

Cyclin A (antibody)

RRID:AB_395286

This monoclonal targets Cyclin A

View all literature mentions

Androgen Receptor (D6F11) XP Rabbit mAb (antibody)

RRID:AB_10691711

This monoclonal targets Androgen Receptor (D6F11) XP Rabbit mAb

View all literature mentions

p63 antibody [EPR5701] (antibody)

RRID:AB_10971840

This monoclonal targets p63 antibody [EPR5701]

View all literature mentions

Estrogen Receptor α (D6R2W) Rabbit mAb #13258 (antibody)

RRID:AB_2632959

This monoclonal targets Estrogen Receptor alpha

View all literature mentions

Phospho-Smad2 (Ser465/467)/Smad3 (Ser423/425) (D27F4) Rabbit mAb (antibody)

RRID:AB_2631089

This monoclonal targets Phospho-Smad2 (Ser465/467)/Smad3 (Ser423/425)

View all literature mentions