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SUPPLEMENTARY INFORMATIONdoi:10.1038/nature21408

Table S3. Cell lines, media and source  

Cell line Media Source HME MEGM (Lonza) HMEC-Clonetics HMLER MEGM (Lonza) HMEC-Clonetics MCF10A DME+F12 (1:1), 5% Horse

Serum+EGF+Hydrocortisone+Cholera Toxin+Insulin

Dr. Joan Brugge (Harvard Medical School)

BJ-1 DME:Medium199 (3:1)+15%IFS ATCC HUVEC EBM+0.1% hEGF+0.1%

hydrocortisone, 2% FBS, 0.4% bovine brain extract (BBE), 30 μg/ml Gentamicin+15 ng/ml Amphotericin

ATCC

BPLER WIT Media (Stemgent) Dr. Tan Ince (University of Miami)

MCF7ras DME 10%IFS ATCC CAMA1 DME 10%IFS ATCC SKBR3 DME 10%IFS ATCC BT20 DME 10%IFS ATCC MDA-MB-436 DME 10%IFS ATCC HCC38 RPMI 10%FBS ATCC BT474 RPMI 10%FBS ATCC MDA-MB-361 RPMI 10%FBS ATCC T47D RPMI 10%FBS ATCC MDA-MB-231 RPMI 10%FBS ATCC MDA-MB-157 RPMI 10%FBS ATCC HS578t RPMI 10%FBS ATCC HCC1806 RPMI 10%FBS ATCC SUM149 F12 5%IFS, Insulin, Hydrocortisone Dr. Steve Ethier

(University of Michigan)

SUM159 F12 5%IFS, Insulin, Hydrocortisone Dr. Steve Ethier SUM1315 F12 5%IFS, Insulin, Hydrocortisone Dr. Steve Ethier C2C12 DME+15%FBS ATCC Human myoblasts Commercial media Cell Applications  

 

 

 

 

 

 

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Table S4. Primer sequences

Primer Forward Reverse GAPDH CGTATTGGGCGCCTGGTCAC ATGATGACCCTTTTGGCTCC CDKN1A ATGTCAGAACCGGCTGGGGATG

TCC CGTGGGAAGGTAGAGCTTGGGCAGG

CDKN1B ATGTCAAACGTGCGAGTGTCTAACG

CTCCACCTCTTGCCACTCGTACTTG

CDKN2A AGCAGCATGGAGCCTTCGGCTGACT

ACCACCAGCGTGTCCAGGAAGCCCT

CDKN2B GAGGAGAACAAGGGCATGCCCAGTG

GAGAGTGGCAGGGTCTGCGCAGTTG

CDKN2C ATGGCCGAGCCTTGGGGGAACGAGT

GGAAACCTGCTCTGGCCGCATCATG

RB1 GCAGCAGTTGACCTAGATGAGATGT

CTTTGAGCAACATGGGAGGTGAGAG

RBL1 GAAGCCCTGGACGACTTTACTGCCA

CTCTCTAGCCTTTCTATACGTTCAC

RBL2 GACAGCTACCGCAGCATGAGCGAAA

TGCCATGTCTTCCCACTTCTTCATC

BRCA1 ATGGATTTATCTGCTCTTCGCGTTG

AATCTCGTACTTTCTTGTAGGCTCC

TP53 ATGGAGGAGCCGCAGTCAGATCCTA

TAGCTGCCCTGGTAGGTTTTCTGGG

ATM GCTTATCTGCTGCCGTCAACTAGAA

CTGATTTCCTGCATCTTTTTCTGCC

CAP2 (cloning and RT)

CAGACGAATTCCACCATGGCCAACATGCAGGGACTGGTGGAAA

GTCTGGGATCCTTAGGCCATAATTTCTGCAGGTTCA

LACTB (RT-1)

GTGGTTGGAGTTTCTGTAGATGGAA

AGTAATCTTGTTGTGACAGAAACCT

LACTB (RT-2)

AAACCTGGTAGTCAGTTTTTGTATT

TGTTAGGGACTGGGGTCCACATCAT

LACTB (cloning)

CAGACGAATTCCACCATGTACCGGCTCATGTCAGCAGTGA

GTCTGGGATCCTCAGTCTGATCTGTCTTTATCAAAT

dS-LACTB GTTATGCGAATTGCTATCATCAGCAAAAGTCTCACC

GGTGAGACTTTTGCTGATGATAGCAATTCGCATAAC

d1-97-LACTB

CAGACGGATCCACCATGCCGCCCTGCTCCAGGTGCTTCGCCA

GTCTGGGATCCTCAGTCTGATCTGTCTTTATCAAAT

REEP1 (cloning and RT)

CAGACGAATTCCACCATGGTGTCATGGATCATCTCCAGGC

GTCTGGGATCCCTAGGCGGTGCCTGAGCTGCTAGCG

PDLIM3 (cloning and RT)

CAGACGAATTCCACCATGCCCCAGACGGTGATCCTCCCGG

GTCTGGGATCCTTAAGCTTTGGGATACAGAGTGACC

SMPX (cloning and

CAGACGAATTCCACCATGAATATGTCGAAACAGCCAGTTTCC

GTCTGGGATCCCTACTGTTCAGCTTTGGGGACATAT

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RT) HER2 AGGTGGTGCAGGGAAACCTG CAGGGGTGGTATTGTTCAGC c-MYC CGACGAGACCTTCATCAAAA CTGCTGTCGTTGAGAGGGTA PISD ATGATGTGTCAGTCAGAGGC CACTGACTTGTACAAAGCCA SNAIL AAGATGCACATCCGAAGCCA CTCTTGGTGCTTGTGGAGCA TWIST CTGCCCTCGGACAAGCTGAG CTAGTGGGACGCGGACATGG SLUG GTTTCAGTGCAATTTATGCA TTCTAATGTGTCCTTGAAGC ZEB1 GTTCTGCCAACAGTTGGTTT GCTCAAGACTGTAGTTGATG SIP1 TCTGAAGATGAAGAAGGCTG AGTGAATGAGCCTCAGGTAA E-cadherin TGCCCAGAAAATGAAAAAGG GTGTATGTGGCAATGCGTTC N-cadherin GACAATGCCCCTCAAGTGTT CCATTAAGCCGAGTGATGGT Vimentin GAGAACTTTGCCGTTGAAGC TCCAGCAGCTTCCTGTAGGT Fibronectin GAGATTGGACCTGCAAGCCCA AGTGCAAGTGATGCGTCCGC ZO-1 AGAGCTGCGGCCGCCAAGAGCA

CAG ATACTGGTTCAGGATCAGGACGACT

CK5 CAGCCGGAGCCTCTACAACC CGCCGAAACCAAATCCACTAC CK8 GATGCTGGAGACCAAGTGGAG GCCGCCTAAGGTTGTTGATG  

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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Table S5. Antibodies, source and dilution  

Antibody Source Dilution (application)

LACTB Proteintech Group # 18195-1-AP 1:5 000 (WB) 1:250 (IF)

PISD Proteintech Group # 16401-1-AP 1:1000 (WB) GAPDH Cell Signaling Technology # 2118S 1:5000 (WB) COX4 Cell Signaling Technology # 4850S 1:5000 (WB) β-actin Cell Signaling Technology # 4970P 1:5000 (WB) Mitochondrial marker EMD Millipore # MAB1273 1:200 (IF) KI-67 BD Pharmingen # 550609 1:200 (IF) CCP3* read below Cell Signaling Technology # 9661S 1:250 (IF) α-actinin Sigma Aldrich # A7811 1:250 (IF) phalloidin Invitrogen # A22283 1:100 (IF) CD44-PeCy7 eBioscience # 25-0441-81 1:200 (FACS) CD24-APC BioLegend # 311118 1:50 (FACS) EPCAM-Pacific Blue BioLegend # 324218 1:100 (FACS) PGS1 Proteintech Group # 17149-1-AP 1:1000 (WB) PGP Proteintech Group # 25081-1-AP 1:1000 (WB) E-cadherin Cell signaling # 3195 1:100 (IF) β-catenin BD Biosciences # 610154 1:100 (IF) Cytokeratin 8 Covance # MMS-162P-250 1:1000 (IF) Zeb1 Cell Signaling # 3396 1:100 (IF) Vimentin Cell signaling # 5741 1:100 (IF) Fibronectin BD Biosciences # 610078 1:100 (IF) h-Ras Santa Cruz #sc-520 1:500 (WB) Calnexin Enzo # ADI-SPA-865 1:2000 (WB) Fis1 Proteintech Group # 10956-1-AP 1:1000 (WB) Opa1 Abcam # ab55772 1:500 (WB) Mfn1 Cell Signaling Technology # 14739 1:1000 (WB) Mfn2 Cell Signaling Technology # 11925 1:1000 (WB) OXPHOS Abcam # ab110411 1:1000 (WB) Drp1 Cell Signaling # 8570 1:500 (WB)  

* This CCP3 antibody also recognizes other caspase substrates (such as caspase 9 substrates) apart from cleaved caspase 3. This has been reported on the Cell Signaling website and also in a published report (Yun Fan and Andreas Bergmann, Cell Death Differ., 2010), which specifically describes the cross-reactivity of this antibody with other components of apoptotic pathway. Therefore, in our text we refer to this antibody as “Cleaved Caspase” antibody.

 

 

 

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Table S6. Abbreviations  

ATM ataxia-telangiectasia mutated protein CAP2 adenylate cyclase-associated protein 2 CD24 cluster of differentiation 24 CD44 cluster of differentiation 44 CDKN1A cyclin-dependent Kinase Inhibitor 1A CDKN1B cyclin-dependent Kinase Inhibitor 1B CDKN2A cyclin-dependent Kinase Inhibitor 2A CDKN2B cyclin-dependent Kinase Inhibitor 2B cDNA complementary DNA CK5 cytokeratin 5 CK8 cytokeratin 8 COX4 cytochrome c oxidase subunit 4 CSC cancer stem cell DAPI 4',6-diamidino-2-phenylindole DMEM dulbecco's modied Eagle's medium DMSO dimethyl sulfoxide DOX doxycycline dsiRNA dicer-substrate RNAs Edu 5-ethynyl-2'-deoxyuridine EPCAM epithelial cellular adhesion molecule FACS fluorescence-activated cell sorting FBS fetal bovine serum GAPDH glyceraldehyde 3-phosphate dehydrogenase H&E hematoxylin and eosin stain HBSS Hanks' Balanced Salt Solution HME human mammary epithelial cells HRP horseradish peroxidase hTERT human telomerase reverse transcriptase IFS heat inactivated fetal serum LACTB beta-lactamase-like LC-MS liquid chromatography-tandem mass spectrometry LPC lysophosphatidylcholine LPE lysophosphatidylethanolamine mRNA messenger RNA MTUS1 mitochondrial tumor suppressor 1 NOD/SCID nonobese diabetic/severe combined immunodeficiency PBS phosphate-buffered saline PDLIM3 PDZ and LIM domain protein 3 PE phosphatidylethanolamine PG phosphatidylglycerol

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PGP phosphatidylglycerophosphatase PGS1 phosphatidylglycerophosphate synthase 1 PISD phosphatidylserine decarboxylase pRB retinoblastoma 1 protein PS phosphatidylserine qRT-PCR quantitative reverse transcription polymerase chain

reaction RBL2 retinoblastoma-like protein 2 REEP1 receptor accessory protein 1 RIPA radioimmunoprecipitation assay buffer RPM revolutions per minute RT-PCR reverse transcription polymerase chain reaction shRNA short hairpin RNA siRNA short interfering RNA SMPX small muscle protein X-linked TP53 tumor protein P53 ZEB1 zinc finger E-Box binding homeobox 1

 

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38 KDa31 KDa

52 KDa

76 KDa

38 KDa31 KDa

52 KDa

76 KDa

38 KDa31 KDa

52 KDa

LACTB+GAPDHLACTB

GAPDH

A

AC

C

CB

38 KDa52 KDa

76 KDa

B LACTB

GAPDHB

38 KDa31 KDa

52 KDa

Figure 1a

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Figure 5a

ABCDEF

Raw Western blot image for E (PISD) is shown in Extended Data Fig. 8d

F

A

LACTB

CActinPGS1

PGPD

38 KDa31 KDa

52 KDa

38 KDa52 KDa

76 KDa

38 KDa31 KDa

52 KDa

76 KDa

38 KDa52 KDa

76 KDa

COX4B

38 KDa31 KDa

52 KDa

24 KDa17 KDa

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Figure 5d A B

A BPISD PISD

BLACTB

BCOX4

38 KDa

52 KDa

24 KDa17 KDa

ACOX4

ALACTB

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Extended Data Fig. 2fLACTB+GAPDH

38 KDa31 KDa

52 KDa

76 KDa

Extended Data Fig. 4a

A CB

LACTB+GAPDH

38 KDa31 KDa

52 KDa

76 KDaA B C

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Extended Data Fig. 4f,g,h

A CB

AA

B B

C C

c‐myc

H‐Ras

her2

GAPDH

COX4

actin

38 KDa52 KDa

76 KDa

38 KDa31 KDa

52 KDa

38 KDa

52 KDa

24 KDa17 KDa

102 KDa76 KDa

150 KDa225 KDa

38 KDa31 KDa24 KDa17 KDa

38 KDa31 KDa

52 KDa

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Extended Data Fig. 7e

Raw Western blot images for actin, COX4 and LACTB are shown in Source Data Fig 5a above.

F OXPHOS

ABCDE

F

38 KDa

52 KDa

24 KDa17 KDa

Mfn2E

102 KDa76 KDa

150 KDa225 KDa

Mfn1D

102 KDa76 KDa

150 KDa225 KDa

Fis1A

38 KDa

52 KDa

24 KDa17 KDa

C

Opa1

38 KDa31 KDa

52 KDa

B

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SUPPLEMENTARY INFORMATION RESEARCH

Extended Data Fig. 8g

ABC PISD

calnexinLACTB

A

BC

Extended Data Fig. 8f

ABC

A

B C

LACTB

PISD GAPDH

38 KDa31 KDa

52 KDa

38 KDa31 KDa

52 KDa

76 KDa

31 KDa52 KDa

76 KDa

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Extended Data Fig. 9a

ABC

A PISD

38 KDa31 KDa

52 KDa

76 KDa

COX4C

38 KDa

52 KDa

24 KDa17 KDa

B LACTB

Extended Data Fig. 9d

ABC

A PISD

38 KDa31 KDa

52 KDa

C COX4B LACTB

38 KDa52 KDa

24 KDa17 KDa

38 KDa52 KDa

76 KDa

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Extended Data Fig. 9g

A

B

A LACTB+GAPDH

38 KDa52 KDa

76 KDa

PISDB

38 KDa31 KDa

52 KDa

Extended Data Fig. 10dLACTB+actin

38 KDa52 KDa

76 KDa

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Extended Data Fig.10f

AB

C

C COX4

38 KDa31 KDa

52 KDa

PISDA

B LACTB

38 KDa52 KDa

76 KDa

38 KDa52 KDa

24 KDa17 KDa

Extended Data Fig.10g

A

B 38 KDa31 KDa

52 KDa

PISDBLACTBA

38 KDa52 KDa

76 KDa