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A B D Relative TAp73 mrna p73 Supplementary Figure 1 25 2 15 1 5 p63 _-tub. MDA-468 HCC1143 HCC38 SUM149 MDA-468 HCC1143 HCC38 SUM149 HCC-1937 MDA-MB-468 ΔNp63_ TAp73_ TAp73β E C Relative ΔNp63 mrna TAp73 mrna Levels 18 16 14 12 1 8 6 4 2 3 25 R 2 =.9121 2 15 1 5 MDA-468 HCC1143 HCC38 SUM149 1 1 1 TAp73 Protein levels MDA-468

Supplementary Figure 2 A Relative ΔNp63 mrna 1.2 1..8.6.4.2. p63si B p63si 12 Fold Change 1 8 6 4 2 PUMA NOXA Bax p53aip1 FAS

Supplementary Figure 3 V p63 8 TAp73_ TAp73b p73 6 4 PARP 2 C 1 TAp73 PUMA ΔNp73 p63si _-tubulin D % Apoptosis Relative mrna Levels 12 p6 3s i B p6 3s i V A 4 p63si 3 2 1 TAp63si

Supplementary Figure 4 A IP p73 p73 MDA-468 TAp73_ TAp73β B Cell Lines Cisplatin (um) Doxorubicin (nm) Paclitaxel (nm) 6. ±.57 < 1..59 ±.4 9.22 ±.19 < 1..59 ±.6 2.8 ± 1.48 4.14 ± 1.5.78 ±.8 43.75 ±.59 2.31 ± 9.26.53 ±.5 MDA-MB-468 1.15 ±.4 38.43 ± 7.7.56 ±.2 12.86 ± 3.1 69.28 ± 2.76.64 ±.6 C 12 1 % Viability 8 6 4 2 Allp73si.1.1 1 1 1 Cisplatin (µm) D MCF-1A E p73 TAp73_ MCF-1A Cisplatin ( µ M) Doxorubicin (nm) Paclitaxel (nm) 6.6 ±.55 57.44 ± 2.73 8.23 ± 1.26 TAp73b.74 ±.3 73.29 ± 6.88 8.12 ±.15

Supplementary Figure Legends Supplementary Figure 1 Correlation between p73 and p63 mrna and protein levels in breast cancer cells. (A) TAp73 protein level by IP/Immunoblot of 2.5mg protein lysate from the indicated human breast cancer-derived cell lines. Little or no ΔNp73 is detected based on transfected isoform size controls and on isoform-specific QRT-PCR (not shown). (B) Quantitation of TAp73 by isoform-specific QRT-PCR, normalized to GAPDH. (C) Correlation of TAp73 mrna and protein levels in breast cancer cells. (D) Expression of ΔNp63α protein by immunoblot. (E) Expression of ΔNp63 mrna by isoform-specific QRT-PCR in the indicated cell lines. Error bars in B and E show SD for two experiments. Supplementary Figure 2 Controls for apoptosis following p63 inhibition by lentiviral shrna. (A) Knockdown of endogenous ΔNp63 mrna by lentiviral p63-directed shrna (p63si) in HCC-1937. RNA was prepared at 72 hours following lentiviral infection and assayed by isoform-specific QRT-PCR, normalized to GAPDH levels. (B) Neither gene induction nor apoptosis is observed in p63-negative cells. Left, photomicrographs (1X) taken at 72 hours post lentiviral shrna infection. Right, QRT- PCR for the indicated genes. For gene expression graphs, error bars represent SD from two independent experiments performed in duplicate. Supplementary Figure 3 Puma induction, PARP cleavage, and apoptosis following p63 knockdown are TAp73-dependent in cells. (A) TAp73-directed shrna targets TAp73 but not ΔNp73. Expression of endogenous TAp73 and ΔNp73 was assessed by QRT-PCR following lentiviral shrna infection. Error bars indicate SD from three measurements. (B) Cells expressing a TAp73-directed shrna or control were subsequently infected with a p63-directed lentiviral shrna and harvested at 72 hours for immunoblot and IP/immunoblot (for p73). (C) Photomicrograph (1X) taken 72 hours post lentiviral infection as in B show that morphologic features of apoptosis correlate with Puma induction and PARP cleavage. (D) Rescue from apoptosis following ablation of TAp73 but not TAp63. Quantitation of apoptosis by Annexin/PI staining of cells 1

treated as in B and harvested 72 hours following p63 knockdown. Error bars show SD for 3 independent experiments. Supplementary Figure 4 TAp73 mediates cisplatin sensitivity in breast cancer cells. (A) Knockdown of endogenous TAp73 protein by lentiviral shrna in the indicated cell lines, assessed by IP/immunoblot. (B) IC 5 values determined by cell viability (MTT) assay 5 days following treatment of control or TAp73-directed shrna-expressing cells with the indicated agents. Values indicate the mean + SD for 3 independent experiments. (C) Knockdown of TAp73 or All p73 isoforms induces cisplatin resistance in breast cancer cells. MTT assay performed as in B. (D) Stable retroviral expression of TAp73β in MCF-1A cells, assessed by immunoblot. (E) TAp73β expression in mammary epithelial cells conveys specific sensitivity to cisplatin. IC 5 values determined and expressed as in B. 2

Supplementary Table 1. p53 Status in Clinical Breast Cancer Samples Sample ID ER Status P53 Status Codon 72 polymorphism Codon nucleotide Codon Amino Acid 282 Positive WT Pro 432 Positive WT Pro 481 Positive WT Pro 48 Positive WT Pro 398 Positive WT Pro 298 Positive WT Pro 469 Positive WT Pro 436 Positive WT Pro 477 Positive WT Pro 426 Positive WT Pro 43 Positive WT Pro 242 Positive WT Pro 356 Positive WT Pro 253 Positive WT Pro 588 Negative WT Unknown 1274 Negative Mutant Pro 151 (G to T) 152 (A to G) Stop E51G 164 Negative Mutant Arg 523 (C to G) R175G 72 Negative Mutant Arg 639 (A to G) R213R 29 Negative Mutant Arg 818 (G to A) R273H 1196 Negative Mutant Pro 73 (G to A) G244S 465 Negative Mutant Arg Del (529-546) 1322 Negative WT Arg 1278 Negative WT Arg 116 Negative WT Arg 222 Negative WT Unknown 1321 Negative WT Arg 715 Negative Mutant Pro 577 (C to T) H193Y 999 Negative WT Arg 158 Negative WT Arg 489 Negative Mutant Pro 469 (G to T) V157F 152 Negative WT Arg 289 Negative WT Pro 1325 Negative WT Pro 1273 Negative Mutant Pro 817 (C to T) R273C 756 Negative WT Arg 159 Negative WT Pro 488 Negative WT Pro Mutational status was determined based on bi-directional sequencing (exon 1-7), and was verified by the presence of nucleotide changes in both strands.

Supplementary Table 2. Primer sequences for QRT-PCR Gene Forward primer Reverse primer Product (bp) ΔNp63 5 -GGAAAACAATGCCCAGACTC-3 5 -GTGGAATACGTCCAGGTGGC -3 294 TAp63 5 -AAGATGGTGCGACAAACAAG-3 5 -AGAGAGCATCGAAGGTGGAG -3 234 TAp73 5'-GCACCACGTTTGAGCACCTCT -3' 5 -GCAGATTGAACTGGGCCATGA -3' 168 ΔNp73 5'-CAAACGGCCCGCATGTTCCC-3' 5'-TTGAACTGGGCCGTGGCGAG -3' 232 Bax 5 -TGACATGTTTTCTGACGGCAAC-3 5 -GGAGGCTTGAGGAGTCTCAC C-3 24 Noxa 5 -GAGATGCCTGGGAAGAAGG-3 5 -ACGTGCACCTCCTGAGAAAA -3 228 P53AIP1 5 -AGCTCACTCCGAAAGCCTCTGCTC-3 5 -GCATCACCGAGAGGTTCTGG TCTC-3 28 FAS 5 -GGGCATCTGGACCCTCCTAC-3 5 -TCCTTTCACCTGGAGGACAG -3 2 PUMA 5 -ACGACCTCAACGCACAGTACGAG-3 5 -AGGAGTCCGCATCTCCGTCA GTG-3 345 HER2 5 -AGCGGTGTGAAACCTGACC-3 5 -TTGATGAGGATCCCAAAGACC -3 224 B2M 5 - AGCTGTGCTCGCGCTACTCT C-3 5 -CACACGGCAGGCATACTCAT C-3 286 GAPDH 5 -CACCCAGAAGACTGTGGATGG-3 5 -GTCTACATGGCAACTGTGAG G-3 587

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