Whole-Exome Sequencing and Data Analysis
Supplemental Information Methods
Whole-exome Sequencing and Data Analysis
Whole-exome sequencing (WES) analysis on the Illumina platform with the SureSelect Human All Exon V4+UTRs capture library (Agilent Technologies, Inc.) was previously performed for several bladder cancer PDX models (BL0269, BL0293, BL0440) used in this study as described in Pan et al.The raw sequence data files are publicly available through the NCBI BioProject database ( with Accession Number PRJNA352282.For BL0645, targeted sequencing of 358 genes was performed with the JAX Cancer Treatment Profile. Variant discovery and annotation were performed with a standard Burrows-Wheeler Aligner (BWA) and Genome Analysis Toolkit (GATK) pipeline(1-3).The results were filtered for variants in DNA repair genes (Supplementary Table S6) and subsequently for resulting in a non-synonymous base substitution. Variants were classified as somatic mutations by satisfying one or more criteria, including 1) annotated as a confirmed somatic variant in the COSMIC (Catalogue of Somatic Mutations in Cancer) (4) or TCGA (The Cancer Genome Atlas) databases, 2) alternate allele fraction within the range of 0.1-0.5 or 0.6-0.9, and/or 3) not listed as a reference SNP in the dbSNP database. Furthermore, potential, functionally impactful variants were selected on the basis of SnpEff predictions (e.g., Moderate, High) (5).
Supplemental Information Figures and Tables
Supplementary Figure 1SI Figure 1: Diagram showing the formation of cisplatin, carboplatin and gemcitabine-DNA adducts. A) Formation of cisplatin DNA-monoadducts and diadducts. B) Formation of carboplatin DNA-monoadducts and diadducts.The 14C label in carboplatin is included in the cyclobutane dicarboxylate (CBDCA) ligand, which is released upon diadduct formation, therefore only carboplatin-monoadducts can be measured via AMS.Cisplatin does not contain carbon atoms and cannot be [14C] labeled. Note that cisplatin and carboplatin form the same final diadduct.C) Following gemcitabine activation through dCK, difluorodeoxyfluorocytisine is incorporated into DNA.
Supplementary Figure 2
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B
SI Figure 2:Schema of the clinical trial sample collection and processing.A) Microdosing sample collection schema for patients participating in the pharmacokinetics study. B) Experimental design overview schema. Bladder cancer patients are administered one [14C]-labeled carboplatin microdose prior to blood sampling and tumor biopsy. DNA is then isolated from PBMC and tumor tissue and assayed for drug-DNA damage using AMS. Within four weeks patients begin a standard platinum-based regimen with collection of objective cancer response and patient toxicity. The drug-DNA damage levels are being evaluated for correlation to response and to patient toxicity.
Supplementary Figure 3
A B / A
C D
C
SI Figure 3:PDX tumor response curves towards chemotherapy. A-D)Tumor response curves from drug response study comparing different treatments in tumor-bearing NSG mice of A) BL0269, B) BL0293 C) BL0440 and D) BL0645. Black line = Vehicle D5W IV Q7Dx3, blue line = cisplatin 2mg/kg IV Q7Dx3 or carboplatin 30 mg/kg IP Q7Dx4, red line = gemcitabine 150 mg/kg IP Q7Dx4, green line = G/C combination. NSG mice were implanted with indicated PDX models 14 to 30 days before treatment start, dotted lines indicate treatment days.
Supplementary Figure 4
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C / D
SI Figure 4: Gene expression of RRM1+2, hENT1 and ERCC1 does not correlate to tumor resistance toward cisplatin or gemcitabine chemotherapy. Total RNA was isolated from indicated PDX tumor tissue and subjected to reverse transcription followed by real time PCR for indicated genes. Expression was normalized to GAPDH expression as internal control. Relative gene expression of BL0269 compared to indicated tumor models of A) RRM1, B) RRM2, C) hENT1, D) ERCC1. The 2-ΔΔCt method was used
Supplementary Table 1: Relevant data on patients participating in clinical study
Patient # / Tumor Type / Stage before chemo / Neoadjuvant Therapy / Patient response
1 / Urothelial / cT2N0M0 / Gemzar/Carboplatin / CR
2 / Urothelial / cT2N0M0 / Gemzar/Cisplatin / CR
5* / Urothelial / cT1N0M0 / no chemo, NMIBC / NC
8 / Urothelial / cT3N0M1 / Gemzar/Carboplatin / DP
10 / Urothelial / cT2N0M0 / Gemzar/Carboplatin / CR
11 / Urothelial / cT2N0M0 / MVAC / CR
14 / Urothelial / cT2N0M0 / DD MAVC / DP
15 / Urothelial / cT2N0M0 / Gemzar/Carboplatin / CR
16* / Urothelial / cT2N0M0 / no chemo, NMIBC / NC
17 / Urothelial / pT3N1M0 / MVAC / DP
18 / Urothelial / cT2N0M0 / no chemo, kidney failure / NC
19 / Urothelial / pT3N0Mx / MVAC / PR
20 / Urothelial / cT3N3Mx / Gemzar/Cisplatin / PR
PR= partial response, CR= complete response, DP=disease progression, NC= no chemo, NMIBC= non-muscle invasive bladder cancer, MVAC= methotrexate, vinblastine, doxorubicin and cisplatin, DD MVAC= dose dense MVAC. * clinical diagnosis of myoinvasive bladder cancer, biopsy during the microdosing study showed they had T1 disease,hence, no chemotherapy was given.
Supplemental Table 2: Summary of [14C]carboplatin dosing PK and adduct data
Patient / Dose / T ½ alpha* / T ½ beta** / AUC 0-t# / 24h PBMC Adducts+ / 24h Tumor Adducts+
1 / micro / 43.2 / 8.14 / 714.06 / 0.329 / -
thera / 43.8 / 8.71 / 67501 / 61.16 / -
2 / micro / 42.6 / 7.83 / 1610.3 / 0.978 / -
5 / micro / 41.4 / 8.25 / 2832.6 / 0.443 / 20.2
8 / micro / 48.6 / 7.56 / 1078.8 / 0.081 / 14.8
-
thera / 54.6 / 7.83 / 116365 / 68.77
10 / micro / 45.0 / 8.08 / 783.40 / 0.930 / 5.37
-
thera / 20.4 / 6.63 / 65698 / 35.18
11 / micro / 46.2 / 7.26 / 1124.3 / 0.154 / 3.13
14 / micro / 47.4 / 7.96 / 945.68 / 0.283 / 0.31
15 / micro / 45.6 / 7.84 / 3840.4 / 0.968 / 42.5
16 / micro / 37.8 / 6.94 / 1608.2 / 0.499 / 8.79
17 / micro / 46.2 / 7.18 / 2217.2 / 0.485 / -
18 / micro / 13.2 / 4.47 / 1023.7 / - / -
19 / micro / - / - / - / 0.923 / -
20 / micro / - / - / - / 0.908 / -
* min, ** hours, microdose (micro), therapeutic dose (thera), # area under the curve (AUC) in ng-hour/mL,+ adducts/ 108 nt,- = not determined
Supplementary Table 3: Characteristics of donor patients and xenograft tissue
PDX / Sex / Age / Diagnosis / Tumor Stage / Surgery / Prior Chemo / PDX sensitivity
median survival (days)
Control / Gem / Carbo / Cis / Gem/ Carbo / Gem/Cis
BL0269 / M / 58 / Urothelial Carcinoma / pT4 N0 Mx / Cystectomy / no / 34/36 / Res41/32 / Res 39 / Res 38 / Res 39 / Res 44
BL0293 / F / 77 / Urothelial Carcinoma / pT2a N2 Mx / Cystectomy / no / 35/25 / Sen 68/58 / Res 28 / Res 35 / Sen 67 / Sen >70
BL0440 / M / 71 / Urothelial Carcinoma / pT4 N2 Mx / Cystectomy / G/Cis / 22/13 / Sen 46/39 / Sen 64 / Sen 80 / Sen >62 / Sen >83
BL0645 / F / 75 / Urothelial Carcinoma / pT4a N2 Mx / Cystectomy / MVAC / 18 / Res 28 / Res 21 / Sen >32
PDX = patient derived xenograft, M = male, F = female, Gem = gemcitabine, Carbo = carboplatin, Cis = cisplatin, MVAC= methotrexate, vinblastine, doxorubicin and cisplatin, Sen = sensitive, Res = resistant,
SupplementaryTable4:Relative mRNA expression of four genes implemented in chemotherapy resistance
PDX / RRM1 / RRM2 / hENT1 / ERCC1
BL0269 / 1.003 ± 0.078 / 1.004 ± 0.096 / 1.008 ± 0.133 / 1.003 ± 0.080
BL0293 / 0.477 ± 0.152 / 0.408 ± 0.098 / 5.637 ± 0.871 / 2.270 ± 0.777
BL0440 / 1.598 ± 0.475 / 1.763 ± 0.486 / 72.70 ± 27.77 / 5.037 ± 1.310
BL0645 / 0.825 ± 0.181 / 1.875 ± 0.349 / 9.225 ± 2.334 / 1.098 ± 0.367
RRM1 = ribonucleotide reductase 1 and 2, hENT1 = human equilibrative nucleoside transporter-1, ERCC1 = excision repair cross complementing group 1
Supplementary Table 5: Mutation status of genes associated with sensitivity to cisplatin in four bladder cancer PDX models.
PDX Model
Gene Symbol / BL0269 / BL0293 / BL0440 / BL0645 / Prediction Rule
ATM / D1853N / - / - / - / ATM/FANCC/RB1 Decision Rule
RB1 / - / R358* / L88fs / -
FANCC / - / - / - / -
ERCC1 / - / - / - / - / ERCC1/2
ERCC2 / D288N / - / - / -
RRM1 / - / - / - / - / RRM1/2
RRM2 / - / - / S59A / -
BRCA1 / - / - / S1566G / P824L / Homologous Recombination Deficiency
BRCA2 / R2488K / R2034C / - / N372H, T1915M
RAD51C / - / - / R370Q / -
TP53 / - / - / E126K / - / TP53 Status
Mutations in genes associated with sensitivity to cisplatin in bladder cancer PDX models. Whole-exome sequencing (WES), or targeted sequencing with the JAX Cancer Treatment Profile panel, was previously performed for each bladder cancer PDX model used in this study and the resulting data analyzed for somatic mutations in 184 DNA repair-associated genes (Supplementary Table S6). Mutations (i.e., amino acid change) in genes described to be associated with sensitivity to cisplatin are presented in the table. Confirmed somatic variants are indicated in Bold type.
Supplementary Table 6: DNA repair-associated genes analyzed by targeted sequencing in this study
Gene Symbol / DNA Repair Category / Activity / Location / Accession / Drug Sensitivity / Cancer Type / Comment / Reference
ALKBH2 / Direct reversal of damage / 1-meA dioxygenase / 12q24.11 / NM001001655
ALKBH3 / Direct reversal of damage / 1-meA dioxygenase / 11p11.2 / NM139178
APEX1 / BER strand break joiningfactors / AP endonuclease / 14q11.2 / NM001641
APEX2 / BER strand break joining factors / AP endonuclease / Xp11.21 / NM014481
APLF / BER strand break joining factors / Accessory factor for DNA end-joining / 2p13.3 / NM173545
APTX / Editingandprocessingnucleases / Processing of DNA single-strand interruptions / 9p21.1 / NM175073
ATM / Genesdefective in diseases associated withsensitivityto DNA damaging agents / ataxia telangiectasia / 11q22.3 / NM000051 / Cisplatin, Olaparib / Bladder, Prostate / (6, 7)
ATR / OtherconservedDNAdamageresponsegenes / ATM- and PI-3K-like essential kinase / 3q23 / NM001184
ATRIP / OtherconservedDNAdamageresponsegenes / ATR-interacting protein / 3p21.31 / NM130384
BLM / Genesdefectivein diseases associatedwith sensitivity toDNA damagingagents / Bloom syndrome helicase / 15q26.1 / NM000057
BRCA1 / Homologousrecombination / Accessory factor for transcription and recombination, E3 Ubiquitin ligase / 17q21.31 / NM007295 / Cisplatin, Olaparib / Breast, Prostate / Inactivation is predictive of Homologous Recombination Deficiency (HRD) in breast cancer and is necessary for cisplatin sensitivity. / (7, 8)
BRCA2 / Fanconianemia / Cooperation with RAD51, essential function / 13q13.1 / NM000059 / Cisplatin, Olaparib / Breast, Prostate
BRIP1 / Fanconi anemia / DNA helicase, BRCA1-interacting / 17q23 / NM032043
CCNH / Nucleotide excision repair / Kinase subunits of TFIIH / 5q14.3 / NM001239
CDK7 / Nucleotide excision repair / Kinase subunits of TFIIH / 5q13.2 / NM001799
CETN2 / Nucleotide excision repair / Binds DNA distortions / Xq28 / NM004344
CHAF1A / Chromatin StructureandModification / Chromatin assembly factor / 19p13.3 / NM005483
CHEK1 / Other conservedDNAdamage response genes / Effector kinases / 11q24.2 / NM001274
CHEK2 / Other conservedDNAdamage response genes / Effector kinases / 22q12.1 / NM007194 / Olaparib / Prostate / (7)
CLK2 / Other conservedDNAdamage response genes / S-phase check point and biological clock protein / 1q21 / NM003993
DCLRE1A / Otheridentified genes with known or suspectedDNArepairfunction / DNA crosslink repair / 10q25.3 / NM014881
DCLRE1B / Otheridentified genes with known or suspectedDNArepairfunction / Related to SNM1 / 1p13.2 / NM022836
DCLRE1C / Non homologousendjoining / Nuclease / 10p13 / NM022487
DDB1 / Nucleotide excision repair / Complex defective in XP group E / 11q12.2 / NM001923
DDB2 / Nucleotide excision repair / Complex defective in XP group E / 11p11.2 / NM000107
DMC1 / Homologousrecombination / Rad51 homolog, meiosis / 22q13.1 / NM007068
DUT / Modulation ofnucleotidepools / dUTPase / 15q21.1 / NM001948
EME1 / Homologousrecombination / Subunits of structure-specific DNA nuclease / 17q21.33 / NM152463
EME2 / Homologousrecombination / Subunits of structure-specific DNA nuclease / 16p13.3 / NM001010865
ENDOV / Editing andprocessingnucleases / incision 3' of hypoxanthine and uracil in DNA and inosine in RNA / 17q25.3 / NM173627
ERCC1 / Nucleotideexcisionrepair / 5' incision DNA binding subunit / 19q13.32 / NM001983 / Cisplatin / Bladder / Patients with resected ERCC1-negative TCC bladder cancer, benefited more from adjuvant gemcitabine plus cisplatin chemotherapy than those with ERCC1-positive tumors. High ERCC1 expression was associated with shorter disease-free and overall survival in patients with bladder cancer who received NAC. / (9, 10)
ERCC2 / Nucleotideexcisionrepair / 5' to 3' DNA helicase / 19q13.32 / NM000400 / Cisplatin / Bladder / ERCC2 substantially increases the odds of a complete or near-complete response and improved survival, but is not 100% specific as a biomarker / (11)
ERCC3 / Nucleotideexcisionrepair / 3' to 5' DNA helicase / 2q14.3 / NM000122 / Olaparib / Prostate / (7)
ERCC4 / Nucleotideexcisionrepair / 5' incision catalytic subunit / 16p13.12 / NM005236
ERCC5 / Nucleotideexcisionrepair / 3' incision / 13q33.1 / NM000123
ERCC6 / Nucleotideexcisionrepair / Cockayne syndrome and UV-Sensitive Syndrome; Needed for transcription-coupled NER / 10q11.23 / NM000124
ERCC8 / Nucleotideexcisionrepair / Cockayne syndrome and UV-Sensitive Syndrome; Needed for transcription-coupled NER / 5q12.1 / NM000082
EXO1 / Editingandprocessingnucleases / 5' exonuclease / 1q43 / NM003686
FAAP20 / Fanconianemia / FANCA-associated / 1p36.33 / NM182533.2
FAAP24 / Fanconianemia / FAAP24 / 19q13.11 / NM152266
FAN1 / Editingandprocessingnucleases / 5' nuclease interacting with FANCD2 / 15q13.2 / NM014967
FANCA / Fanconianemia / FANCA / 16q24.3 / NM000135 / Olaparib / Prostate / (7)
FANCB / Fanconianemia / FANCB / Xp22.31 / NM152633
FANCC / Fanconianemia / FANCC / 9q22.32 / NM000136 / Cisplatin / Bladder / (6)
FANCD2 / Fanconianemia / target for monoubiquitination / 3p25.3 / NM033084
FANCD2OS
FANCE / Fanconianemia / FANCE / 6p21.31 / NM021922
FANCF / Fanconianemia / FANCF / 11p14.3 / NM022725
FANCG / Fanconianemia / FANCG / 9p13.3 / NM004629
FANCI / Fanconianemia / target for monoubiquitination / 15q26.1 / NM018193
FANCL / Fanconianemia / FANCL / 2p16.1 / NM018062
FANCM / Fanconianemia / helicase/translocase / 14q21.3 / NM020937
FEN1 / Editingandprocessingnucleases / 5' nuclease / 11q12.2 / NM004111
GEN1 / Homologousrecombination / Nuclease cleaving Holliday junctions / 2p24.2 / NM182625
GIYD1 / Homologousrecombination / Subunit of SLX1-SLX4 structure-specific nuclease, two identical tandem genes in the human genome / 16p11.2 / NM001014999
GIYD2 / Homologousrecombination / Subunit of SLX1-SLX4 structure-specific nuclease, two identical tandem genes in the human genome / 16p11.2 / NM024044
GTF2H1 / Nucleotideexcisionrepair / Core TFIIH subunit p62 / 11p15.1 / NM005316
GTF2H2 / Nucleotideexcisionrepair / Core TFIIH subunit p44 / 5q13.2 / NM001515
GTF2H3 / Nucleotideexcisionrepair / Core TFIIH subunit p34 / 12q24.31 / NM001516
GTF2H4 / Nucleotideexcisionrepair / Core TFIIH subunit p52 / 6p21.33 / NM001517
GTF2H5 / Nucleotideexcisionrepair / Core TFIIH subunit p8 / 6p25.3 / NM207118
H2AFX / ChromatinStructureandModification / Histone, phosphorylated after DNA damage / 11q23.3 / NM002105
HDAC2 / Olaparib / Prostate / (7)
HELQ / Other identifiedgenes with known or suspected DNA repairfunction / DNA helicase / 4q21.23 / NM133636
HLTF / Ubiquitinationandmodification / E3 ubiquitin ligase, SWI/SNF related, homolog of S. cerevisiae Rad5 / 3q25.1-q26.1 / NM003071
HUS1 / OtherconservedDNAdamageresponsegenes / subunits of PCNA-like sensor of damaged DNA / 7p12.3 / NM004507
LIG1 / Nucleotideexcisionrepair / DNA ligase / 19q13.32 / NM000234
LIG3 / BERstrandbreak joiningfactors / DNA Ligase III / 17q12 / NM013975
LIG4 / Nonhomologousendjoining / Ligase / 13q33.3 / NM002312
MAD2L2 / DNApolymerasescatalyticsubunits / DNA pol zeta subunit / 1p36.22 / NM006341
MBD4 / Baseexcisionrepair / U or T opposite G at CpG sequences / 3q21.3 / NM003925
MDC1 / OtherconservedDNAdamageresponsegenes / Mediator of DNA damage checkpoint / 6p21.3 / NM014641
MGMT / Directreversalofdamage / O6-meG alkyltransferase / 10q26.3 / NM002412
MLH1 / MismatchexcisionrepairMMR / MutL homologs, forming heterodimer / 3p22.3 / NM000249
MLH3 / MismatchexcisionrepairMMR / MutL homologs of unknown function / 14q24.3 / NM014381 / Olaparib / Prostate / (7)
MMS19 / Nucleotideexcisionrepair / Iron-sulfur cluster loading and transport / 10q24.1 / NM022362
MNAT1 / Nucleotideexcisionrepair / Kinase subunits of TFIIH / 14q23.1 / NM002431
MPG / Baseexcisionrepair / 3-meA, ethenoA, hypoxanthine / 16p13.3 / NM002434
MRE11 / Olaparib / Prostate / (7)
MRE11A / Homologousrecombination / 3' exonuclease, defective in ATLD (ataxia-telangiectasia-like disorder) / 11q21 / NM005590
MSH2 / MismatchexcisionrepairMMR / Mismatch (MSH2-MSH6) and loop (MSH2-MSH3) recognition / 2p21 / NM000251
MSH3 / MismatchexcisionrepairMMR / Mismatch (MSH2-MSH6) and loop (MSH2-MSH3) recognition / 5q14.1 / NM002439
MSH4 / MismatchexcisionrepairMMR / MutS homologs specialized for meiosis / 1p31.1 / NM002440
MSH5 / MismatchexcisionrepairMMR / MutS homologs specialized for meiosis / 6p21.33 / NM002441
MSH6 / MismatchexcisionrepairMMR / Mismatch (MSH2-MSH6) and loop (MSH2-MSH3) recognition / 2p16.3 / NM000179
MUS81 / Homologousrecombination / Subunits of structure-specific DNA nuclease / 11q13.1 / NM025128
MUTYH / Baseexcisionrepair / A opposite 8-oxoG / 1p34.1 / NM012222
NBN / Homologous recombination / Mutated in Nijmegen breakage syndrome / 8q21.3 / NM002485 / Olaparib / Prostate / (7)
NEIL1 / Baseexcisionrepair / Removes thymine glycol / 15q24.2 / NM024608
NEIL2 / Baseexcisionrepair / Removes oxidative products of pyrimidines / 8p23.1 / NM145043
NEIL3 / Baseexcisionrepair / Removes oxidative products of pyrimidines / 4q34 / NM018248
NHEJ1 / Nonhomologousendjoining / End-joining factor / 2q35 / NM024782
NTHL1 / Baseexcisionrepair / Ring-saturated or fragmented pyrimidines / 16p13.3 / NM002528
NUDT1 / Modulationofnucleotidepools / 8-oxoGTPase / 7p22.3 / NM002452
OBFC2B / OtheridentifiedgeneswithknownorsuspectedDNArepairfunction / Single-stranded DNA binding protein / 12q13.2 / NM024068
OGG1 / Baseexcisionrepair / 8-oxoG opposite C / 3p25.3 / NM016821
PALB2 / Fanconianemia / co-localizes with BRCA2 (FANCD1) / 16p12.1 / NM024675 / Olaparib / Prostate / (7)
PARP1 / PARPenzymesthatbindtoDNA / Protects strand interruptions / 1q42.12 / NM001618
PARP2 / PARPenzymesthatbindtoDNA / PARP-like enzyme / 14q11.2 / NM005484
PARP3 / PARPenzymesthatbindtoDNA / PARP-like enzyme / 3p21.1 / NM001003931
PCNA / DNApolymerasescatalyticsubunits / Sliding clamp for pol delta and pol epsilon / 20p12.3 / NM002592
PER1 / OtherconservedDNAdamageresponsegenes / S-phase check point and biological clock protein / 17p12 / NM002616
PMS1 / MismatchexcisionrepairMMR / MutL homologs of unknown function / 2q32.2 / NM000534
PMS2 / MismatchexcisionrepairMMR / MutL homologs, forming heterodimer / 7p22.1 / NM000535
PMS2L3 / MismatchexcisionrepairMMR / MutL homologs of unknown function / 7q11.23 / NM005395
PNKP / BERstrandbreak joiningfactors / Converts some DNA breaks to ligatable ends / 19q13.33 / NM007254
POLB / DNApolymerasescatalyticsubunits / BER in nuclear DNA / 8p11.21 / NM002690
POLD1 / DNApolymerasescatalyticsubunits / NER and MMR / 19q13.33 / NM002691
POLE / DNApolymerasescatalyticsubunits / NER and MMR / 12q24.33 / NM006231
POLG / DNApolymerasescatalyticsubunits / BER in mitochondrial DNA / 15q26.1 / NM002693
POLH / DNApolymerasescatalyticsubunits / xerodermapigmentosum (XP) variant / 6p21.1 / NM006502
POLI / DNApolymerasescatalyticsubunits / Lesion bypass / 18q21.2 / NM007195
POLK / DNApolymerasescatalyticsubunits / Lesion bypass and NER / 5q13.3 / NM016218
POLL / DNApolymerasescatalyticsubunits / Gap-filling during non-homologous end-joining / 10q24.32 / NM013274
POLM / DNApolymerasescatalyticsubunits / Gap filling during non-homologous end-joining / 7p13 / NM013284
POLN / DNApolymerasescatalyticsubunits / DNA crosslink repair? / 4p16.3 / NM181808
POLQ / DNApolymerasescatalyticsubunits / Sensitivity to ionizing radiation / 3q13.33 / NM199420
PRKDC / Nonhomologousendjoining / DNA-dependent protein kinase catalytic subunit / 8q11.21 / NM006904
PRPF19 / OtheridentifiedgeneswithknownorsuspectedDNArepairfunction / DNA crosslink repair; binding to SETMAR / 11q12.2 / NM014502
RAD1 / OtherconservedDNAdamageresponsegenes / subunits of PCNA-like sensor of damaged DNA / 5p13.2 / NM002853
RAD17 / OtherconservedDNAdamageresponsegenes / RFC-like DNA damage sensor / 5q13.2 / NM002873
RAD18 / Ubiquitinationandmodification / E3 ubiquitin ligase / 3p25.3 / NM020165
RAD23A / Nucleotideexcisionrepair / Substitutes for RAD23B / 19p13.13 / NM005053
RAD23B / Nucleotideexcisionrepair / Binds DNA distortions / 9q31.2 / NM002874
RAD50 / Homologousrecombination / ATPase in complex with MRE11A, NBS1 / 5q23.3 / NM005732
RAD51 / Homologousrecombination / Homologous pairing / 15q15.1 / NM002875 / Olaparib / Prostate / (7)
RAD51B / Homologousrecombination / Rad51 homolog / 14q24.1 / NM002877
RAD51C / Fanconianemia / Rad51 homolog FANCO / 17q23.2 / NM002876 / Cisplatin / Breast / Inactivation is predictive of Homologous Recombination Deficiency (HRD) in breast cancer and is necessary for cisplatin sensitivity. / (8)
RAD51D / Homologousrecombination / Rad51 homolog / 17q12 / NM002878
RAD52 / Homologousrecombination / Accessory factors for recombination / 12p13.33 / NM002879
RAD54B / Homologousrecombination / Accessory factors for recombination / 8q22.1 / NM012415
RAD54L / Homologousrecombination / Accessory factors for recombination / 1p34.1 / NM003579
RAD9A / OtherconservedDNAdamageresponsegenes / subunits of PCNA-like sensor of damaged DNA / 11q13.2 / NM004584
RB1 / Cisplatin / Bladder / (6)
RBBP8 / Homologousrecombination / Promotes DNA end resection / 18q11.2 / NM002894
RDM1 / OtheridentifiedgeneswithknownorsuspectedDNArepairfunction / Similar to RAD52 / 17q12 / NM145654
RECQL / OtheridentifiedgeneswithknownorsuspectedDNArepairfunction / DNA helicase / 12p12.1 / NM002907
RECQL4 / GenesdefectiveindiseasesassociatedwithsensitivitytoDNAdamagingagents / Rothmund-Thompson syndrome / 8q24.3 / NM004260
RECQL5 / OtheridentifiedgeneswithknownorsuspectedDNArepairfunction / DNA helicase / 17q25.1 / NM001003715
REV1L / DNApolymerasescatalyticsubunits / dCMPtransferase / 2q11.2 / NM016316
REV3L / DNApolymerasescatalyticsubunits / DNA pol zeta catalytic subunit, essential function / 6q21 / NM002912
RIF1 / OtherconservedDNAdamageresponsegenes / suppressor of 5'-end-resection / 2q23.3 / NM001177665
RNF168 / Ubiquitinationandmodification / E3 ubiquitin ligase for DSB repair; ATM-like and RIDDLE syndrome / 3q29 / NM152617
RNF4 / Ubiquitinationandmodification / E3 ubiquitin ligase / 4p16.3 / NM001185009
RNF8 / Ubiquitinationandmodification / E3 ubiquitin ligase for DSB repair / 6p21 / NM152617
RPA1 / Nucleotideexcisionrepair / Binds DNA in preincision complex / 17p13.3 / NM002945
RPA2 / Nucleotideexcisionrepair / Binds DNA in preincision complex / 1p35.3 / NM002946
RPA3 / Nucleotideexcisionrepair / Binds DNA in preincision complex / 7p21.3 / NM002947
RPA4 / OtheridentifiedgeneswithknownorsuspectedDNArepairfunction / Similar to RPA2 / Xp21.33 / NM013347
RRM1
RRM2
RRM2B / Modulationofnucleotidepools / p53-inducible ribonucleotide reductase small subunit 2 homolog / 8q22.3 / NM015713
SETMAR / ChromatinStructureandModification / DNA damage-associated histone methylase and nuclease / 3p26 / NM006515
SHFM1 / Homologousrecombination / BRCA2 associated / 7q21.3 / NM006304
SHPRH / Ubiquitinationandmodification / E3 ubiquitin ligase, SWI/SNF related, homolog of S. cerevisiae Rad5 / 6q24.3 / NM001042683
SLX4 / Fanconianemia / nuclease subunit/scaffold BTBD12 (SLX4) FANCP / 16p13.3 / NM032444
SMUG1 / Baseexcisionrepair / U / 12q13.13 / NM014311
SPO11 / Editingandprocessingnucleases / endonuclease / 20q13.32 / NM012444
SPRTN / Ubiquitinationandmodification / Reads ubiquitylation / 1q42.12-q43 / NM032018
TDG / BaseexcisionrepairBER / U, T or ethenoC opposite G / 12q23.3 / NM003211
TDP1 / RepairofDNAtopoisomerasecrosslinks / Removes 3'-tyrosylphosphate and 3'-phosphoglycolate from DNA; human disorder SCAN1 / 14q32.11 / NM018319
TDP2 / RepairofDNAtopoisomerasecrosslinks / 5'- and 3'-tyrosyl DNA phosphodiesterase / 6p22.3 / NM016614
TOPBP1 / OtherconservedDNAdamageresponsegenes / DNA damage checkpoint control / 3q22.1 / NM007027
TP53 / OtherconservedDNAdamageresponsegenes / Regulation of the cell cycle / 17p13.1 / NM000546 / Cisplatin / Bladder / Enhancement of chemo-sensitivity in human bladder cancer cells by adenoviral-mediated p53 gene transfer. Overexpres-sion of mutant p53 and Bcl-2 in bladder cancer cells synergistically interferes with the therapeutic effect of cisplatin. TL and p53 mutation did not predict response or toxicity. / (6, 12, 13)
TP53BP1 / OtherconservedDNAdamageresponsegenes / chromatin-binding checkpoint protein / 15q15-q21 / NM001141980
TREX1 / Editingandprocessingnucleases / 3' exonuclease / 3p21.31 / NM033629
TREX2 / Editingandprocessingnucleases / 3' exonuclease / Xq28 / NM007205
TTDN1 / GenesdefectiveindiseasesassociatedwithsensitivitytoDNAdamagingagents / non-photosensitive form of trichothiodystrophy / 7p14 / NM138701
UBE2A / Ubiquitinationandmodification / Ubiquitin-conjugating enzyme / Xq24-q25 / NM003336
UBE2B / Ubiquitinationandmodification / Ubiquitin-conjugating enzyme / 5q31.1 / NM003337
UBE2N / Ubiquitinationandmodification / Ubiquitin-conjugating complex / 12q22 / NM003348
UBE2V2 / Ubiquitinationandmodification / Ubiquitin-conjugating complex / 8q11.21 / NM003350
UNG / Baseexcisionrepair / U / 12q24.11 / NM080911
UVSSA / Nucleotideexcisionrepair / Cockayne syndrome and UV-Sensitive Syndrome; Needed for transcription-coupled NER / 4p16.3 / NM020894
WRN / Genesdefective in diseasesassociatedwithsensitivity to DNAdamagingagents / Werner syndrome helicase / 3' - exonuclease / 8p12 / NM000553
XAB2 / Nucleotideexcisionrepair / XAB2 / 19p13.2 / NM020196
XPA / Nucleotideexcisionrepair / Binds damaged DNA in preincision complex / 9q22.33 / NM000380
XPC / Nucleotideexcisionrepair / Binds DNA distortions / 3p25.1 / NM004628
XRCC1 / BERstrandbreak joiningfactors / LIG3 accessory factor / 19q13.31 / NM006297
XRCC2 / Homologousrecombination / DNA break and crosslink repair / 7q36.1 / NM005431
XRCC3 / Homologousrecombination / DNA break and crosslink repair / 14q32.33 / NM005432
XRCC4 / Nonhomologous end joining / Ligase accessory factor / 5q14.2 / NM003401
XRCC5 / Nonhomologous end joining / DNA end binding subunit / 2q35 / NM021141
XRCC6 / Nonhomologous end joining / DNA end binding subunit / 22q13.2 / NM001469
DNA repair-associated genes analyzed by targeted sequencing in this study. A comprehensive list of DNA repair genes was
compiled primarily from references from Wood et al.(14)and references describing cisplatin-sensitivity genes.
Supplementary Table 7 : Mutations found in DNA repair genes in MIBC PDX models
Supplementary Information References
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