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Miral Dizdaroglu Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with liquid chromatography-tandem mass spectrometry with isotope-dilution isotope-dilution National Institute of Standards and National Institute of Standards and Technology Technology Gaithersburg, Maryland, USA Gaithersburg, Maryland, USA

Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

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Page 1: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Miral DizdarogluMiral Dizdaroglu

Measurement of DNA repair proteins in human tissues by Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with liquid chromatography-tandem mass spectrometry with

isotope-dilutionisotope-dilution

National Institute of Standards and National Institute of Standards and TechnologyTechnology

Gaithersburg, Maryland, USAGaithersburg, Maryland, USA

Page 2: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

N

NN

N

NH2

O

HO

HH

HH

O

NH

N

N

O

NH2N

O

H

HH

HHO

OP

O-

O

O

H

HH

HH

N

N

NH2

O

OP

O-

O

O

P

O-

OO

H

HH

HH

HN

N

O

O

O

O

O

P

O-

O

P

O-

O O

CH3

sugar- phosphate backbone

adenine

guanine

cytosine

thymine

Sites of oxidatively induced damage in DNASites of oxidatively induced damage in DNA

OH, eOH, eaqaq――, H, HOH, eOH, eaqaq――, H, H

OHOHOHOHDNA base damageDNA sugar damage 8,5'-cyclopurine-2'-

deoxynucleosidesTandem lesionsClustered sitesDNA-protein cross-linksSingle- and double-strand breaksAbasic sites

Reviewed in:Dizdaroglu, M. and Jaruga, P., Free Radic. Res. 46, 382-419, 2012

Page 3: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Products of oxidatively induced damage to DNA Products of oxidatively induced damage to DNA bases bases

Reviewed in:Dizdaroglu, M. and Jaruga, P., Free Radic. Res. 46, 382-419, 2012

N

N NH2

H2N

O

2,5-diamino-4H-imidazol-4-one

O

N NH2

H2NO

H2N

2,2,4-triamino-5(2H)-oxazolone

HN

N NH

NHN

N NH2

NHCHO

8-hydroxyguanine 2,6-diamino-4-hydroxy-5-formamidopyrimidine

H2N

OH

O O

H2N

guanine-derived products

NH

NN

N

O

O

HO

HH

HH

O

H

DNA

DNANH2

(5'R)-8,5'-cyclo-2'-deoxyguanosine

NH

NN

N

O

O

HO

HH

HH

O

H

DNA

DNA

NH2

(5'S)-8,5'-cyclo-2'-deoxyguanosine

N

N NH

NN

N NH2

NHCHO

H

N

N NH

N

HO

8-hydroxyadenine 4,6-diamino-5-form-amidopyrimidine

2-hydroxyadenine

NH2

OH

NH2

H

NH2

H

adenine-derived productsN

NN

N

NH2

O

HO

HH

HH

O

H

DNA

DNA

(5'R)-8,5'-cyclo-2'-deoxyadenosine

N

NN

N

NH2

O

HO

HH

HH

H

O

DNA

DNA

(5'S)-8,5'-cyclo-2'-deoxyadenosine

NH

N

NH

N

OHNH

N

NH

N

5-hydroxy-6-hydrocytosine

cytosine glycol 5-hydroxycytosine 5,6-dihydroxy-cytosine

NH2

H

OH

OH

H

NH2

O H

NH2

OHH

O H

OH

NH2

O

OH

OHNH

N

5,6-dihydrocytosine

NH2H

OH

H

H

NH

HNO

5-hydroxy-hydantoin

O OHH

NH

HN

OH

uracil glycol

O

H

H

OH

O

NH

HN

O

H

5,6-dihydrouracil

H

HO

H

NH

HN

5-hydroxyuracil

O

O H

OH

NH

HN

5-hydroxy-6-hydrouracil

O

O H

H

H

OH

NH

HN

alloxan

O

O

O

O NH

HN

isodialuric acid

O

O

OH

O

H

NH

HN

dialuric acid

O

OH

O

OH

cytosine-derived products

NH

HN

O

HNH

HN

O

CH2OH

NH

HNO

NH

HN

O

HNH

HN

OH

thymine glycol

3

5-(hydroxymethyl)- uracil

5,6-dihydrothymine

3

5-hydroxy-5-methylhydantoin

3

5-hydroxy-6-hydro- thymine

NH

HN

O

CHO

5-formyluracil

H

OH

O

CH

H

H

H OOCH

O

CH

OHH

OH

O

O

CH3

HO

thymine-derived products

Page 4: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Reviewed in:Madhusudan, S. and Middleton, M. R., Cancer Treatment Reviews 31, 603-617, 2005.Helleday, T., Petermann, E., Lunding, C., Hodgson, B. and Sharma, R.A., Nature Reviews Cancer 8, 193-204, 2008Helleday, T., European J. Cancer 44, 921-927, 2008Raffoul, J.J., Heydari, S.R. and Hillman, G.G., Journal of Oncology , 2012Kelley, M., DNA Repair in Cancer Therapy, Elsevier, 2012

One important mechanism by which cancer cells can develop resistance to therapy is to increase their DNA repair capacity.

DNA repair in cancer therapyDNA repair in cancer therapy

The efficacy of anticancer drugs and radiation can be reduced in cancer cells by increased DNA repair that remove DNA lesions before they become toxic.

DNA repair pathways are promising targets for novel cancer treatments

Inhibition of DNA Inhibition of DNA repairrepair

Page 5: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Poly(ADP-ribose) polymerase 1 (PARP1)

PARP1 is required for the efficient repair of AP sites and single-stranded DNA breaks.

Cells deficient in BRCA1 or BRCA2 are highly sensitive to PARP1 inhibition.

Apurinic/apyrimidic endonuclease 1 (APE1)

APE1 hydrolyzes the phosphate bond at 5' to AP site, causing a strand breaks and leaving a 3'-OH group and a 5‘-deoxyribose-phosphate terminus.

Targeted DNA repair proteins in base excision repair pathwayTargeted DNA repair proteins in base excision repair pathway

MTH1

MTH1 dephosporylates modified 2‘-deoxynucleoside triphosphates in the nucleotide pool to prevent

incorporation of DNA lesions during DNA replication.

Reviewed in:Helleday, T., Petermann, E., Lunding, C., Hodgson, B. and Sharma, R.A., Nature Reviews Cancer 8, 193-204, 2008Wilson III, D.M. and Simeonov, A., Cell. Mol. Life Sci. 67, 3621-3631, 2010Kelley, M., DNA Repair in Cancer Therapy, Elsevier, 2012Gad, H., et al. Nature 508, 215-221, 2014

DNA glycosylases

NEIL1, NEIL2, NEIL3, OGG1, NTH1

Page 6: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

DNA repair in cancer therapyDNA repair in cancer therapy

To use DNA repair proteins as disease biomarkers or to determine the DNA repair capacity in tissues, the measurement of the levels of DNA repair proteins in vivo will be necessary.

Mass spectrometric techniques with isotope-dilution will be the techniques of choice for accurate measurement of DNA repair proteins in tissues.

“A knowledge of DNA repair proteins’ overexpression or underexpression in cancers will help predict and guide development of treatments, and yield the greatest therapeutic response.”

Kelley, M. R., DNA Repair in Cancer Therapy, Elsevier, 2012

Page 7: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Apurinic/apyrimidinic endonuclease 1 Apurinic/apyrimidinic endonuclease 1 (APE1)(APE1)

DNA repair activity of APE1 is critical for cell viability.1. Complete absence of APE1 is associated with embryonic lethality in mice2. APE1 depletion hypersensitizes cells to DNA damage3. Overexpression of APE1 protects cells from DNA damage

APE1 expression is increased in human cancers1. Nuclear and/or cytoplasmic overexpression of APE1 occurs in breast, cervical, colon, head & neck, lung, melanoma, ovarian, prostate, etc., cancers2. Increased APE1 expression is associated with resistance to chemo- and radiation

therapies

APE1 as a predictive and prognostic biomarker1. Alterations in APE expression levels and subcellular localization may have predictive

and prognostic significance in many human cancers2. Nuclear localization is associated with good prognostic features3. Cytoplasmic localization is associated with poor survival outcomes

Positive identification and accurate quantification of APE1 in tissues is Positive identification and accurate quantification of APE1 in tissues is essential for its use as an efficient biomarker essential for its use as an efficient biomarker

Reviewed in:Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A. and Ellenberger, T., DNA Repair and Mutagenesis, 2006Abbotts, R. and Madhusudan, S., Cancer Treat Rev. 36, 425-435, 2010

Page 8: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

repaired DNA

DNA-damaging agent

APE1

DNA repair activity of APE1DNA repair activity of APE1

Reviewed in: Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A. and Ellenberger, T., DNA Repair and Mutagenesis, 2006

APE1 hydrolyzes the O-P bond 5' to the AP site, yielding 2'-deoxyribose-

5'-phosphate and 3'-OH end

APE1AP site

excision of a modified base

Approximately 10000 AP sites are formed per day per cell

spontaneous hydrolysis

base excision repair pathway

Page 9: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Production, isolation and purification of Production, isolation and purification of 1515N-N-hAPE1hAPE1

proteinmarkers

(kDa)

15N-hAPE1

175

80

58

46

30

25

54321

Lane 1: Uninduced cell extractLane 2: Induced cell extractLane 3: 70,000 x g supernatant fractionLane 4: Flow through from DEAE cellulose columnLane 5: Flow through from CM cellulose columnLane 6: Purified 15N-hAPE1

6

Kirkali, G., Jaruga, P., Reddy, P. T., Tona, A., Nelson, B. C., Li, M., Wilson III, D. M. and Dizdaroglu, M., PLOS ONE 8 (7), e69894, 2013

hAPE1 15N-hAPE1

proteinmarkers

(kDa)

250

150

100

75

50

37

25

20

35.532 kDa35.970 kDa

SDS-PAGE analysis of hAPE1 and 15N-hAPE1

Page 10: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Measurement of molecular masses of hAPE1 and Measurement of molecular masses of hAPE1 and 1515N-N-hAPE1 by Orbitrap mass spectrometryhAPE1 by Orbitrap mass spectrometry

hAPE1 15N-hAPE1average mass 35554 35992

loss of Met 131 13235423 35860

found 35421 35854difference -2 -6

% labeling99.98

200002100022000230002400025000260002700028000290003000031000320003300034000350003600037000380003900040000Mass 35854

mass-to-charge (m/z)

15N-hAPE1

200002100022000230002400025000260002700028000290003000031000320003300034000350003600037000380003900040000Mass 35421

mass-to-charge (m/z)

hAPE1

Kirkali, G., Jaruga, P., Reddy, P. T., Tona, A., Nelson, B. C., Li, M., Wilson III, D. M. and Dizdaroglu, M., PLOS ONE 8 (7), e69894, 2013

Page 11: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Calculation of fragment masses of tryptic peptides Calculation of fragment masses of tryptic peptides using using NIST Mass and Fragment CalculatorNIST Mass and Fragment Calculator

Page 12: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Measurement of human APE1 by LC-MS/MS with isotope-Measurement of human APE1 by LC-MS/MS with isotope-dilutiondilution

unlabeled peptide 15N-labeled peptide

peak peptide MH+ (M+2H)2+ MH+ (M+2H)2+

1 GLASR 503.2 252.1 511.2 256.1

2 TSPSGKPATLK 1086.6 543.8 1099.6 550.3

3 GLVR 444.2 222.6 452.2 226.6

4 NAGFTPQER 1019.4 510.2 1033.4 517.2

5 NVGWR 631.3 316.1 641.3 321.1

6 GAVAEDGDELR 1131.5 566.2 1145.5 573.2

7 VSYGIGDEEHDQEGR 1690.7 845.8 1711.7 856.3

8 AWIK 517.3 259.1 523.3 262.1

9 EAAGEGPALYEDPPDQK 1786.8 893.9 1805.8 903.4

10 WDEAFR 823.3 412.1 833.3 417.1

11 GLDWVK 717.3 359.1 725.3 363.1

12 EGYSGVGLLSR 1137.5 569.2 1151.5 576.2

13 EEAPDILCLQETK 1488.7 744.8 1503.7 752.3

14 QGFGELLQAVPLADSFR 1847.9 924.4 1869.9 935.4

inte

ns

ity

20e7

40e7

60e7

80e7

100e7

2 4 6 8 10 12 14 16time (min)

1

2

3

4

57

8

9

11

12

13

6 14

10

15N-hAPE1

2 4 6 8 10 12 14 16time (min)

5e7

15e7

25e7

35e7

45e7

inte

ns

ity

12

3

4

5

7

8

9

11

12

13

6

14

10

hAPE1

Total-ion-current profiles of tryptic peptidesTotal-ion-current profiles of tryptic peptides

Identified peptides

Kirkali, G., Jaruga, P., Reddy, P. T., Tona, A., Nelson, B. C., Li, M., Wilson III, D. M. and Dizdaroglu, M., PLOS ONE 8 (7), e69894, 2013

Molecular mass 35.5 kDa

Sequence of hAPE1

MPKRGKK GAVAEDGDELR TEPEAK K SK TAAK K NDK EAAGEGPALYEDPPDQK TSPSGKPATLK ICSWNVDGLR AWIK K K GLDWVK EEAPD ILCLQETK CSENK LPAELQELPGLSHQYWSAPSDK EGYSGVGLLSR QCPLK VSYGIGDEEHDQEGR VIVAEFDSFVLVTAYVPNAGR GLVR LEYR QR WDEAFR K FLK GLASR KPLVLCGDLNVAHEEIDLR NPK GNK K NAGFTPQER QGFGELLQAVPLADSFR HLYPNTPYAYTFWTYMMNAR SK NVGWR LDYFLLSHSLLPALCDSK IR SK ALGSDHCPITLYLAL318

Page 13: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

100

600 700 800 900 1000 1100 1200 1300 14000

10

20

30

40

50

60

70

80

90

652.1

1303.1

VQEGETIEDGARVQEGETIEDGAR

(M+2H)2+

MH+

mass-to-charge (m/z)

Rel

ati

ve

Ab

un

da

nc

e (

%)

600 700 800 900 1000 1100 1200 1300 14000

10

20

30

40

50

60

70

80

90

100 659.9

1319.1

15N-VQEGETIEDGAR15N-VQEGETIEDGAR

(M+2H)2+

MH+

mass-to-charge (m/z)

Rel

ati

ve

Ab

un

da

nc

e (

%)

Full scan-mass spectrum of a tryptic peptide of hAPE1 and its Full scan-mass spectrum of a tryptic peptide of hAPE1 and its 1515N-N-labeled analoglabeled analog

659.9

1319.1

Kirkali, G., Jaruga, P., Reddy, P. T., Tona, A., Nelson, B. C., Li, M., Wilson III, D. M. and Dizdaroglu, M., PLOS ONE 8 (7), e69894, 2013

Page 14: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

200 400 600 800 1000 1200 14000

10

20

30

40

50

60

70

80

90

100

rela

tive

ab

un

dan

ce (

%)

805.1

975.4

915.7

595.3

409.2

1087.11216.6

186.0

708.31329.8

1458.8

mass-to-charge (m/z)

333.1

904.4

y5 y6

y7

y8

b2

b3

y9

y3

y10 –NH3

y10

y11

y12

y13

1103.5

a9

614.4

b6 –H2O

501.14b5 –H2O

745.3b7

y7

Q–G–F–G–E–L–L–Q–A–V–P–L–A–D–S–F–R

y3y13 y5y6

b3

y8

b4

y9y10y12 y11

b7

Product ion spectra of a tryptic peptide of hAPE1 and its Product ion spectra of a tryptic peptide of hAPE1 and its 1515N-labeled N-labeled analoganalog

200 400 600 800 1000 1200 14000

10

20

30

40

50

60

70

80

90

100

rela

tive

ab

un

dan

ce (

%)

815.2

925.93415.14 987.5336.6

1231.3

1117.4

717.41345.9

603.04

1476.0

mass-to-charge (m/z)

189.1

915.4

y5

y6

y7

y8

b2

b3 y9y3

y10 –NH3

y10

y11

y12

y13

1099.4

a9

620.0b6 –H2O

506.6b5 –H2O

753.4

b7

y7

15N-Q–G–F–G–E–L–L–Q–A–V–P–L–A–D–S–F–R

y3y13 y5y6

b3

y8

b4

y9y10y12 y11

b7

MH+ m/z 1848.0 (M + 2H)2+ m/z 924.5

Mass transitionsm/z 924.5 → m/z 805.4m/z 924.5 → m/z 904.5m/z 924.5 → m/z 975.5

m/z 924.5 → m/z 1103.6 m/z 924.5 → m/z 1216.7 m/z 924.5 → m/z 1329.8 m/z 924.5 → m/z 1458.8

MH+ m/z 1870.0(M + 2H)2+ m/z 935.5

Mass transitions m/z 935.5 → m/z 815.4 m/z 935.5 → m/z 915.5m/z 935.5 → m/z 987.5

m/z 935.5 → m/z 1117.6 m/z 935.5 → m/z 1231.7 m/z 935.5 → m/z 1345.8 m/z 935.5 → m/z 1475.8

Kirkali, G., Jaruga, P., Reddy, P. T., Tona, A., Nelson, B. C., Li, M., Wilson III, D. M. and Dizdaroglu, M., PLOS ONE 8 (7), e69894, 2013

Page 15: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

M. Kinter and N.E. Sherman, Protein Sequencing and Identification Using Tandem Mass Spectrometry, Wiley, 2000

Collision energy (V)

Inte

nsi

ty

0 5 10 15 20 25 30 35 40 45 50 55 600

2.0107

4.0107

6.0107

m/z 429 m/z 402

m/z 698 m/z 956

m/z 811 m/z 1041

m/z 763 m/z 679

m/z 503 m/z 695

m/z 315 m/z 288

m/z 322 m/z 272

m/z 508 m/z 603

m/z 382 m/z 564

Determination of optimal collision energiesDetermination of optimal collision energies

Reddy, P.T., Jaruga, P., Kirkali, G., Tuna, G., Nelson, B.C. and Dizdaroglu, M., J. Proteome Res. 12, 1049-1061, 2013

m/z

Co

llis

ion

en

erg

y (

V)

300 400 500 600 700 8000

10

20

30

40

Page 16: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

0

100

200

300

400

500

600

Time (min)

10 12 14 16 18 20 22 24 26

cytoplasmic extractMCF-7 cells

Time (min)

10 12 14 16 18 20 22 24 26

100

150

200

250

300

350

400

450

500 nuclear extractMCF-7 cells

Enrichment of APE1 by HPLC from protein extracts of human cellsEnrichment of APE1 by HPLC from protein extracts of human cells

hAPE1

hAPE1

Kirkali, G., Jaruga, P., Reddy, P. T., Tona, A., Nelson, B. C., Li, M., Wilson III, D. M. and Dizdaroglu, M., PLOS ONE 8 (7), e69894, 2013

Page 17: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Inte

nsi

ty

5000

100000

1000

3000

0

10000

20000

0

5000

15000

0

50000

0

50000

0

10000

20000

0

10000

20000

4.84

4.84

5.14

5.13

5.30

5.30

7.06

7.04

m/z 510.2 → m/z 834.4

NAGFTPQER

m/z 517.2 → m/z 845.4

15N-NAGFTPQER

m/z 566.3 → m/z 904.4

GAVAEDGDELR

m/z 573.3 → m/z 915.4

15N-GAVAEDGDELR

m/z 893.9 → m/z 584.3

EAAGEGPALYEDPPDQK

m/z 903.4 → m/z 591.3

15N-EAAGEGPALYEDPPDQK

m/z 316.2 → m/z 418.2

NVGWR

m/z 321.2 → m/z 425.2

15N-NVGWR

0 2 4 6 8 10 12 14 16Time (min)

0

7.36

0 2 4 6 8 10 12 14 16Time (min)

0

2000

4000

0

1000

3000

0

10000

30000

0

20000

40000

0

50000

1000000

20000

40000

0

10000

20000

0

5000

15000

7.37

8.27

8.27

8.80

8.80

14.70

14.69

m/z 359.2 → m/z 547.3

GLDWVK

m/z 363.2 → m/z 553.3

15N-GLDWVK

m/z 569.3 → m/z 545.3

EGYSGVGLLSR

m/z 576.3 → m/z 553.3

15N-EGYSGVGLLSR

m/z 924.5 → m/z 805.4

QGFGELLQAVPLADSFR

m/z 935.5 → m/z 815.4

15N-QGFGELLQAVPLADSFR

m/z 412.2 → m/z 637.3

WDEAFR

m/z 417.2 → m/z 645.3

15N-WDEAFR

Inte

nsi

ty

Identification and quantification of APE1 in human MCF-10A cellsIdentification and quantification of APE1 in human MCF-10A cells

Kirkali, G., Jaruga, P., Reddy, P. T., Tona, A., Nelson, B. C., Li, M., Wilson III, D. M. and Dizdaroglu, M., PLOS ONE 8 (7), e69894, 2013

Page 18: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Identification and quantification of APE1 in human cultured cells and Identification and quantification of APE1 in human cultured cells and mouse livermouse liver

Kirkali, G., Jaruga, P., Reddy, P. T., Tona, A., Nelson, B. C., Li, M., Wilson III, D. M. and Dizdaroglu, M., PLOS ONE 8 (7), e69894, 2013

0

1

2

3

4

hA

PE

1 l

ev

el (

pg

/ g

pro

tein

)

MCF-10A

MCF-7

HepG-2

MCF-10A: mammary gland epithelial cell lineMCF-7: mammary gland epithelial adenocarcinoma

cell lineHepG-2: hepatocellular carcinoma cell line

hA

PE

1 le

vel

(ng

/μg

pro

tein

)

p 0.0001

p 0.0001

p 0.0015

p 0.0001

p 0.0001

Levels of hAPE1 in human normal and cancer cell lines

p 0.0001

0.00

0.04

0.08

0.12

mA

PE

1 l

ev

el

(pg

/ g

pro

tein

)h

AP

E1

leve

l (n

g/μ

g p

rote

in)

Levels of hAPE1 in mouse liver

Page 19: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Identification and quantification of APE1 in human breast Identification and quantification of APE1 in human breast tissuestissues

Unpublished results

p 0.0001

normal cancer0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

AP

E1

leve

l (n

g/

g p

rote

in)

Levels of hMTH1 in human disease-free breast tissues and malignant breast tumors

disease-free breast tissue malignant breast tissue

Page 20: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Sanitation of the nucleotide Sanitation of the nucleotide poolpool

MTH1MTH1 hydrolyzes oxidized 2’-deoxynucleoside triphosphates to monophosphates in the nucleotide pool. As a result, DNA polymerases cannot insert the wrong base across from the normal base, maintaining transcription fidelity, thus inhibiting mutagenesis.

8-OH-dGMP8-OH-dGTPMTH1

hydrolysis8-OH-dG

nucleotidase

8-OH-dGMP cannot be rephosphorylated by guanylate kinase, which phosphorylates dGMP.

Reviewed in:Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A. and Ellenberger, T., DNA Repair and Mutagenesis, 2006

Page 21: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Inhibition of MTH1 in cancer therapyInhibition of MTH1 in cancer therapy

Nature, 508, 215-221, 2014

Page 22: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Production, isolation and purification of Production, isolation and purification of 1515N-N-hNTH1hNTH1

Coskun, E., Jaruga, P., Jemth, A.-S., Loseva, O., Scanlan, L.D., Tona, A., Lowenthal, M.S., Helleday, T. and Dizdaroglu, M., DNA Repair ( in press).

SDS-PAGE analysis of hMTH1 and 15N-hMTH1

Separation of hMTH1 and 15N-hMTH1 by HPLC. The elution profiles were superimposed.

Page 23: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Measurement of the masses of hMTH1 and Measurement of the masses of hMTH1 and 1515N-hMTH1 by QToF N-hMTH1 by QToF LC/MSLC/MS

Coskun, E., Jaruga, P., Jemth, A.-S., Loseva, O., Scanlan, L.D., Tona, A., Lowenthal, M.S., Helleday, T. and Dizdaroglu, M., DNA Repair ( in press).

Page 24: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

  unlabeled 15N-labeled

peak tryptic peptide MH+ (M+2H)2+ MH+ (M+2H)2+

1 GFGAGR 564.2 282.6 573.2 287.1

2 VQEGETIEDGAR 1303.6 652.3 1319.5 660.2

3 FHGYFK 798.3 399.7 807.3 404.2

4 WNGFGGK 765.3 383.1 775.3 388.2

5 VLLGMK 660.4 330.7 667.3 334.2

6 ELQEESGLTVDALHK 1668.8 834.9 1687.7 844.4

7 FQGQDTILDYTLR 1569.7 785.4 1587.7 794.4

Measurement of human MTH1 by LC-MS/MS with isotope-Measurement of human MTH1 by LC-MS/MS with isotope-dilutiondilution

Sequences of the identified peptides

Coskun, E., Jaruga, P., Jemth, A.-S., Loseva, O., Scanlan, L.D., Tona, A., Lowenthal, M.S., Helleday, T. and Dizdaroglu, M., DNA Repair ( in press).

Total-ion-current profiles of tryptic peptidesTotal-ion-current profiles of tryptic peptides

hMTH1

15N-hMTH1

Sequence of hMTH1 p18 isoform

molecular mass 17.95 kDa

156

Page 25: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Determination of optimal collision energiesDetermination of optimal collision energies

Coskun, E., Jaruga, P., Jemth, A.-S., Loseva, O., Scanlan, L.D., Tona, A., Lowenthal, M.S., Helleday, T. and Dizdaroglu, M., DNA Repair ( in press).

Page 26: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Identification and quantification of MTH1 in human Identification and quantification of MTH1 in human cultured cellscultured cells

Coskun, E., Jaruga, P., Jemth, A.-S., Loseva, O., Scanlan, L.D., Tona, A., Lowenthal, M.S., Helleday, T. and Dizdaroglu, M., DNA Repair ( in press).

MCF-10A cells MCF-7 cells

MCF-1

0A

MCF-7

HeLa

HepG2

0.00

0.05

0.10

0.15

0.20

leve

l of

MT

H1

(ng

/ g

pro

tein

)

Levels of hMTH1 in human normal and cancer cell lines

p 0.0001

p 0.0001

MCF-10A: mammary gland epithelial cell lineMCF-7: mammary gland epithelial

adenocarcinoma cell lineHeLa: cervix epithelial adenocarcinoma

cell lineHepG-2: hepatocellular carcinoma cell line

Page 27: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Coskun, E., Jaruga, P., Jemth, A.-S., Loseva, O., Scanlan, L.D., Tona, A., Lowenthal, M.S., Helleday, T. and Dizdaroglu, M., DNA Repair ( in press).

Identification and quantification of MTH1 in human breast Identification and quantification of MTH1 in human breast tissuestissues

A: disease-free breast tissuesB: malignant breast tumors

Levels of hMTH1 in human disease-free breast tissues and malignant breast tumors

normal cancer0.000

0.002

0.004

0.006

0.008

0.010

0.012

0.014

leve

l o

f M

TH

1 (n

g/

g p

rote

in)

p 0.0001

Page 28: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

ConclusionsConclusions

Oxidative stress caused in vivo by endogenous and exogenous DNA-damaging agents leads to the formation of a plethora of lesions in DNA.

DNA lesions are repaired in vivo by a variety of DNA repair mechanisms.

Cancer cells resist to therapy by greater DNA repair capacity than in normal cells.

DNA repair proteins are promising targets for novel cancer treatments. DNA repair inhibitors are being developed worldwide as potential drugs.

Accurate measurement of DNA repair proteins’ overexpression or underexpression in cancers may help predict and guide development of treatments, and yield the greatest therapeutic response.

LC-MS/MS with isotope-dilution using stable isotope-labeled analogs is well suited for the positive identification and accurate quantification of DNA repair proteins in human tissues.

Page 29: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Pawel Jaruga, NISTErdem Coskun, NISTGüldal Kirkali, NIST and

NIHPrasad T. Reddy, NISTBryant C. Nelson, NISTMark S. Lowenthal, NISTLeona D. Scanlan, NISTAlex Tona, NISTGamze Tuna, NISTThomas Helleday, SwedenAnn-Sofie Jemth, SwedenOlga Loseva, Sweden

Collaborators Collaborators

Page 30: Miral Dizdaroglu Measurement of DNA repair proteins in human tissues by liquid chromatography-tandem mass spectrometry with isotope-dilution National Institute

Thank youThank you

National Institute of Standards and National Institute of Standards and TechnologyTechnology

Gaithersburg, Maryland, USAGaithersburg, Maryland, USA