Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps

Mariana Paes Dias; Vivek Tripathi; Ingrid van der Heijden; Ke Cong; Eleni Maria Manolika; Jinhyuk Bhin; Ewa Gogola; Panagiotis Galanos; Stefano Annunziato; Cor Lieftink; Miguel Andújar-Sánchez; Sanjiban Chakrabarty; Graeme C.M. Smith; Marieke van de Ven; Roderick L. Beijersbergen; Jirina Bartkova; Sven Rottenberg; Sharon Cantor; Jiri Bartek; Arnab Ray Chaudhuri; Jos Jonkers

doi:10.1016/j.molcel.2021.09.005

Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps

Mariana Paes Dias, Vivek Tripathi, Ingrid van der Heijden, Ke Cong, Eleni Maria Manolika, Jinhyuk Bhin, Ewa Gogola, Panagiotis Galanos, Stefano Annunziato, Cor Lieftink, Miguel Andújar-Sánchez, Sanjiban Chakrabarty, Graeme C.M. Smith, Marieke van de Ven, Roderick L. Beijersbergen, Jirina Bartkova, Sven Rottenberg, Sharon Cantor, Jiri Bartek, Arnab Ray Chaudhuri^*Jos Jonkers^*

^*Corresponding author for this work

Molecular Genetics

Research output: Contribution to journal › Article › Academic › peer-review

46 Citations (Scopus)

Abstract

Inhibitors of poly(ADP-ribose) (PAR) polymerase (PARPi) have entered the clinic for the treatment of homologous recombination (HR)-deficient cancers. Despite the success of this approach, preclinical and clinical research with PARPi has revealed multiple resistance mechanisms, highlighting the need for identification of novel functional biomarkers and combination treatment strategies. Functional genetic screens performed in cells and organoids that acquired resistance to PARPi by loss of 53BP1 identified loss of LIG3 as an enhancer of PARPi toxicity in BRCA1-deficient cells. Enhancement of PARPi toxicity by LIG3 depletion is dependent on BRCA1 deficiency but independent of the loss of 53BP1 pathway. Mechanistically, we show that LIG3 loss promotes formation of MRE11-mediated post-replicative ssDNA gaps in BRCA1-deficient and BRCA1/53BP1 double-deficient cells exposed to PARPi, leading to an accumulation of chromosomal abnormalities. LIG3 depletion also enhances efficacy of PARPi against BRCA1-deficient mammary tumors in mice, suggesting LIG3 as a potential therapeutic target.

Original language	English
Pages (from-to)	4692-4708.e9
Journal	Molecular Cell
Volume	81
Issue number	22
DOIs	https://doi.org/10.1016/j.molcel.2021.09.005
Publication status	Published - 18 Nov 2021

Bibliographical note

Funding Information:
We thank Peter Bouwman for sharing the mESCs, Sylvie Noordermeer and Dan Durocher for the RPE1-TERT cells, and Madalena Tarsounas for the DLD1 isogenic cells. We thank Wei Zhao for helping with image analysis and Hanneke van der Gulden, the NKI Preclinical Intervention Unit, digital microscopy facility, genomics core facility, and animal facility for technical assistance. This work was supported by grants from the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant (agreement 722729); Dutch Research Council (Vici 91814643, Vidi 193.131); Dutch Cancer Society (KWF grant 11008); Oncode Institute; Swiss National Science Foundation (310030_179360); Swiss Cancer League (KLS-4282-08-2017); Danish Cancer Society (R204-A12617-B153, R167-A11068); Danish Council for Independent Research (DFF-7016-00313); Novo Nordisk Foundation (16854, 0060590); Danish National Research Foundation (DNRF 125); LundbeckFonden (R322-2019-2577); Swedish Research Council (VR-MH 2014-46602-117891-30); Swedish Cancer Foundation (170176); and grant R01 CA254037. Conceptualization, M.P.D. A.R.C. and J.J.; Methodology, M.P.D. I.v.d.H. and A.R.C.; Investigation, M.P.D. V.T. I.v.d.H. E.-M.M. K.C. P.G. S.A. J. Bartkova, G.C.M.S. and M.A.S.; Supervision of in vivo experiments, M.v.d.V.; Data analysis, C.L. R.L.B. J. Bhin, and S. Chakrabarty; Writing of original draft, review & editing, M.P.D. A.R.C. and J.J.; Supervision, E.G. S.R. S. Cantor, J. Bartek, A.R.C. and J.J. G.C.M.S. is an employee and shareholder of ArtiosPharma Ltd. and of AstraZeneca PLC. All other authors declare no competing interests.

Funding Information:
We thank Peter Bouwman for sharing the mESCs, Sylvie Noordermeer and Dan Durocher for the RPE1-TERT cells, and Madalena Tarsounas for the DLD1 isogenic cells. We thank Wei Zhao for helping with image analysis and Hanneke van der Gulden, the NKI Preclinical Intervention Unit, digital microscopy facility, genomics core facility, and animal facility for technical assistance. This work was supported by grants from the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant (agreement 722729 ); Dutch Research Council ( Vici 91814643 , Vidi 193.131 ); Dutch Cancer Society (KWF grant 11008 ); Oncode Institute ; Swiss National Science Foundation ( 310030_179360 ); Swiss Cancer League ( KLS-4282-08-2017 ); Danish Cancer Society ( R204-A12617-B153 , R167-A11068 ); Danish Council for Independent Research ( DFF-7016-00313 ); Novo Nordisk Foundation ( 16854 , 0060590 ); Danish National Research Foundation ( DNRF 125 ); LundbeckFonden ( R322-2019-2577 ); Swedish Research Council ( VR-MH 2014-46602-117891-30 ); Swedish Cancer Foundation ( 170176 ); and grant R01 CA254037 .

Publisher Copyright:
© 2021 Elsevier Inc.

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10.1016/j.molcel.2021.09.005

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9098260

Cite this

Paes Dias, M., Tripathi, V., van der Heijden, I., Cong, K., Manolika, E. M., Bhin, J., Gogola, E., Galanos, P., Annunziato, S., Lieftink, C., Andújar-Sánchez, M., Chakrabarty, S., Smith, G. C. M., van de Ven, M., Beijersbergen, R. L., Bartkova, J., Rottenberg, S., Cantor, S., Bartek, J., ... Jonkers, J. (2021). Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps. Molecular Cell, 81(22), 4692-4708.e9. https://doi.org/10.1016/j.molcel.2021.09.005

@article{2ce39a2af71c4db39a33ba218d4f74a2,

title = "Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps",

abstract = "Inhibitors of poly(ADP-ribose) (PAR) polymerase (PARPi) have entered the clinic for the treatment of homologous recombination (HR)-deficient cancers. Despite the success of this approach, preclinical and clinical research with PARPi has revealed multiple resistance mechanisms, highlighting the need for identification of novel functional biomarkers and combination treatment strategies. Functional genetic screens performed in cells and organoids that acquired resistance to PARPi by loss of 53BP1 identified loss of LIG3 as an enhancer of PARPi toxicity in BRCA1-deficient cells. Enhancement of PARPi toxicity by LIG3 depletion is dependent on BRCA1 deficiency but independent of the loss of 53BP1 pathway. Mechanistically, we show that LIG3 loss promotes formation of MRE11-mediated post-replicative ssDNA gaps in BRCA1-deficient and BRCA1/53BP1 double-deficient cells exposed to PARPi, leading to an accumulation of chromosomal abnormalities. LIG3 depletion also enhances efficacy of PARPi against BRCA1-deficient mammary tumors in mice, suggesting LIG3 as a potential therapeutic target.",

author = "{Paes Dias}, Mariana and Vivek Tripathi and {van der Heijden}, Ingrid and Ke Cong and Manolika, {Eleni Maria} and Jinhyuk Bhin and Ewa Gogola and Panagiotis Galanos and Stefano Annunziato and Cor Lieftink and Miguel And{\'u}jar-S{\'a}nchez and Sanjiban Chakrabarty and Smith, {Graeme C.M.} and {van de Ven}, Marieke and Beijersbergen, {Roderick L.} and Jirina Bartkova and Sven Rottenberg and Sharon Cantor and Jiri Bartek and {Ray Chaudhuri}, Arnab and Jos Jonkers",

note = "Funding Information: We thank Peter Bouwman for sharing the mESCs, Sylvie Noordermeer and Dan Durocher for the RPE1-TERT cells, and Madalena Tarsounas for the DLD1 isogenic cells. We thank Wei Zhao for helping with image analysis and Hanneke van der Gulden, the NKI Preclinical Intervention Unit, digital microscopy facility, genomics core facility, and animal facility for technical assistance. This work was supported by grants from the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant (agreement 722729); Dutch Research Council (Vici 91814643, Vidi 193.131); Dutch Cancer Society (KWF grant 11008); Oncode Institute; Swiss National Science Foundation (310030_179360); Swiss Cancer League (KLS-4282-08-2017); Danish Cancer Society (R204-A12617-B153, R167-A11068); Danish Council for Independent Research (DFF-7016-00313); Novo Nordisk Foundation (16854, 0060590); Danish National Research Foundation (DNRF 125); LundbeckFonden (R322-2019-2577); Swedish Research Council (VR-MH 2014-46602-117891-30); Swedish Cancer Foundation (170176); and grant R01 CA254037. Conceptualization, M.P.D. A.R.C. and J.J.; Methodology, M.P.D. I.v.d.H. and A.R.C.; Investigation, M.P.D. V.T. I.v.d.H. E.-M.M. K.C. P.G. S.A. J. Bartkova, G.C.M.S. and M.A.S.; Supervision of in vivo experiments, M.v.d.V.; Data analysis, C.L. R.L.B. J. Bhin, and S. Chakrabarty; Writing of original draft, review & editing, M.P.D. A.R.C. and J.J.; Supervision, E.G. S.R. S. Cantor, J. Bartek, A.R.C. and J.J. G.C.M.S. is an employee and shareholder of ArtiosPharma Ltd. and of AstraZeneca PLC. All other authors declare no competing interests. Funding Information: We thank Peter Bouwman for sharing the mESCs, Sylvie Noordermeer and Dan Durocher for the RPE1-TERT cells, and Madalena Tarsounas for the DLD1 isogenic cells. We thank Wei Zhao for helping with image analysis and Hanneke van der Gulden, the NKI Preclinical Intervention Unit, digital microscopy facility, genomics core facility, and animal facility for technical assistance. This work was supported by grants from the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant (agreement 722729 ); Dutch Research Council ( Vici 91814643 , Vidi 193.131 ); Dutch Cancer Society (KWF grant 11008 ); Oncode Institute ; Swiss National Science Foundation ( 310030_179360 ); Swiss Cancer League ( KLS-4282-08-2017 ); Danish Cancer Society ( R204-A12617-B153 , R167-A11068 ); Danish Council for Independent Research ( DFF-7016-00313 ); Novo Nordisk Foundation ( 16854 , 0060590 ); Danish National Research Foundation ( DNRF 125 ); LundbeckFonden ( R322-2019-2577 ); Swedish Research Council ( VR-MH 2014-46602-117891-30 ); Swedish Cancer Foundation ( 170176 ); and grant R01 CA254037 . Publisher Copyright: {\textcopyright} 2021 Elsevier Inc.",

year = "2021",

month = nov,

day = "18",

doi = "10.1016/j.molcel.2021.09.005",

language = "English",

volume = "81",

pages = "4692--4708.e9",

journal = "Molecular Cell",

issn = "1097-2765",

publisher = "Cell Press",

number = "22",

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Paes Dias, M, Tripathi, V, van der Heijden, I, Cong, K, Manolika, EM, Bhin, J, Gogola, E, Galanos, P, Annunziato, S, Lieftink, C, Andújar-Sánchez, M, Chakrabarty, S, Smith, GCM, van de Ven, M, Beijersbergen, RL, Bartkova, J, Rottenberg, S, Cantor, S, Bartek, J, Ray Chaudhuri, A & Jonkers, J 2021, 'Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps', Molecular Cell, vol. 81, no. 22, pp. 4692-4708.e9. https://doi.org/10.1016/j.molcel.2021.09.005

TY - JOUR

T1 - Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps

AU - Paes Dias, Mariana

AU - Tripathi, Vivek

AU - van der Heijden, Ingrid

AU - Cong, Ke

AU - Manolika, Eleni Maria

AU - Bhin, Jinhyuk

AU - Gogola, Ewa

AU - Galanos, Panagiotis

AU - Annunziato, Stefano

AU - Lieftink, Cor

AU - Andújar-Sánchez, Miguel

AU - Chakrabarty, Sanjiban

AU - Smith, Graeme C.M.

AU - van de Ven, Marieke

AU - Beijersbergen, Roderick L.

AU - Bartkova, Jirina

AU - Rottenberg, Sven

AU - Cantor, Sharon

AU - Bartek, Jiri

AU - Ray Chaudhuri, Arnab

AU - Jonkers, Jos

N1 - Funding Information: We thank Peter Bouwman for sharing the mESCs, Sylvie Noordermeer and Dan Durocher for the RPE1-TERT cells, and Madalena Tarsounas for the DLD1 isogenic cells. We thank Wei Zhao for helping with image analysis and Hanneke van der Gulden, the NKI Preclinical Intervention Unit, digital microscopy facility, genomics core facility, and animal facility for technical assistance. This work was supported by grants from the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant (agreement 722729); Dutch Research Council (Vici 91814643, Vidi 193.131); Dutch Cancer Society (KWF grant 11008); Oncode Institute; Swiss National Science Foundation (310030_179360); Swiss Cancer League (KLS-4282-08-2017); Danish Cancer Society (R204-A12617-B153, R167-A11068); Danish Council for Independent Research (DFF-7016-00313); Novo Nordisk Foundation (16854, 0060590); Danish National Research Foundation (DNRF 125); LundbeckFonden (R322-2019-2577); Swedish Research Council (VR-MH 2014-46602-117891-30); Swedish Cancer Foundation (170176); and grant R01 CA254037. Conceptualization, M.P.D. A.R.C. and J.J.; Methodology, M.P.D. I.v.d.H. and A.R.C.; Investigation, M.P.D. V.T. I.v.d.H. E.-M.M. K.C. P.G. S.A. J. Bartkova, G.C.M.S. and M.A.S.; Supervision of in vivo experiments, M.v.d.V.; Data analysis, C.L. R.L.B. J. Bhin, and S. Chakrabarty; Writing of original draft, review & editing, M.P.D. A.R.C. and J.J.; Supervision, E.G. S.R. S. Cantor, J. Bartek, A.R.C. and J.J. G.C.M.S. is an employee and shareholder of ArtiosPharma Ltd. and of AstraZeneca PLC. All other authors declare no competing interests. Funding Information: We thank Peter Bouwman for sharing the mESCs, Sylvie Noordermeer and Dan Durocher for the RPE1-TERT cells, and Madalena Tarsounas for the DLD1 isogenic cells. We thank Wei Zhao for helping with image analysis and Hanneke van der Gulden, the NKI Preclinical Intervention Unit, digital microscopy facility, genomics core facility, and animal facility for technical assistance. This work was supported by grants from the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant (agreement 722729 ); Dutch Research Council ( Vici 91814643 , Vidi 193.131 ); Dutch Cancer Society (KWF grant 11008 ); Oncode Institute ; Swiss National Science Foundation ( 310030_179360 ); Swiss Cancer League ( KLS-4282-08-2017 ); Danish Cancer Society ( R204-A12617-B153 , R167-A11068 ); Danish Council for Independent Research ( DFF-7016-00313 ); Novo Nordisk Foundation ( 16854 , 0060590 ); Danish National Research Foundation ( DNRF 125 ); LundbeckFonden ( R322-2019-2577 ); Swedish Research Council ( VR-MH 2014-46602-117891-30 ); Swedish Cancer Foundation ( 170176 ); and grant R01 CA254037 . Publisher Copyright: © 2021 Elsevier Inc.

PY - 2021/11/18

Y1 - 2021/11/18

N2 - Inhibitors of poly(ADP-ribose) (PAR) polymerase (PARPi) have entered the clinic for the treatment of homologous recombination (HR)-deficient cancers. Despite the success of this approach, preclinical and clinical research with PARPi has revealed multiple resistance mechanisms, highlighting the need for identification of novel functional biomarkers and combination treatment strategies. Functional genetic screens performed in cells and organoids that acquired resistance to PARPi by loss of 53BP1 identified loss of LIG3 as an enhancer of PARPi toxicity in BRCA1-deficient cells. Enhancement of PARPi toxicity by LIG3 depletion is dependent on BRCA1 deficiency but independent of the loss of 53BP1 pathway. Mechanistically, we show that LIG3 loss promotes formation of MRE11-mediated post-replicative ssDNA gaps in BRCA1-deficient and BRCA1/53BP1 double-deficient cells exposed to PARPi, leading to an accumulation of chromosomal abnormalities. LIG3 depletion also enhances efficacy of PARPi against BRCA1-deficient mammary tumors in mice, suggesting LIG3 as a potential therapeutic target.

AB - Inhibitors of poly(ADP-ribose) (PAR) polymerase (PARPi) have entered the clinic for the treatment of homologous recombination (HR)-deficient cancers. Despite the success of this approach, preclinical and clinical research with PARPi has revealed multiple resistance mechanisms, highlighting the need for identification of novel functional biomarkers and combination treatment strategies. Functional genetic screens performed in cells and organoids that acquired resistance to PARPi by loss of 53BP1 identified loss of LIG3 as an enhancer of PARPi toxicity in BRCA1-deficient cells. Enhancement of PARPi toxicity by LIG3 depletion is dependent on BRCA1 deficiency but independent of the loss of 53BP1 pathway. Mechanistically, we show that LIG3 loss promotes formation of MRE11-mediated post-replicative ssDNA gaps in BRCA1-deficient and BRCA1/53BP1 double-deficient cells exposed to PARPi, leading to an accumulation of chromosomal abnormalities. LIG3 depletion also enhances efficacy of PARPi against BRCA1-deficient mammary tumors in mice, suggesting LIG3 as a potential therapeutic target.

UR - http://www.scopus.com/inward/record.url?scp=85119597645&partnerID=8YFLogxK

U2 - 10.1016/j.molcel.2021.09.005

DO - 10.1016/j.molcel.2021.09.005

M3 - Article

C2 - 34555355

AN - SCOPUS:85119597645

SN - 1097-2765

VL - 81

SP - 4692-4708.e9

JO - Molecular Cell

JF - Molecular Cell

IS - 22

ER -

Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps

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