Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance

Dalia Tarantino; Callum Walker; Daniel Weekes; Helen Pemberton; Kathryn Davidson; Gonzalo Torga; Jessica Frankum; Ana M. Mendes-Pereira; Cynthia Prince; Riccardo Ferro; Rachel Brough; Stephen J. Pettitt; Christopher J. Lord; Anita Grigoriadis; Andrew NJ  Tutt

doi:10.1038/s41388-022-02369-9

Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance

Dalia Tarantino, Callum Walker, Daniel Weekes, Helen Pemberton, Kathryn Davidson, Gonzalo Torga, Jessica Frankum, Ana M. Mendes-Pereira, Cynthia Prince, Riccardo Ferro, Rachel Brough, Stephen J. Pettitt, Christopher J. Lord, Anita Grigoriadis, Andrew NJ Tutt^*

^*Corresponding author for this work

Comprehensive Cancer Centre

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

1 Citation (Scopus)

Abstract

HORMAD1 expression is usually restricted to germline cells, but it becomes mis-expressed in epithelial cells in ~60% of triple-negative breast cancers (TNBCs), where it is associated with elevated genomic instability (1). HORMAD1 expression in TNBC is bimodal with HORMAD1-positive TNBC representing a biologically distinct disease group. Identification of HORMAD1-driven genetic dependencies may uncover novel therapies for this disease group. To study HORMAD1-driven genetic dependencies, we generated a SUM159 cell line model with doxycycline-inducible HORMAD1 that replicated genomic instability phenotypes seen in HORMAD1-positive TNBC (1). Using small interfering RNA screens, we identified candidate genes whose depletion selectively inhibited the cellular growth of HORMAD1-expressing cells. We validated five genes (ATR, BRIP1, POLH, TDP1 and XRCC1), depletion of which led to reduced cellular growth or clonogenic survival in cells expressing HORMAD1. In addition to the translesion synthesis (TLS) polymerase POLH, we identified a HORMAD1-driven dependency upon additional TLS polymerases, namely POLK, REV1, REV3L and REV7. Our data confirms that out-of-context somatic expression of HORMAD1 can lead to genomic instability and reveals that HORMAD1 expression induces dependencies upon replication stress tolerance pathways, such as translesion synthesis. Our data also suggest that HORMAD1 expression could be a patient selection biomarker for agents targeting replication stress.

Original language	English
Pages (from-to)	3969-3977
Number of pages	9
Journal	Oncogene
Volume	41
Issue number	32
Early online date	29 Jun 2022
DOIs	https://doi.org/10.1038/s41388-022-02369-9
Publication status	Published - 5 Aug 2022

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Tarantino, D., Walker, C., Weekes, D., Pemberton, H., Davidson, K., Torga, G., Frankum, J., Mendes-Pereira, A. M., Prince, C., Ferro, R., Brough, R., Pettitt, S. J., Lord, C. J., Grigoriadis, A., & Tutt, A. NJ. (2022). Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance. Oncogene, 41(32), 3969-3977. https://doi.org/10.1038/s41388-022-02369-9

@article{1ddda29bb72a490f8ff893b7501bdd43,

title = "Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance",

abstract = "HORMAD1 expression is usually restricted to germline cells, but it becomes mis-expressed in epithelial cells in ~60% of triple-negative breast cancers (TNBCs), where it is associated with elevated genomic instability (1). HORMAD1 expression in TNBC is bimodal with HORMAD1-positive TNBC representing a biologically distinct disease group. Identification of HORMAD1-driven genetic dependencies may uncover novel therapies for this disease group. To study HORMAD1-driven genetic dependencies, we generated a SUM159 cell line model with doxycycline-inducible HORMAD1 that replicated genomic instability phenotypes seen in HORMAD1-positive TNBC (1). Using small interfering RNA screens, we identified candidate genes whose depletion selectively inhibited the cellular growth of HORMAD1-expressing cells. We validated five genes (ATR, BRIP1, POLH, TDP1 and XRCC1), depletion of which led to reduced cellular growth or clonogenic survival in cells expressing HORMAD1. In addition to the translesion synthesis (TLS) polymerase POLH, we identified a HORMAD1-driven dependency upon additional TLS polymerases, namely POLK, REV1, REV3L and REV7. Our data confirms that out-of-context somatic expression of HORMAD1 can lead to genomic instability and reveals that HORMAD1 expression induces dependencies upon replication stress tolerance pathways, such as translesion synthesis. Our data also suggest that HORMAD1 expression could be a patient selection biomarker for agents targeting replication stress.",

author = "Dalia Tarantino and Callum Walker and Daniel Weekes and Helen Pemberton and Kathryn Davidson and Gonzalo Torga and Jessica Frankum and Mendes-Pereira, {Ana M.} and Cynthia Prince and Riccardo Ferro and Rachel Brough and Pettitt, {Stephen J.} and Lord, {Christopher J.} and Anita Grigoriadis and Tutt, {Andrew NJ}",

note = "Funding Information: This work was funded by Programme Grants from Breast Cancer Now as part of Programme Funding to the Breast Cancer Now Toby Robins Research Centre and by funding from Cancer Research UK, the National Institute for Health Research (NIHR) Biomedical Research Centre at Guy{\textquoteright}s and St Thomas{\textquoteright} NHS Foundation Trust and the NIHR Royal Marsden Hospital Biomedical Research Centre to Prof. Andrew Tutt. We thank King{\textquoteright}s College London Genomic Core Facility for supporting the RT-qPCR data acquisition and analysis. We thank the Nikon Imaging Centre (KCL) for access to and assistance with the microscope facilities. We thank Sorapun Utting, Melanie Ferrao and Caroline Carey for technical and administrative assistance. We thank Dr. Rebecca Marlow for providing training in immunofluorescence image processing. We thank Dr. Tencho Tenev for providing assistance with the design and optimisation of the CRISPR-Cas9 based gene editing experiments. We thank Dr. Olivia Rossanese and the Cancer Therapeutics Unit (ICR) for kindly providing laboratory space for conducting part of the experimental work. Funding Information: This work was funded by Programme Grants from Breast Cancer Now as part of Programme Funding to the Breast Cancer Now Toby Robins Research Centre and by funding from Cancer Research UK, the National Institute for Health Research (NIHR) Biomedical Research Centre at Guy{\textquoteright}s and St Thomas{\textquoteright} NHS Foundation Trust and the NIHR Royal Marsden Hospital Biomedical Research Centre to Prof. Andrew Tutt. We thank King{\textquoteright}s College London Genomic Core Facility for supporting the RT-qPCR data acquisition and analysis. We thank the Nikon Imaging Centre (KCL) for access to and assistance with the microscope facilities. We thank Sorapun Utting, Melanie Ferrao and Caroline Carey for technical and administrative assistance. We thank Dr. Rebecca Marlow for providing training in immunofluorescence image processing. We thank Dr. Tencho Tenev for providing assistance with the design and optimisation of the CRISPR-Cas9 based gene editing experiments. We thank Dr. Olivia Rossanese and the Cancer Therapeutics Unit (ICR) for kindly providing laboratory space for conducting part of the experimental work. Funding Information: ANJT is/has been a consultant for AstraZeneca, Merck KGaA, Artios, Pfizer, Vertex, GE Healthcare, Inbiomotion, Prime Oncology, Medscape Education, EMPartners, VJ Oncology, Gilead and MD Anderson Cancer Centre; has received grant/research support from AstraZeneca, Myriad, Medivation and Merck KGaA; is a stockholder in Inbiomotion; and stands to gain from the use of PARPi as part of the Institute of Cancer Research {\textquoteleft}rewards to inventors{\textquoteright} scheme. CJL makes the following disclosures: receives and/or has received research funding from: AstraZeneca, Merck KGaA, Artios. Received consultancy, SAB membership or honoraria payments from: Syncona, Sun Pharma, Gerson Lehrman Group, Merck KGaA, Vertex, AstraZeneca, Tango, 3rd Rock, Ono Pharma, Artios, Abingworth, Tesselate. Has stock in: Tango, Ovibio, Enedra Tx., Hysplex, Tesselate. CJL is also a named inventor on patents describing the use of DNA repair inhibitors and stands to gain from their development and use as part of the ICR “Rewards to Inventors” scheme. The remaining authors declare no competing interests. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = aug,

day = "5",

doi = "10.1038/s41388-022-02369-9",

language = "English",

volume = "41",

pages = "3969--3977",

journal = "Oncogene",

issn = "0950-9232",

publisher = "Springer Nature [academic journals on nature.com]",

number = "32",

}

Tarantino, D, Walker, C, Weekes, D, Pemberton, H, Davidson, K, Torga, G, Frankum, J, Mendes-Pereira, AM, Prince, C, Ferro, R, Brough, R, Pettitt, SJ, Lord, CJ, Grigoriadis, A & Tutt, ANJ 2022, 'Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance', Oncogene, vol. 41, no. 32, pp. 3969-3977. https://doi.org/10.1038/s41388-022-02369-9

TY - JOUR

T1 - Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance

AU - Tarantino, Dalia

AU - Walker, Callum

AU - Weekes, Daniel

AU - Pemberton, Helen

AU - Davidson, Kathryn

AU - Torga, Gonzalo

AU - Frankum, Jessica

AU - Mendes-Pereira, Ana M.

AU - Prince, Cynthia

AU - Ferro, Riccardo

AU - Brough, Rachel

AU - Pettitt, Stephen J.

AU - Lord, Christopher J.

AU - Grigoriadis, Anita

AU - Tutt, Andrew NJ

N1 - Funding Information: This work was funded by Programme Grants from Breast Cancer Now as part of Programme Funding to the Breast Cancer Now Toby Robins Research Centre and by funding from Cancer Research UK, the National Institute for Health Research (NIHR) Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and the NIHR Royal Marsden Hospital Biomedical Research Centre to Prof. Andrew Tutt. We thank King’s College London Genomic Core Facility for supporting the RT-qPCR data acquisition and analysis. We thank the Nikon Imaging Centre (KCL) for access to and assistance with the microscope facilities. We thank Sorapun Utting, Melanie Ferrao and Caroline Carey for technical and administrative assistance. We thank Dr. Rebecca Marlow for providing training in immunofluorescence image processing. We thank Dr. Tencho Tenev for providing assistance with the design and optimisation of the CRISPR-Cas9 based gene editing experiments. We thank Dr. Olivia Rossanese and the Cancer Therapeutics Unit (ICR) for kindly providing laboratory space for conducting part of the experimental work. Funding Information: This work was funded by Programme Grants from Breast Cancer Now as part of Programme Funding to the Breast Cancer Now Toby Robins Research Centre and by funding from Cancer Research UK, the National Institute for Health Research (NIHR) Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and the NIHR Royal Marsden Hospital Biomedical Research Centre to Prof. Andrew Tutt. We thank King’s College London Genomic Core Facility for supporting the RT-qPCR data acquisition and analysis. We thank the Nikon Imaging Centre (KCL) for access to and assistance with the microscope facilities. We thank Sorapun Utting, Melanie Ferrao and Caroline Carey for technical and administrative assistance. We thank Dr. Rebecca Marlow for providing training in immunofluorescence image processing. We thank Dr. Tencho Tenev for providing assistance with the design and optimisation of the CRISPR-Cas9 based gene editing experiments. We thank Dr. Olivia Rossanese and the Cancer Therapeutics Unit (ICR) for kindly providing laboratory space for conducting part of the experimental work. Funding Information: ANJT is/has been a consultant for AstraZeneca, Merck KGaA, Artios, Pfizer, Vertex, GE Healthcare, Inbiomotion, Prime Oncology, Medscape Education, EMPartners, VJ Oncology, Gilead and MD Anderson Cancer Centre; has received grant/research support from AstraZeneca, Myriad, Medivation and Merck KGaA; is a stockholder in Inbiomotion; and stands to gain from the use of PARPi as part of the Institute of Cancer Research ‘rewards to inventors’ scheme. CJL makes the following disclosures: receives and/or has received research funding from: AstraZeneca, Merck KGaA, Artios. Received consultancy, SAB membership or honoraria payments from: Syncona, Sun Pharma, Gerson Lehrman Group, Merck KGaA, Vertex, AstraZeneca, Tango, 3rd Rock, Ono Pharma, Artios, Abingworth, Tesselate. Has stock in: Tango, Ovibio, Enedra Tx., Hysplex, Tesselate. CJL is also a named inventor on patents describing the use of DNA repair inhibitors and stands to gain from their development and use as part of the ICR “Rewards to Inventors” scheme. The remaining authors declare no competing interests. Publisher Copyright: © 2022, The Author(s).

PY - 2022/8/5

Y1 - 2022/8/5

N2 - HORMAD1 expression is usually restricted to germline cells, but it becomes mis-expressed in epithelial cells in ~60% of triple-negative breast cancers (TNBCs), where it is associated with elevated genomic instability (1). HORMAD1 expression in TNBC is bimodal with HORMAD1-positive TNBC representing a biologically distinct disease group. Identification of HORMAD1-driven genetic dependencies may uncover novel therapies for this disease group. To study HORMAD1-driven genetic dependencies, we generated a SUM159 cell line model with doxycycline-inducible HORMAD1 that replicated genomic instability phenotypes seen in HORMAD1-positive TNBC (1). Using small interfering RNA screens, we identified candidate genes whose depletion selectively inhibited the cellular growth of HORMAD1-expressing cells. We validated five genes (ATR, BRIP1, POLH, TDP1 and XRCC1), depletion of which led to reduced cellular growth or clonogenic survival in cells expressing HORMAD1. In addition to the translesion synthesis (TLS) polymerase POLH, we identified a HORMAD1-driven dependency upon additional TLS polymerases, namely POLK, REV1, REV3L and REV7. Our data confirms that out-of-context somatic expression of HORMAD1 can lead to genomic instability and reveals that HORMAD1 expression induces dependencies upon replication stress tolerance pathways, such as translesion synthesis. Our data also suggest that HORMAD1 expression could be a patient selection biomarker for agents targeting replication stress.

AB - HORMAD1 expression is usually restricted to germline cells, but it becomes mis-expressed in epithelial cells in ~60% of triple-negative breast cancers (TNBCs), where it is associated with elevated genomic instability (1). HORMAD1 expression in TNBC is bimodal with HORMAD1-positive TNBC representing a biologically distinct disease group. Identification of HORMAD1-driven genetic dependencies may uncover novel therapies for this disease group. To study HORMAD1-driven genetic dependencies, we generated a SUM159 cell line model with doxycycline-inducible HORMAD1 that replicated genomic instability phenotypes seen in HORMAD1-positive TNBC (1). Using small interfering RNA screens, we identified candidate genes whose depletion selectively inhibited the cellular growth of HORMAD1-expressing cells. We validated five genes (ATR, BRIP1, POLH, TDP1 and XRCC1), depletion of which led to reduced cellular growth or clonogenic survival in cells expressing HORMAD1. In addition to the translesion synthesis (TLS) polymerase POLH, we identified a HORMAD1-driven dependency upon additional TLS polymerases, namely POLK, REV1, REV3L and REV7. Our data confirms that out-of-context somatic expression of HORMAD1 can lead to genomic instability and reveals that HORMAD1 expression induces dependencies upon replication stress tolerance pathways, such as translesion synthesis. Our data also suggest that HORMAD1 expression could be a patient selection biomarker for agents targeting replication stress.

UR - http://www.scopus.com/inward/record.url?scp=85133200205&partnerID=8YFLogxK

U2 - 10.1038/s41388-022-02369-9

DO - 10.1038/s41388-022-02369-9

M3 - Article

C2 - 35768547

AN - SCOPUS:85133200205

SN - 0950-9232

VL - 41

SP - 3969

EP - 3977

JO - Oncogene

JF - Oncogene

IS - 32

ER -

Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance

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