Computational modelling identifies primary mediators of crosstalk between DNA damage and oxidative stress responses

Cells exposed to toxicants, such as drugs, activate a wide variety of stress pathways, often simultaneously. Two important pathways that can influence cell fate and consequently adverse reactions are the oxidative stress response (OSR) and the DNA damage response (DDR). Previous studies have present...

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Published in:	PLoS computational biology Vol. 21; no. 3; p. e1012844
Main Authors:	Burgers, Elsje J., Sharma, Raju P., Eugenio, Carl Joshua S., Heldring, Muriel M., Wijaya, Lukas S., van de Water, Bob, Beltman, Joost B.
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 01.03.2025 Public Library of Science (PLoS)
Subjects:	BTG2 protein Cell culture Cell fate Cell research Cellular signal transduction Cellular stress response Complications and side effects Computational Biology Computer applications Computer Simulation Computer-generated environments Crosstalk Cyclin-dependent kinase inhibitor p21 Damage Deoxyribonucleic acid Diethyl maleate DNA DNA damage DNA Damage - physiology DNA repair Drug dosages Etoposide Etoposide - pharmacology Hep G2 Cells Hepatocytes Humans Kinases Liver Maleates - pharmacology Mathematical models MDM2 protein Methods Models, Biological Ordinary differential equations Oxidative stress Oxidative Stress - drug effects Oxidative Stress - physiology p53 Protein Pharmaceutical industry Proteins Signal Transduction - drug effects Signal Transduction - physiology Toxicants Toxicity Tumor proteins Netherlands Timor-Leste
ISSN:	1553-7358, 1553-734X, 1553-7358
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Abstract	Cells exposed to toxicants, such as drugs, activate a wide variety of stress pathways, often simultaneously. Two important pathways that can influence cell fate and consequently adverse reactions are the oxidative stress response (OSR) and the DNA damage response (DDR). Previous studies have presented evidence of crosstalk between the OSR and DDR. We aimed to develop computational models to describe experimentally observed dynamics of both OSR and DDR proteins in liver (HepG2) cells in vitro upon exposure to various concentrations of either diethyl maleate (DEM; an agent primarily invoking oxidative stress) or etoposide (an agent primarily causing DNA damage). With these models, we aimed to identify the key interactions that cause crosstalk and their importance in describing protein dynamics. We developed a new model for the OSR pathway, coupled it to a previously developed model for the DDR pathway, and extended the resulting combined model based on multiple potential modes of crosstalk described in the literature. The different models were applied to previously published data of HepG2 GFP-reporter cells with time-dynamic information on the relative amount of proteins important for the OSR (NRF2, SRXN1) or DDR (p53, p21, BTG2 and MDM2). The developed models properly described key OSR and DDR protein dynamics, and in silico knockdowns of key model components in most cases led to a moderate effect on the connected pathway. The largest effect occurred after knockdown of p21, which resulted in a substantial decrease in NRF2 and SRXN1. We expect these models could play a role in adversity predictions by coupling our models with other models that predict cell fate or adversity based on the expression of specific proteins.
AbstractList	Cells exposed to toxicants, such as drugs, activate a wide variety of stress pathways, often simultaneously. Two important pathways that can influence cell fate and consequently adverse reactions are the oxidative stress response (OSR) and the DNA damage response (DDR). Previous studies have presented evidence of crosstalk between the OSR and DDR. We aimed to develop computational models to describe experimentally observed dynamics of both OSR and DDR proteins in liver (HepG2) cells in vitro upon exposure to various concentrations of either diethyl maleate (DEM; an agent primarily invoking oxidative stress) or etoposide (an agent primarily causing DNA damage). With these models, we aimed to identify the key interactions that cause crosstalk and their importance in describing protein dynamics. We developed a new model for the OSR pathway, coupled it to a previously developed model for the DDR pathway, and extended the resulting combined model based on multiple potential modes of crosstalk described in the literature. The different models were applied to previously published data of HepG2 GFP-reporter cells with time-dynamic information on the relative amount of proteins important for the OSR (NRF2, SRXN1) or DDR (p53, p21, BTG2 and MDM2). The developed models properly described key OSR and DDR protein dynamics, and in silico knockdowns of key model components in most cases led to a moderate effect on the connected pathway. The largest effect occurred after knockdown of p21, which resulted in a substantial decrease in NRF2 and SRXN1. We expect these models could play a role in adversity predictions by coupling our models with other models that predict cell fate or adversity based on the expression of specific proteins. Cells exposed to toxicants, such as drugs, activate a wide variety of stress pathways, often simultaneously. Two important pathways that can influence cell fate and consequently adverse reactions are the oxidative stress response (OSR) and the DNA damage response (DDR). Previous studies have presented evidence of crosstalk between the OSR and DDR. We aimed to develop computational models to describe experimentally observed dynamics of both OSR and DDR proteins in liver (HepG2) cells in vitro upon exposure to various concentrations of either diethyl maleate (DEM; an agent primarily invoking oxidative stress) or etoposide (an agent primarily causing DNA damage). With these models, we aimed to identify the key interactions that cause crosstalk and their importance in describing protein dynamics. We developed a new model for the OSR pathway, coupled it to a previously developed model for the DDR pathway, and extended the resulting combined model based on multiple potential modes of crosstalk described in the literature. The different models were applied to previously published data of HepG2 GFP-reporter cells with time-dynamic information on the relative amount of proteins important for the OSR (NRF2, SRXN1) or DDR (p53, p21, BTG2 and MDM2). The developed models properly described key OSR and DDR protein dynamics, and in silico knockdowns of key model components in most cases led to a moderate effect on the connected pathway. The largest effect occurred after knockdown of p21, which resulted in a substantial decrease in NRF2 and SRXN1. We expect these models could play a role in adversity predictions by coupling our models with other models that predict cell fate or adversity based on the expression of specific proteins.Cells exposed to toxicants, such as drugs, activate a wide variety of stress pathways, often simultaneously. Two important pathways that can influence cell fate and consequently adverse reactions are the oxidative stress response (OSR) and the DNA damage response (DDR). Previous studies have presented evidence of crosstalk between the OSR and DDR. We aimed to develop computational models to describe experimentally observed dynamics of both OSR and DDR proteins in liver (HepG2) cells in vitro upon exposure to various concentrations of either diethyl maleate (DEM; an agent primarily invoking oxidative stress) or etoposide (an agent primarily causing DNA damage). With these models, we aimed to identify the key interactions that cause crosstalk and their importance in describing protein dynamics. We developed a new model for the OSR pathway, coupled it to a previously developed model for the DDR pathway, and extended the resulting combined model based on multiple potential modes of crosstalk described in the literature. The different models were applied to previously published data of HepG2 GFP-reporter cells with time-dynamic information on the relative amount of proteins important for the OSR (NRF2, SRXN1) or DDR (p53, p21, BTG2 and MDM2). The developed models properly described key OSR and DDR protein dynamics, and in silico knockdowns of key model components in most cases led to a moderate effect on the connected pathway. The largest effect occurred after knockdown of p21, which resulted in a substantial decrease in NRF2 and SRXN1. We expect these models could play a role in adversity predictions by coupling our models with other models that predict cell fate or adversity based on the expression of specific proteins.
Audience	Academic
Author	Wijaya, Lukas S. Eugenio, Carl Joshua S. Heldring, Muriel M. Beltman, Joost B. Sharma, Raju P. Burgers, Elsje J. van de Water, Bob
Author_xml	– sequence: 1 givenname: Elsje J. orcidid: 0000-0002-0863-0774 surname: Burgers fullname: Burgers, Elsje J. – sequence: 2 givenname: Raju P. surname: Sharma fullname: Sharma, Raju P. – sequence: 3 givenname: Carl Joshua S. orcidid: 0009-0005-7947-8860 surname: Eugenio fullname: Eugenio, Carl Joshua S. – sequence: 4 givenname: Muriel M. surname: Heldring fullname: Heldring, Muriel M. – sequence: 5 givenname: Lukas S. surname: Wijaya fullname: Wijaya, Lukas S. – sequence: 6 givenname: Bob surname: van de Water fullname: van de Water, Bob – sequence: 7 givenname: Joost B. orcidid: 0000-0001-9215-3087 surname: Beltman fullname: Beltman, Joost B.
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/40063860$$D View this record in MEDLINE/PubMed
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SubjectTerms	BTG2 protein Cell culture Cell fate Cell research Cellular signal transduction Cellular stress response Complications and side effects Computational Biology Computer applications Computer Simulation Computer-generated environments Crosstalk Cyclin-dependent kinase inhibitor p21 Damage Deoxyribonucleic acid Diethyl maleate DNA DNA damage DNA Damage - physiology DNA repair Drug dosages Etoposide Etoposide - pharmacology Hep G2 Cells Hepatocytes Humans Kinases Liver Maleates - pharmacology Mathematical models MDM2 protein Methods Models, Biological Ordinary differential equations Oxidative stress Oxidative Stress - drug effects Oxidative Stress - physiology p53 Protein Pharmaceutical industry Proteins Signal Transduction - drug effects Signal Transduction - physiology Toxicants Toxicity Tumor proteins
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Title	Computational modelling identifies primary mediators of crosstalk between DNA damage and oxidative stress responses
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