MS CETSA deep functional proteomics uncovers DNA repair programs leading to gemcitabine resistance
Abstract Mechanisms for resistance to cytotoxic cancer drugs are dependent on dynamic changes in the biochemistry of cellular pathways, information which is hard to obtain at the systems level. Here we use a deep functional proteomics implementation of the Cellular Thermal Shift Assay to reveal a ra...
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Nature Portfolio
2025-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-59505-8 |
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| author | Ying Yu Liang Khalidah Khalid Hai Van Le Hui Min Vivian Teo Mindaugas Raitelaitis Marc-Antoine Gerault Jane Jia Hui Lee Jiawen Lyu Allison Chan Anand Devaprasath Jeyasekharan Wai Leong Tam Pär Nordlund Nayana Prabhu |
| author_facet | Ying Yu Liang Khalidah Khalid Hai Van Le Hui Min Vivian Teo Mindaugas Raitelaitis Marc-Antoine Gerault Jane Jia Hui Lee Jiawen Lyu Allison Chan Anand Devaprasath Jeyasekharan Wai Leong Tam Pär Nordlund Nayana Prabhu |
| author_sort | Ying Yu Liang |
| collection | DOAJ |
| description | Abstract Mechanisms for resistance to cytotoxic cancer drugs are dependent on dynamic changes in the biochemistry of cellular pathways, information which is hard to obtain at the systems level. Here we use a deep functional proteomics implementation of the Cellular Thermal Shift Assay to reveal a range of induced biochemical responses to gemcitabine in resistant and sensitive diffuse large B cell lymphoma cell lines. Initial responses in both, gemcitabine resistant and sensitive cells, reflect known targeted effects by gemcitabine on ribonucleotide reductase and DNA damage responses. However, later responses diverge dramatically where sensitive cells show induction of characteristic CETSA signals for early apoptosis, while resistant cells reveal biochemical modulations reflecting transition through a distinct DNA-damage signaling state, including opening of cell cycle checkpoints and induction of translesion DNA synthesis programs, allowing bypass of damaged DNA-adducts. The results also show the induction of a protein ensemble, labeled the Auxiliary DNA Damage Repair, likely supporting DNA replication at damaged sites that can be attenuated in resistant cells by an ATR inhibitor, thus re-establishing gemcitabine sensitivity and demonstrating ATR as a key signaling node of this response. |
| format | Article |
| id | doaj-art-abfc0f04ac9c45b0b6e126399cc382de |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-abfc0f04ac9c45b0b6e126399cc382de2025-08-20T03:45:35ZengNature PortfolioNature Communications2041-17232025-05-0116111510.1038/s41467-025-59505-8MS CETSA deep functional proteomics uncovers DNA repair programs leading to gemcitabine resistanceYing Yu Liang0Khalidah Khalid1Hai Van Le2Hui Min Vivian Teo3Mindaugas Raitelaitis4Marc-Antoine Gerault5Jane Jia Hui Lee6Jiawen Lyu7Allison Chan8Anand Devaprasath Jeyasekharan9Wai Leong Tam10Pär Nordlund11Nayana Prabhu12Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis DriveInstitute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis DriveInstitute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis DriveGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis StreetDepartment of Oncology and Pathology, Karolinska InstitutetDepartment of Oncology and Pathology, Karolinska InstitutetGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis StreetDepartment of Oncology and Pathology, Karolinska InstitutetCancer Science Institute of Singapore, National University of SingaporeCancer Science Institute of Singapore, National University of SingaporeGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis StreetInstitute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis DriveInstitute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis DriveAbstract Mechanisms for resistance to cytotoxic cancer drugs are dependent on dynamic changes in the biochemistry of cellular pathways, information which is hard to obtain at the systems level. Here we use a deep functional proteomics implementation of the Cellular Thermal Shift Assay to reveal a range of induced biochemical responses to gemcitabine in resistant and sensitive diffuse large B cell lymphoma cell lines. Initial responses in both, gemcitabine resistant and sensitive cells, reflect known targeted effects by gemcitabine on ribonucleotide reductase and DNA damage responses. However, later responses diverge dramatically where sensitive cells show induction of characteristic CETSA signals for early apoptosis, while resistant cells reveal biochemical modulations reflecting transition through a distinct DNA-damage signaling state, including opening of cell cycle checkpoints and induction of translesion DNA synthesis programs, allowing bypass of damaged DNA-adducts. The results also show the induction of a protein ensemble, labeled the Auxiliary DNA Damage Repair, likely supporting DNA replication at damaged sites that can be attenuated in resistant cells by an ATR inhibitor, thus re-establishing gemcitabine sensitivity and demonstrating ATR as a key signaling node of this response.https://doi.org/10.1038/s41467-025-59505-8 |
| spellingShingle | Ying Yu Liang Khalidah Khalid Hai Van Le Hui Min Vivian Teo Mindaugas Raitelaitis Marc-Antoine Gerault Jane Jia Hui Lee Jiawen Lyu Allison Chan Anand Devaprasath Jeyasekharan Wai Leong Tam Pär Nordlund Nayana Prabhu MS CETSA deep functional proteomics uncovers DNA repair programs leading to gemcitabine resistance Nature Communications |
| title | MS CETSA deep functional proteomics uncovers DNA repair programs leading to gemcitabine resistance |
| title_full | MS CETSA deep functional proteomics uncovers DNA repair programs leading to gemcitabine resistance |
| title_fullStr | MS CETSA deep functional proteomics uncovers DNA repair programs leading to gemcitabine resistance |
| title_full_unstemmed | MS CETSA deep functional proteomics uncovers DNA repair programs leading to gemcitabine resistance |
| title_short | MS CETSA deep functional proteomics uncovers DNA repair programs leading to gemcitabine resistance |
| title_sort | ms cetsa deep functional proteomics uncovers dna repair programs leading to gemcitabine resistance |
| url | https://doi.org/10.1038/s41467-025-59505-8 |
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