1
|
Bedia JS, Huang YW, Gonzalez AD, Gonzalez VD, Funingana IG, Rahil Z, Mike A, Lowber A, Vias M, Ashworth A, Brenton JD, Fantl WJ. Coordinated protein modules define DNA damage responses to carboplatin at single cell resolution in human ovarian carcinoma models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.21.624591. [PMID: 39605494 PMCID: PMC11601625 DOI: 10.1101/2024.11.21.624591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Tubo-ovarian high-grade serous carcinoma (HGSC) is the most lethal gynecological malignancy and frequently responds to platinum-based chemotherapy because of common genetic and somatic impairment of DNA damage repair (DDR) pathways. The mechanisms of clinical platinum resistance are diverse and poorly molecularly defined. Consequently, there are no biomarkers or medicines that improve patient outcomes. Herein we use single cell mass cytometry (CyTOF) to systematically evaluate the phosphorylation and abundance of proteins known to participate in the DNA damage response (DDR). Single cell analyses of highly characterized HGSC cell lines that phenocopy human patients show that cells with comparable levels of intranuclear platinum, a proxy for carboplatin uptake, undergo different cell fates. Unsupervised analyses revealed a continuum of DDR responses. Decompositional methods were used to identify eight distinct protein modules of carboplatin resistance and sensitivity at single cell resolution. CyTOF profiling of primary and secondary platinum-resistance patient models shows that a complex DDR sensitivity module is strongly associated with response, suggesting it as a potential tool to clinically characterize complex drug resistance phenotypes.
Collapse
Affiliation(s)
- Jacob S. Bedia
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ying-Wen Huang
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Veronica D. Gonzalez
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ionut-Gabriel Funingana
- Department of Oncology, University of Cambridge, Cambridgeshire, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire, CB2 0RE, UK
- Department of Oncology, Addenbrooke’s Hospital, Cambridge University Hospitals, NHS Foundation Trust, Cambridge, UK
| | - Zainab Rahil
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alyssa Mike
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexis Lowber
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maria Vias
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire, CB2 0RE, UK
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 Third Street, San Francisco, CA 94158, USA
| | - James D. Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire, CB2 0RE, UK
- Department of Oncology, Addenbrooke’s Hospital, Cambridge University Hospitals, NHS Foundation Trust, Cambridge, UK
| | - Wendy J. Fantl
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Comprehensive Cancer Institute
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
2
|
Li Z, Gu H, Xu X, Tian Y, Huang X, Du Y. Unveiling the novel immune and molecular signatures of ovarian cancer: insights and innovations from single-cell sequencing. Front Immunol 2023; 14:1288027. [PMID: 38022625 PMCID: PMC10654630 DOI: 10.3389/fimmu.2023.1288027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Ovarian cancer is a highly heterogeneous and lethal malignancy with limited treatment options. Over the past decade, single-cell sequencing has emerged as an advanced biological technology capable of decoding the landscape of ovarian cancer at the single-cell resolution. It operates at the level of genes, transcriptomes, proteins, epigenomes, and metabolisms, providing detailed information that is distinct from bulk sequencing methods, which only offer average data for specific lesions. Single-cell sequencing technology provides detailed insights into the immune and molecular mechanisms underlying tumor occurrence, development, drug resistance, and immune escape. These insights can guide the development of innovative diagnostic markers, therapeutic strategies, and prognostic indicators. Overall, this review provides a comprehensive summary of the diverse applications of single-cell sequencing in ovarian cancer. It encompasses the identification and characterization of novel cell subpopulations, the elucidation of tumor heterogeneity, the investigation of the tumor microenvironment, the analysis of mechanisms underlying metastasis, and the integration of innovative approaches such as organoid models and multi-omics analysis.
Collapse
Affiliation(s)
- Zhongkang Li
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Haihan Gu
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaotong Xu
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanpeng Tian
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xianghua Huang
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanfang Du
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| |
Collapse
|
3
|
Esimbekova AR, Palkina NV, Zinchenko IS, Belenyuk VD, Savchenko AA, Sergeeva EY, Ruksha T. Focal adhesion alterations in
G0
‐positive melanoma cells. Cancer Med 2022; 12:7294-7308. [PMID: 36533319 PMCID: PMC10067123 DOI: 10.1002/cam4.5510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Melanoma is a highly heterogeneous malignant tumor that exhibits various forms of drug resistance. Recently, reversal transition of cancer cells to the G0 phase of the cell cycle under the influence of therapeutic drugs has been identified as an event associated with tumor dissemination. In the present study, we investigated the ability of chemotherapeutic agent dacarbazine to induce a transition of melanoma cells to the G0 phase as a mechanism of chemoresistance. METHODS We used the flow cytometry to analyze cell distribution within cell cycle phases after dacarbazine treatment as well as to identifyG0 -positive cells population. Transcriptome profiling was provided to determine genes associated with dacarbazine resistance. We evaluated the activity of β-galactosidase in cells treated with dacarbazine by substrate hydrolysis. Cell adhesion strength was measured by centrifugal assay application with subsequent staining of adhesive cells with Ki-67 monoclonal antibodies. Ability of melanoma cells to metabolize dacarbazine was determined by expressional analysis of CYP1A1, CYP1A2, CYP2E1 followed by CYP1A1 protein level evaluation by the ELISA method. RESULTS The present study determined that dacarbazine treatment of melanoma cells could induce an increase in the percentage of cells in G0 phase without alterations of β-galactosidase positive cells which corresponded to the fraction of the senescent cells. Transcriptomic profiling of cells under dacarbazine induction of G0 -positive cells percentage revealed that 'VEGFA-VEGFR2 signaling pathway' and 'Cell cycle' signaling were mostly enriched by dysregulated genes. 'Focal adhesion' signaling was also found to be triggered by dacarbazine. In melanoma cells treated with dacarbazine, an increase in G0 -positive cells among adherent cells was found. CONCLUSIONS Dacarbazine induces the alteration in a percentage of melanoma cells residing in G0 phase of a cell cycle. The altered adhesive phenotype of cancer cells under transition in the G0 phase may refer to a specific intercellular communication pattern of quiescent/senescent cancer cells.
Collapse
Affiliation(s)
| | - Nadezhda V. Palkina
- Department of Pathophysiology Krasnoyarsk State Medical University Krasnoyarsk Russia
| | - Ivan S. Zinchenko
- Department of Pathophysiology Krasnoyarsk State Medical University Krasnoyarsk Russia
| | - Vasiliy D. Belenyuk
- Laboratory of Cell Molecular Physiology and Pathology Federal Research Center, Krasnoyarsk Science Center of The Siberian Branch of The Russian Academy of Sciences Krasnoyarsk Russia
| | - Andrey A. Savchenko
- Laboratory of Cell Molecular Physiology and Pathology Federal Research Center, Krasnoyarsk Science Center of The Siberian Branch of The Russian Academy of Sciences Krasnoyarsk Russia
| | - Ekaterina Yu Sergeeva
- Department of Pathophysiology Krasnoyarsk State Medical University Krasnoyarsk Russia
| | - Tatiana G. Ruksha
- Department of Pathophysiology Krasnoyarsk State Medical University Krasnoyarsk Russia
| |
Collapse
|