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Burtscher ML, Gade S, Garrido-Rodriguez M, Rutkowska A, Werner T, Eberl HC, Petretich M, Knopf N, Zirngibl K, Grandi P, Bergamini G, Bantscheff M, Fälth-Savitski M, Saez-Rodriguez J. Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition. Mol Syst Biol 2024; 20:458-474. [PMID: 38454145 PMCID: PMC10987601 DOI: 10.1038/s44320-024-00025-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
Complex disease phenotypes often span multiple molecular processes. Functional characterization of these processes can shed light on disease mechanisms and drug effects. Thermal Proteome Profiling (TPP) is a mass-spectrometry (MS) based technique assessing changes in thermal protein stability that can serve as proxies of functional protein changes. These unique insights of TPP can complement those obtained by other omics technologies. Here, we show how TPP can be integrated with phosphoproteomics and transcriptomics in a network-based approach using COSMOS, a multi-omics integration framework, to provide an integrated view of transcription factors, kinases and proteins with altered thermal stability. This allowed us to recover consequences of Poly (ADP-ribose) polymerase (PARP) inhibition in ovarian cancer cells on cell cycle and DNA damage response as well as interferon and hippo signaling. We found that TPP offers a complementary perspective to other omics data modalities, and that its integration allowed us to obtain a more complete molecular overview of PARP inhibition. We anticipate that this strategy can be used to integrate functional proteomics with other omics to study molecular processes.
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Affiliation(s)
- Mira L Burtscher
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | | | - Martin Garrido-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | | | | | - Katharina Zirngibl
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
| | | | | | | | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany.
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Rajawat J, Awasthi P, Banerjee M. PARP inhibitor olaparib induced differential protein expression in cervical cancer cells. J Proteomics 2023; 275:104823. [PMID: 36646275 DOI: 10.1016/j.jprot.2023.104823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
PARP inhibitors are a potential class of chemotherapeutic drugs but PARP inhibitor response has not been explored systematically. We lack a specific understanding of the subset of the proteome preferentially modified in various cancers by PARP inhibitors. Implications of PARP inhibitor and PARP1 in cervical cancer treatment and resistance are not fully elucidated. We conducted a mass spectrometry-based proteomic analysis of cervical cancer Hela cells treated with olaparib. We aimed to identify the alteration in the protein signaling pathway induced by PARP inhibitors beyond the DNA damage response pathway. Our data demonstrate a significant reduction in PARP activity and enhanced cell death after olaparib treatment. We further observed articulated proteomic changes with a significant enrichment of proteins in diverse cellular processes. The differentially expressed proteins were predominantly associated with RNA metabolism, mRNA splicing, processing, and RNA binding. Our data also identified proteins that could probably contribute to survival mechanisms resulting in resistance to PARP inhibitors. Hence, we put forth the overview of proteomic changes induced by PARP inhibitor olaparib in cervical cancer cells. This study highlights the significant proteins modified during PARP inhibition and thus could be a probable target for combination therapies with PARP inhibitors in cervical cancer. SIGNIFICANCE.
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Affiliation(s)
- Jyotika Rajawat
- Molecular & Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow 226007, U.P, India
| | - Poorwa Awasthi
- CSIR-Indian Institute of Toxicology Research, Lucknow 226001, U.P, India
| | - Monisha Banerjee
- Molecular & Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow 226007, U.P, India..
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Duda JM, Twigg CAI, Thomas SN. Differential histone deacetylase inhibitor-induced perturbations of the global proteome landscape in the setting of high-grade serous ovarian cancer. Proteomics 2023; 23:e2100372. [PMID: 36193784 PMCID: PMC9957826 DOI: 10.1002/pmic.202100372] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/12/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) is the most lethal gynecologic malignancy in women. Its low survival rate is attributed to late detection, relapse, and drug resistance. The lack of effective second-line therapeutics remains a significant challenge. There is an opportunity to incorporate the use of histone deacetylase inhibitors (HDACi) into HGSOC treatment. However, the mechanism and efficacy of HDACi in the context of BRCA-1/2 mutation status is understudied. Therefore, we set out to elucidate how HDACi perturb the proteomic landscape within HGSOC cells. In this work, we used TMT labeling followed by data-dependent acquisition LC-MS/MS to quantitatively determine differences in the global proteomic landscape across HDACi-treated CAOV3, OVCAR3, and COV318 (BRCA-1/2 wildtype) HGSOC cells. We identified significant differences in the HDACi-induced perturbations of global protein regulation across CAOV3, OVCAR3, and COV318 cells. The HDACi Vorinostat and Romidepsin were identified as being the least and most effective in inhibiting HDAC activity across the three cell lines, respectively. Our results provide a justification for the further investigation of the functional mechanisms associated with the differential efficacy of FDA-approved HDACi within the context of HGSOC. This will enhance the efficacy of targeted HGSOC therapeutic treatment modalities that include HDACi.
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Affiliation(s)
- Jolene M. Duda
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota College of Biological Sciences, Minneapolis, Minnesota, USA
| | - Carly A. I. Twigg
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, Minnesota, USA
| | - Stefani N. Thomas
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, Minnesota, USA
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Zhao Q, Kohut A, Li YJ, Martincuks A, Austria T, Zhang C, Santiago NL, Borrero RM, Phan XT, Melstrom L, Rodriguez-Rodriguez L, Yu H. Niraparib-induced STAT3 inhibition increases its antitumor effects. Front Oncol 2022; 12:966492. [PMID: 36324587 PMCID: PMC9618811 DOI: 10.3389/fonc.2022.966492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 09/21/2022] [Indexed: 11/18/2022] Open
Abstract
Recently, poly(ADP-ribosyl)ation polymerase inhibitors (PARPis), which induce synthetic lethality of tumor cells with DNA damage repair defects, have emerged as a promising therapy for ovarian, breast, and pancreatic cancer. Although the PARPi Olaparib is limited to treating cancer patients with DNA repair deficiencies, the PARPi Niraparib is FDA approved to treat ovarian cancer patients regardless of their status in DNA repair pathways. Despite differences in the affinity to PARP enzymes, the rationale behind the clinical use of Niraparib in patients without DNA repair deficiencies is still lacking. Moreover, only Olaparib has been approved for pancreatic ductal adenocarcinoma (PDAC) patients with BRCA mutations, accounting for only 5-7% of total PDACs. It remains unclear whether Niraparib could be beneficial to PDACs without BRCA mutations. We found that Niraparib inhibits ovarian and PDAC tumor cell growth, regardless of BRCA mutational status, more effectively than Olaparib. Unlike Olaparib, which is known to activate STAT3, Niraparib inhibits STAT3 activity in ovarian and PDAC cancer cell lines and patient tumors. Moreover, Niraparib regulates the expression of several STAT3 downstream genes involved in apoptosis. Overexpression of a constitutively activated STAT3 mutant rescues Niraparib-induced cancer cell apoptosis. Our results suggest that Niraparib inhibits pSTAT3 by interfering with SRC tyrosine kinase. Collectively, our studies provide a mechanism underlying Niraparib's ability to induce tumor cell apoptosis without BRCA mutations, suggesting the potential use of Niraparib for treating PDAC patients regardless of BRCA status.
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Affiliation(s)
- Qianqian Zhao
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope National Medical Center, Duarte, CA, United States
| | - Adrian Kohut
- Department of Surgery, Division of Gynecologic Oncology, City of Hope National Medical Center, Duarte, CA, United States
| | - Yi-Jia Li
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
| | - Antons Martincuks
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
| | - Theresa Austria
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
| | - Chunyan Zhang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
| | - Nicole Lugo Santiago
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
| | - Rosemarie Martinez Borrero
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope National Medical Center, Duarte, CA, United States
| | - Xuan Thuy Phan
- Department of Surgery, Division of Surgical Oncology, City of Hope National Medical Center, Duarte, CA, United States
| | - Laleh Melstrom
- Department of Surgery, Division of Surgical Oncology, City of Hope National Medical Center, Duarte, CA, United States
| | - Lorna Rodriguez-Rodriguez
- Department of Surgery, Division of Gynecologic Oncology, City of Hope National Medical Center, Duarte, CA, United States
| | - Hua Yu
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
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