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Martínez-Val A, Fort K, Koenig C, Van der Hoeven L, Franciosa G, Moehring T, Ishihama Y, Chen YJ, Makarov A, Xuan Y, Olsen JV. Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. Nat Commun 2023; 14:3599. [PMID: 37328457 PMCID: PMC10276052 DOI: 10.1038/s41467-023-39347-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.
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Affiliation(s)
- Ana Martínez-Val
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Kyle Fort
- Thermo Fisher Scientific, Bremen, Germany
| | - Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Leander Van der Hoeven
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Yue Xuan
- Thermo Fisher Scientific, Bremen, Germany.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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Piao S, Lee I, Kim S, Park H, Nagar H, Choi SJ, Vu GH, Kim M, Lee EO, Jeon BH, Kim DW, Seo Y, Kim CS. CRIF1 siRNA-Encapsulated PLGA Nanoparticles Suppress Tumor Growth in MCF-7 Human Breast Cancer Cells. Int J Mol Sci 2023; 24:ijms24087453. [PMID: 37108616 PMCID: PMC10138627 DOI: 10.3390/ijms24087453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) system dysfunction in cancer cells has been exploited as a target for anti-cancer therapeutic intervention. The downregulation of CR6-interacting factor 1 (CRIF1), an essential mito-ribosomal factor, can impair mitochondrial function in various cell types. In this study, we investigated whether CRIF1 deficiency induced by siRNA and siRNA nanoparticles could suppress MCF-7 breast cancer growth and tumor development, respectively. Our results showed that CRIF1 silencing decreased the assembly of mitochondrial OXPHOS complexes I and II, which induced mitochondrial dysfunction, mitochondrial reactive oxygen species (ROS) production, mitochondrial membrane potential depolarization, and excessive mitochondrial fission. CRIF1 inhibition reduced p53-induced glycolysis and apoptosis regulator (TIGAR) expression, as well as NADPH synthesis, leading to additional increases in ROS production. The downregulation of CRIF1 suppressed cell proliferation and inhibited cell migration through the induction of G0/G1 phase cell cycle arrest in MCF-7 breast cancer cells. Similarly, the intratumoral injection of CRIF1 siRNA-encapsulated PLGA nanoparticles inhibited tumor growth, downregulated the assembly of mitochondrial OXPHOS complexes I and II, and induced the expression of cell cycle protein markers (p53, p21, and p16) in MCF-7 xenograft mice. Thus, the inhibition of mitochondrial OXPHOS protein synthesis through CRIF1 deletion destroyed mitochondrial function, leading to elevated ROS levels and inducing antitumor effects in MCF-7 cells.
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Affiliation(s)
- Shuyu Piao
- Department of Physiology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Ikjun Lee
- Department of Physiology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Seonhee Kim
- Department of Physiology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Hyewon Park
- Department of Anatomy and Cell Biology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Harsha Nagar
- Department of Physiology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Su-Jeong Choi
- Department of Physiology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Giang-Huong Vu
- Department of Physiology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Minsoo Kim
- Department of Physiology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Eun-Ok Lee
- Department of Physiology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Byeong-Hwa Jeon
- Department of Physiology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Dong Woon Kim
- Department of Anatomy and Cell Biology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
| | - Youngduk Seo
- Department of Nuclear Medicine, Chungnam National University Sejong Hospital, Sejong 30099, Republic of Korea
| | - Cuk-Seong Kim
- Department of Physiology & Medical Science, School of Medicine, Chungnam National University, Daejeon 35015, Republic of Korea
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Choudhury FK. Mitochondrial Redox Metabolism: The Epicenter of Metabolism during Cancer Progression. Antioxidants (Basel) 2021; 10:antiox10111838. [PMID: 34829708 PMCID: PMC8615124 DOI: 10.3390/antiox10111838] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial redox metabolism is the central component in the cellular metabolic landscape, where anabolic and catabolic pathways are reprogrammed to maintain optimum redox homeostasis. During different stages of cancer, the mitochondrial redox status plays an active role in navigating cancer cells’ progression and regulating metabolic adaptation according to the constraints of each stage. Mitochondrial reactive oxygen species (ROS) accumulation induces malignant transformation. Once vigorous cell proliferation renders the core of the solid tumor hypoxic, the mitochondrial electron transport chain mediates ROS signaling for bringing about cellular adaptation to hypoxia. Highly aggressive cells are selected in this process, which are capable of progressing through the enhanced oxidative stress encountered during different stages of metastasis for distant colonization. Mitochondrial oxidative metabolism is suppressed to lower ROS generation, and the overall cellular metabolism is reprogrammed to maintain the optimum NADPH level in the mitochondria required for redox homeostasis. After reaching the distant organ, the intrinsic metabolic limitations of that organ dictate the success of colonization and flexibility of the mitochondrial metabolism of cancer cells plays a pivotal role in their adaptation to the new environment.
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Affiliation(s)
- Feroza K Choudhury
- Drug Metabolism and Pharmacokinetics Department, Genentech Inc., South San Francisco, CA 94080, USA
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Abstract
Cancer cells accumulate iron to supplement their aberrant growth and metabolism. Depleting cells of iron by iron chelators has been shown to be selectively cytotoxic to cancer cells in vitro and in vivo. Iron chelators are effective at combating a range of cancers including those which are difficult to treat such as androgen insensitive prostate cancer and cancer stem cells. This review will evaluate the impact of iron chelation on cancer cell survival and the underlying mechanisms of action. A plethora of studies have shown iron chelators can reverse some of the major hallmarks and enabling characteristics of cancer. Iron chelators inhibit signalling pathways that drive proliferation, migration and metastasis as well as return tumour suppressive signalling. In addition to this, iron chelators stimulate apoptotic and ER stress signalling pathways inducing cell death even in cells lacking a functional p53 gene. Iron chelators can sensitise cancer cells to PARP inhibitors through mimicking BRCAness; a feature of cancers trademark genomic instability. Iron chelators target cancer cell metabolism, attenuating oxidative phosphorylation and glycolysis. Moreover, iron chelators may reverse the major characteristics of oncogenic transformation. Iron chelation therefore represent a promising selective mode of cancer therapy.
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Doctor A, Seifert V, Ullrich M, Hauser S, Pietzsch J. Three-Dimensional Cell Culture Systems in Radiopharmaceutical Cancer Research. Cancers (Basel) 2020; 12:cancers12102765. [PMID: 32993034 PMCID: PMC7600608 DOI: 10.3390/cancers12102765] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/12/2022] Open
Abstract
In preclinical cancer research, three-dimensional (3D) cell culture systems such as multicellular spheroids and organoids are becoming increasingly important. They provide valuable information before studies on animal models begin and, in some cases, are even suitable for reducing or replacing animal experiments. Furthermore, they recapitulate microtumors, metastases, and the tumor microenvironment much better than monolayer culture systems could. Three-dimensional models show higher structural complexity and diverse cell interactions while reflecting (patho)physiological phenomena such as oxygen and nutrient gradients in the course of their growth or development. These interactions and properties are of great importance for understanding the pathophysiological importance of stromal cells and the extracellular matrix for tumor progression, treatment response, or resistance mechanisms of solid tumors. Special emphasis is placed on co-cultivation with tumor-associated cells, which further increases the predictive value of 3D models, e.g., for drug development. The aim of this overview is to shed light on selected 3D models and their advantages and disadvantages, especially from the radiopharmacist's point of view with focus on the suitability of 3D models for the radiopharmacological characterization of novel radiotracers and radiotherapeutics. Special attention is paid to pancreatic ductal adenocarcinoma (PDAC) as a predestined target for the development of new radionuclide-based theranostics.
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Affiliation(s)
- Alina Doctor
- Department of Radiopharmaceutical and Chemical Biology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany; (A.D.); (V.S.); (M.U.); (S.H.)
- School of Science, Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01069 Dresden, Germany
| | - Verena Seifert
- Department of Radiopharmaceutical and Chemical Biology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany; (A.D.); (V.S.); (M.U.); (S.H.)
- School of Science, Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01069 Dresden, Germany
| | - Martin Ullrich
- Department of Radiopharmaceutical and Chemical Biology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany; (A.D.); (V.S.); (M.U.); (S.H.)
| | - Sandra Hauser
- Department of Radiopharmaceutical and Chemical Biology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany; (A.D.); (V.S.); (M.U.); (S.H.)
| | - Jens Pietzsch
- Department of Radiopharmaceutical and Chemical Biology, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany; (A.D.); (V.S.); (M.U.); (S.H.)
- School of Science, Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01069 Dresden, Germany
- Correspondence: ; Tel.: +49-351-260-2622
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