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Lobo V, Shcherbinina E, Westholm JO, Nowak I, Huang HC, Angeletti D, Anastasakis DG, Sarshad AA. Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression. Sci Data 2024; 11:617. [PMID: 38866801 PMCID: PMC11169490 DOI: 10.1038/s41597-024-03465-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
In this study we examine the impact of cell confluency on gene expression. We focused on Argonaute (AGO) protein dynamics and associated gene and protein expression in HEK293, A375, and SHSY5Y cell lines. As a consequence of cell confluency, AGO2 protein translocates into the nucleus. Therefore, we generated transcriptomic data using RNA sequencing to compare gene expression in subconfluent versus confluent cells, which highlighted significant alterations in gene regulation patterns directly corresponding to changes in cell density. Our study also encompasses miRNA profiling data obtained through small RNA sequencing, revealing miRNA expressional changes dependent on cellular confluency, as well as cellular localization. Finally, we derived proteomic data from mass spectrometry analyses following AGO1-4 immunoprecipitation, providing a comprehensive view of AGO interactome in both nuclear and cytoplasmic compartments under varying confluency. These datasets offer a detailed exploration of the cellular and molecular dynamics, influenced by cell confluency, presenting a valuable resource for further research in cellular biology, particularly in understanding the basic mechanisms of cell density in cancer cells.
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Affiliation(s)
- Vivian Lobo
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden
| | - Evgeniia Shcherbinina
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden
| | - Jakub O Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE, 17121, Solna, Sweden
| | - Iwona Nowak
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden
| | - Hsiang-Chi Huang
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden
| | - Davide Angeletti
- SciLifeLab, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden
| | - Dimitrios G Anastasakis
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Aishe A Sarshad
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.
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Lamnis L, Christofi C, Stark A, Palm H, Roemer K, Vogt T, Reichrath J. Differential Regulation of Circadian Clock Genes by UV-B Radiation and 1,25-Dihydroxyvitamin D: A Pilot Study during Different Stages of Skin Photocarcinogenesis. Nutrients 2024; 16:254. [PMID: 38257148 PMCID: PMC10820546 DOI: 10.3390/nu16020254] [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: 11/27/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Increasing evidence points at an important physiological role of the timekeeping system, known as the circadian clock (CC), regulating not only our sleep-awake rhythm but additionally many other cellular processes in peripheral tissues. It was shown in various cell types that environmental stressors, including ultraviolet B radiation (UV-B), modulate the expression of genes that regulate the CC (CCGs) and that these CCGs modulate susceptibility for UV-B-induced cellular damage. It was the aim of this pilot study to gain further insights into the CCs' putative role for UV-B-induced photocarcinogenesis of skin cancer. METHODS Applying RT-PCR, we analyzed the expression of two core CCGs (brain and muscle ARNT-like 1 (Bmal1) and Period-2 (Per2)) over several time points (0-60 h) in HaCaT cells with and without 1,25-dihydroxyvitamin D (D3) and/or UV-B and conducted a cosinor analysis to evaluate the effects of those conditions on the circadian rhythm and an extended mixed-effects linear modeling to account for both fixed effects of experimental conditions and random inter-individual variability. Next, we investigated the expression of these two genes in keratinocytes representing different stages of skin photocarcinogenesis, comparing normal (Normal Human Epidermal Keratinocytes-NHEK; p53 wild type), precancerous (HaCaT keratinocytes; mutated p53 status), and malignant (Squamous Cell Carcinoma SCL-1; p53 null status) keratinocytes after 12 h under the same conditions. RESULTS We demonstrated that in HaCaT cells, Bmal1 showed a robust circadian rhythm, while the evidence for Per2 was limited. Overall expression of both genes, but especially for Bmal1, was increased following UV-B treatment, while Per2 showed a suppressed overall expression following D3. Both UVB and 1,25(OH)2D3 suggested a significant phase shift for Bmal1 (p < 0.05 for the acrophase), while no specific effect on the amplitude could be evidenced. Differential effects on the expression of BMAL1 and Per2 were found when we compared different treatment modalities (UV-B and/or D3) or cell types (NHEK, HaCaT, and SCL-1 cells). CONCLUSIONS Comparing epidermal keratinocytes representing different stages of skin photocarcinogenesis, we provide further evidence for an independently operating timekeeping system in human skin, which is regulated by UV-B and disturbed during skin photocarcinogenesis. Our finding that this pattern of circadian rhythm was differentially altered by treatment with UV-B, as compared with treatment with D3, does not support the hypothesis that the expression of these CCGs may be regulated via UV-B-induced synthesis of vitamin D but might be introducing a novel photoprotective property of vitamin D through the circadian clock.
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Affiliation(s)
- Leandros Lamnis
- Dermatology, University of Saarland Medical Center, 66421 Homburg, Germany; (L.L.); (T.V.)
| | - Christoforos Christofi
- Dermatology, University of Saarland Medical Center, 66421 Homburg, Germany; (L.L.); (T.V.)
| | - Alexandra Stark
- Dermatology, University of Saarland Medical Center, 66421 Homburg, Germany; (L.L.); (T.V.)
| | - Heike Palm
- Dermatology, University of Saarland Medical Center, 66421 Homburg, Germany; (L.L.); (T.V.)
| | - Klaus Roemer
- José Carreras Center and Internal Medicine I, 66421 Homburg, Germany
| | - Thomas Vogt
- Dermatology, University of Saarland Medical Center, 66421 Homburg, Germany; (L.L.); (T.V.)
| | - Jörg Reichrath
- Dermatology, University of Saarland Medical Center, 66421 Homburg, Germany; (L.L.); (T.V.)
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Tahara H, Sato M, Thurin M, Wang E, Butterfield LH, Disis ML, Fox BA, Lee PP, Khleif SN, Wigginton JM, Ambs S, Akutsu Y, Chaussabel D, Doki Y, Eremin O, Fridman WH, Hirohashi Y, Imai K, Jacobson J, Jinushi M, Kanamoto A, Kashani-Sabet M, Kato K, Kawakami Y, Kirkwood JM, Kleen TO, Lehmann PV, Liotta L, Lotze MT, Maio M, Malyguine A, Masucci G, Matsubara H, Mayrand-Chung S, Nakamura K, Nishikawa H, Palucka AK, Petricoin EF, Pos Z, Ribas A, Rivoltini L, Sato N, Shiku H, Slingluff CL, Streicher H, Stroncek DF, Takeuchi H, Toyota M, Wada H, Wu X, Wulfkuhle J, Yaguchi T, Zeskind B, Zhao Y, Zocca MB, Marincola FM. Emerging concepts in biomarker discovery; the US-Japan Workshop on Immunological Molecular Markers in Oncology. J Transl Med 2009; 7:45. [PMID: 19534815 PMCID: PMC2724494 DOI: 10.1186/1479-5876-7-45] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 06/17/2009] [Indexed: 02/08/2023] Open
Abstract
Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that might be added to the list of known entities applicable in immunotherapy trials. The need for a systematic approach to biomarker discovery that takes advantage of powerful high-throughput technologies was recognized; it was clear from the current state of the science that immunotherapy is still in a discovery phase and only a few of the current biomarkers warrant extensive validation. It was, finally, clear that, while current technologies have almost limitless potential, inadequate study design, limited standardization and cross-validation among laboratories and suboptimal comparability of data remain major road blocks. The institution of an interactive consortium for high throughput molecular monitoring of clinical trials with voluntary participation might provide cost-effective solutions.
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Affiliation(s)
- Hideaki Tahara
- Department of Surgery and Bioengineering, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Marimo Sato
- Department of Surgery and Bioengineering, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Magdalena Thurin
- Cancer Diagnosis Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, Maryland, 20852, USA
| | - Ena Wang
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Center for Human Immunology (CHI), NIH, Bethesda, Maryland, 20892, USA
| | - Lisa H Butterfield
- Departments of Medicine, Surgery and Immunology, Division of Hematology Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, 15213, USA
| | - Mary L Disis
- Tumor Vaccine Group, Center for Translational Medicine in Women's Health, University of Washington, Seattle, Washington, 98195, USA
| | - Bernard A Fox
- Earle A Chiles Research Institute, Robert W Franz Research Center, Providence Portland Medical Center, and Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, 97213, USA
| | - Peter P Lee
- Department of Medicine, Division of Hematology, Stanford University, Stanford, California, 94305, USA
| | - Samir N Khleif
- Cancer Vaccine Section, NCI, NIH, Bethesda, Maryland, 20892, USA
| | - Jon M Wigginton
- Discovery Medicine-Oncology, Bristol-Myers Squibb Inc., Princeton, New Jersey, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center of Cancer Research, NCI, NIH, Bethesda, Maryland, 20892, USA
| | - Yasunori Akutsu
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Damien Chaussabel
- Baylor Institute for Immunology Research and Baylor Research Institute, Dallas, Texas, 75204, USA
| | - Yuichiro Doki
- Department of Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Oleg Eremin
- Section of Surgery, Biomedical Research Unit, Nottingham Digestive Disease Centre, University of Nottingham, NG7 2UH, UK
| | - Wolf Hervé Fridman
- Centre de la Reserche des Cordeliers, INSERM, Paris Descarte University, 75270 Paris, France
| | | | - Kohzoh Imai
- Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - James Jacobson
- Cancer Diagnosis Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, Maryland, 20852, USA
| | - Masahisa Jinushi
- Department of Surgery and Bioengineering, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akira Kanamoto
- Department of Surgery and Bioengineering, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Kazunori Kato
- Department of Molecular Medicine, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Yutaka Kawakami
- Division of Cellular Signaling, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - John M Kirkwood
- Departments of Medicine, Surgery and Immunology, Division of Hematology Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, 15213, USA
| | - Thomas O Kleen
- Cellular Technology Ltd, Shaker Heights, Ohio, 44122, USA
| | - Paul V Lehmann
- Cellular Technology Ltd, Shaker Heights, Ohio, 44122, USA
| | - Lance Liotta
- Department of Molecular Pathology and Microbiology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, 10900, USA
| | - Michael T Lotze
- Illman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, 15213, USA
| | - Michele Maio
- Medical Oncology and Immunotherapy, Department. of Oncology, University, Hospital of Siena, Istituto Toscano Tumori, Siena, Italy
- Cancer Bioimmunotherapy Unit, Department of Medical Oncology, Centro di Riferimento Oncologico, IRCCS, Aviano, 53100, Italy
| | - Anatoli Malyguine
- Laboratory of Cell Mediated Immunity, SAIC-Frederick, Inc. NCI-Frederick, Frederick, Maryland, 21702, USA
| | - Giuseppe Masucci
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, 171 76, Sweden
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shawmarie Mayrand-Chung
- The Biomarkers Consortium (BC), Public-Private Partnership Program, Office of the Director, NIH, Bethesda, Maryland, 20892, USA
| | - Kiminori Nakamura
- Department of Molecular Medicine, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Hiroyoshi Nishikawa
- Department of Cancer Vaccine, Department of Immuno-gene Therapy, Mie University Graduate School of Medicine, Mie, Japan
| | - A Karolina Palucka
- Baylor Institute for Immunology Research and Baylor Research Institute, Dallas, Texas, 75204, USA
| | - Emanuel F Petricoin
- Department of Molecular Pathology and Microbiology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, 10900, USA
| | - Zoltan Pos
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Center for Human Immunology (CHI), NIH, Bethesda, Maryland, 20892, USA
| | - Antoni Ribas
- Department of Medicine, Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, 90095, USA
| | - Licia Rivoltini
- Unit of Immunotherapy of Human Tumors, IRCCS Foundation, Istituto Nazionale Tumori, Milan, 20100, Italy
| | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Shiku
- Department of Cancer Vaccine, Department of Immuno-gene Therapy, Mie University Graduate School of Medicine, Mie, Japan
| | - Craig L Slingluff
- Department of Surgery, Division of Surgical Oncology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Howard Streicher
- Cancer Therapy Evaluation Program, DCTD, NCI, NIH, Rockville, Maryland, 20892, USA
| | - David F Stroncek
- Cell Therapy Section (CTS), Department of Transfusion Medicine, Clinical Center, NIH, Bethesda, Maryland, 20892, USA
| | - Hiroya Takeuchi
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Minoru Toyota
- Department of Biochemistry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Hisashi Wada
- Department of Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Xifeng Wu
- Department of Epidemiology, University of Texas, MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Julia Wulfkuhle
- Department of Molecular Pathology and Microbiology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, 10900, USA
| | - Tomonori Yaguchi
- Division of Cellular Signaling, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | | | - Yingdong Zhao
- Biometric Research Branch, NCI, NIH, Bethesda, Maryland, 20892, USA
| | | | - Francesco M Marincola
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Center for Human Immunology (CHI), NIH, Bethesda, Maryland, 20892, USA
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