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Oeing CU, Pepin ME, Saul KB, Agircan AS, Assenov Y, Merkel TS, Sedaghat-Hamedani F, Weis T, Meder B, Guan K, Plass C, Weichenhan D, Siede D, Backs J. Indirect epigenetic testing identifies a diagnostic signature of cardiomyocyte DNA methylation in heart failure. Basic Res Cardiol 2023; 118:9. [PMID: 36939901 PMCID: PMC10027651 DOI: 10.1007/s00395-022-00954-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 03/21/2023]
Abstract
Precision-based molecular phenotyping of heart failure must overcome limited access to cardiac tissue. Although epigenetic alterations have been found to underlie pathological cardiac gene dysregulation, the clinical utility of myocardial epigenomics remains narrow owing to limited clinical access to tissue. Therefore, the current study determined whether patient plasma confers indirect phenotypic, transcriptional, and/or epigenetic alterations to ex vivo cardiomyocytes to mirror the failing human myocardium. Neonatal rat ventricular myocytes (NRVMs) and single-origin human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and were treated with blood plasma samples from patients with dilated cardiomyopathy (DCM) and donor subjects lacking history of cardiovascular disease. Following plasma treatments, NRVMs and hiPSC-CMs underwent significant hypertrophy relative to non-failing controls, as determined via automated high-content screening. Array-based DNA methylation analysis of plasma-treated hiPSC-CMs and cardiac biopsies uncovered robust, and conserved, alterations in cardiac DNA methylation, from which 100 sites were validated using an independent cohort. Among the CpG sites identified, hypo-methylation of the ATG promoter was identified as a diagnostic marker of HF, wherein cg03800765 methylation (AUC = 0.986, P < 0.0001) was found to out-perform circulating NT-proBNP levels in differentiating heart failure. Taken together, these findings support a novel approach of indirect epigenetic testing in human HF.
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Affiliation(s)
- Christian U Oeing
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
- Department of Internal Medicine and Cardiology, Charité University Medicine, DZHK (German Center for Cardiovascular Research), Partner site Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Mark E Pepin
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Kerstin B Saul
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Ayça Seyhan Agircan
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Yassen Assenov
- Cancer Epigenomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Tobias S Merkel
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Farbod Sedaghat-Hamedani
- Department of Cardiology, University of Heidelberg, DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Tanja Weis
- Department of Cardiology, University of Heidelberg, DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Benjamin Meder
- Department of Cardiology, University of Heidelberg, DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Kaomei Guan
- Institute of Pharmacology and Toxicology, Technische Universität Medical Centre Dresden, Dresden, Germany
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Cancer Epigenomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Dominik Siede
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Johannes Backs
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany.
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2
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Anestopoulos I, Kyriakou S, Tragkola V, Paraskevaidis I, Tzika E, Mitsiogianni M, Deligiorgi MV, Petrakis G, Trafalis DT, Botaitis S, Giatromanolaki A, Koukourakis MI, Franco R, Pappa A, Panayiotidis MI. Targeting the epigenome in malignant melanoma: Facts, challenges and therapeutic promises. Pharmacol Ther 2022; 240:108301. [PMID: 36283453 DOI: 10.1016/j.pharmthera.2022.108301] [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: 06/06/2022] [Revised: 10/03/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022]
Abstract
Malignant melanoma is the most lethal type of skin cancer with high rates of mortality. Although current treatment options provide a short-clinical benefit, acquired-drug resistance highlights the low 5-year survival rate among patients with advanced stage of the disease. In parallel, the involvement of an aberrant epigenetic landscape, (e.g., alterations in DNA methylation patterns, histone modifications marks and expression of non-coding RNAs), in addition to the genetic background, has been also associated with the onset and progression of melanoma. In this review article, we report on current therapeutic options in melanoma treatment with a focus on distinct epigenetic alterations and how their reversal, by specific drug compounds, can restore a normal phenotype. In particular, we concentrate on how single and/or combinatorial therapeutic approaches have utilized epigenetic drug compounds in being effective against malignant melanoma. Finally, the role of deregulated epigenetic mechanisms in promoting drug resistance to targeted therapies and immune checkpoint inhibitors is presented leading to the development of newly synthesized and/or improved drug compounds capable of targeting the epigenome of malignant melanoma.
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Affiliation(s)
- I Anestopoulos
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - S Kyriakou
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - V Tragkola
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - I Paraskevaidis
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - E Tzika
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | | | - M V Deligiorgi
- Laboratory of Pharmacology, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - G Petrakis
- Saint George Hospital, Chania, Crete, Greece
| | - D T Trafalis
- Laboratory of Pharmacology, Medical School, National & Kapodistrian University of Athens, Athens, Greece
| | - S Botaitis
- Department of Surgery, Alexandroupolis University Hospital, Democritus University of Thrace School of Medicine, Alexandroupolis, Greece
| | - A Giatromanolaki
- Department of Pathology, Democritus University of Thrace, University General Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - M I Koukourakis
- Radiotherapy / Oncology, Radiobiology & Radiopathology Unit, Department of Medicine, School of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - R Franco
- Redox Biology Centre, University of Nebraska-Lincoln, Lincoln, NE, USA; School of Veterinary Medicine & Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - A Pappa
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - M I Panayiotidis
- Department of Cancer Genetics, Therapeutics & Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus.
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3
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Carrier A, Desjobert C, Ponger L, Lamant L, Bustos M, Torres-Ferreira J, Henrique R, Jeronimo C, Lanfrancone L, Delmas A, Favre G, Delaunay A, Busato F, Hoon DSB, Tost J, Etievant C, Riond J, Arimondo PB. DNA methylome combined with chromosome cluster-oriented analysis provides an early signature for cutaneous melanoma aggressiveness. eLife 2022; 11:78587. [PMID: 36125262 PMCID: PMC9525058 DOI: 10.7554/elife.78587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/18/2022] [Indexed: 11/24/2022] Open
Abstract
Aberrant DNA methylation is a well-known feature of tumours and has been associated with metastatic melanoma. However, since melanoma cells are highly heterogeneous, it has been challenging to use affected genes to predict tumour aggressiveness, metastatic evolution, and patients’ outcomes. We hypothesized that common aggressive hypermethylation signatures should emerge early in tumorigenesis and should be shared in aggressive cells, independent of the physiological context under which this trait arises. We compared paired melanoma cell lines with the following properties: (i) each pair comprises one aggressive counterpart and its parental cell line and (ii) the aggressive cell lines were each obtained from different host and their environment (human, rat, and mouse), though starting from the same parent cell line. Next, we developed a multi-step genomic pipeline that combines the DNA methylome profile with a chromosome cluster-oriented analysis. A total of 229 differentially hypermethylated genes was commonly found in the aggressive cell lines. Genome localization analysis revealed hypermethylation peaks and clusters, identifying eight hypermethylated gene promoters for validation in tissues from melanoma patients. Five Cytosine-phosphate-Guanine (CpGs) identified in primary melanoma tissues were transformed into a DNA methylation score that can predict survival (log-rank test, p=0.0008). This strategy is potentially universally applicable to other diseases involving DNA methylation alterations.
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Affiliation(s)
- Arnaud Carrier
- Unité de Service et de Recherche USR 3388, CNRS-Pierre Fabre, Toulouse, France
| | - Cécile Desjobert
- Unité de Service et de Recherche USR 3388, CNRS-Pierre Fabre, Toulouse, France
| | | | - Laurence Lamant
- Cancer Research Center of Toulouse, UMR 1037, INSERM, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Matias Bustos
- Department of Translational Molecular Medicine, Providence Saint John's Health Center, Santa Monica, United States
| | - Jorge Torres-Ferreira
- Cancer Biology and Epigenetics Group, Portuguese Oncology Institute, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Portuguese Oncology Institute, Porto, Portugal
| | - Carmen Jeronimo
- Cancer Biology and Epigenetics Group, Portuguese Oncology Institute, Porto, Portugal
| | - Luisa Lanfrancone
- Department of Experimental Oncology, Instituto Europeo di Oncologia, Milan, Italy
| | - Audrey Delmas
- Cancer Research Center of Toulouse, UMR 1037, INSERM, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse, UMR 1037, INSERM, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Antoine Delaunay
- Laboratory for Functional Genomics, Fondation Jean Dausset-CEPH, Paris, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, CNRS, CEA-Institut de Biologie François Jacob, Evry, France
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Providence Saint John's Health Center, Santa Monica, United States
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, CNRS, CEA-Institut de Biologie François Jacob, Evry, France
| | - Chantal Etievant
- Unité de Service et de Recherche USR 3388, CNRS-Pierre Fabre, Toulouse, France
| | - Joëlle Riond
- Unité de Service et de Recherche USR 3388, CNRS-Pierre Fabre, Toulouse, France
| | - Paola B Arimondo
- Department Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3523, Paris, France
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4
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Park JH, de Lomana ALG, Marzese DM, Juarez T, Feroze A, Hothi P, Cobbs C, Patel AP, Kesari S, Huang S, Baliga NS. A Systems Approach to Brain Tumor Treatment. Cancers (Basel) 2021; 13:3152. [PMID: 34202449 PMCID: PMC8269017 DOI: 10.3390/cancers13133152] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022] Open
Abstract
Brain tumors are among the most lethal tumors. Glioblastoma, the most frequent primary brain tumor in adults, has a median survival time of approximately 15 months after diagnosis or a five-year survival rate of 10%; the recurrence rate is nearly 90%. Unfortunately, this prognosis has not improved for several decades. The lack of progress in the treatment of brain tumors has been attributed to their high rate of primary therapy resistance. Challenges such as pronounced inter-patient variability, intratumoral heterogeneity, and drug delivery across the blood-brain barrier hinder progress. A comprehensive, multiscale understanding of the disease, from the molecular to the whole tumor level, is needed to address the intratumor heterogeneity resulting from the coexistence of a diversity of neoplastic and non-neoplastic cell types in the tumor tissue. By contrast, inter-patient variability must be addressed by subtyping brain tumors to stratify patients and identify the best-matched drug(s) and therapies for a particular patient or cohort of patients. Accomplishing these diverse tasks will require a new framework, one involving a systems perspective in assessing the immense complexity of brain tumors. This would in turn entail a shift in how clinical medicine interfaces with the rapidly advancing high-throughput (HTP) technologies that have enabled the omics-scale profiling of molecular features of brain tumors from the single-cell to the tissue level. However, several gaps must be closed before such a framework can fulfill the promise of precision and personalized medicine for brain tumors. Ultimately, the goal is to integrate seamlessly multiscale systems analyses of patient tumors and clinical medicine. Accomplishing this goal would facilitate the rational design of therapeutic strategies matched to the characteristics of patients and their tumors. Here, we discuss some of the technologies, methodologies, and computational tools that will facilitate the realization of this vision to practice.
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Affiliation(s)
- James H. Park
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
| | | | - Diego M. Marzese
- Balearic Islands Health Research Institute (IdISBa), 07010 Palma, Spain;
| | - Tiffany Juarez
- St. John’s Cancer Institute, Santa Monica, CA 90401, USA; (T.J.); (S.K.)
| | - Abdullah Feroze
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA; (A.F.); (A.P.P.)
| | - Parvinder Hothi
- Swedish Neuroscience Institute, Seattle, WA 98122, USA; (P.H.); (C.C.)
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Seattle, WA 98122, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Seattle, WA 98122, USA; (P.H.); (C.C.)
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Seattle, WA 98122, USA
| | - Anoop P. Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA; (A.F.); (A.P.P.)
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
| | - Santosh Kesari
- St. John’s Cancer Institute, Santa Monica, CA 90401, USA; (T.J.); (S.K.)
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
- Departments of Microbiology, Biology, and Molecular Engineering Sciences, University of Washington, Seattle, WA 98105, USA
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5
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Moshe A, Izraely S, Sagi-Assif O, Malka S, Ben-Menachem S, Meshel T, Pasmanik-Chor M, Hoon DS, Witz IP. Inter-Tumor Heterogeneity-Melanomas Respond Differently to GM-CSF-Mediated Activation. Cells 2020; 9:cells9071683. [PMID: 32668704 PMCID: PMC7407964 DOI: 10.3390/cells9071683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022] Open
Abstract
Granulocyte-monocyte colony stimulating factor (GM-CSF) is used as an adjuvant in various clinical and preclinical studies with contradictory results. These were attributed to opposing effects of GM-CSF on the immune or myeloid systems of the treated patients or to lack of optimal dosing regimens. The results of the present study point to inter-tumor heterogeneity as a possible mechanism accounting for the contrasting responses to GM-CSF incorporating therapies. Employing xenograft models of human melanomas in nude mice developed in our lab, we detected differential functional responses of melanomas from different patients to GM-CSF both in vitro as well as in vivo. Whereas cells of one melanoma acquired pro metastatic features following exposure to GM-CSF, cells from another melanoma either did not respond or became less malignant. We propose that inter-melanoma heterogeneity as manifested by differential responses of melanoma cells (and perhaps also of other tumor) to GM-CSF may be developed into a predictive marker providing a tool to segregate melanoma patients who will benefit from GM-CSF therapy from those who will not.
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Affiliation(s)
- Adi Moshe
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (A.M.); (S.I.); (O.S.-A.); (S.M.); (S.B.-M.); (T.M.)
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sivan Izraely
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (A.M.); (S.I.); (O.S.-A.); (S.M.); (S.B.-M.); (T.M.)
| | - Orit Sagi-Assif
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (A.M.); (S.I.); (O.S.-A.); (S.M.); (S.B.-M.); (T.M.)
| | - Sapir Malka
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (A.M.); (S.I.); (O.S.-A.); (S.M.); (S.B.-M.); (T.M.)
| | - Shlomit Ben-Menachem
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (A.M.); (S.I.); (O.S.-A.); (S.M.); (S.B.-M.); (T.M.)
| | - Tsipi Meshel
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (A.M.); (S.I.); (O.S.-A.); (S.M.); (S.B.-M.); (T.M.)
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, The George S. Wise Faculty of Life Science, Tel Aviv University, Tel-Aviv 6997801, Israel;
| | - Dave S.B. Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute, Saint John’s Health Center Providence Health Systems, Santa Monica, CA 90404, USA;
| | - Isaac P. Witz
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 6997801, Israel; (A.M.); (S.I.); (O.S.-A.); (S.M.); (S.B.-M.); (T.M.)
- Correspondence: ; Tel.: +972-3-640-6979
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6
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Prakash R, Izraely S, Thareja NS, Lee RH, Rappaport M, Kawaguchi R, Sagi-Assif O, Ben-Menachem S, Meshel T, Machnicki M, Ohe S, Hoon DS, Coppola G, Witz IP, Carmichael ST. Regeneration Enhances Metastasis: A Novel Role for Neurovascular Signaling in Promoting Melanoma Brain Metastasis. Front Neurosci 2019; 13:297. [PMID: 31024232 PMCID: PMC6465799 DOI: 10.3389/fnins.2019.00297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/15/2019] [Indexed: 12/12/2022] Open
Abstract
Neural repair after stroke involves initiation of a cellular proliferative program in the form of angiogenesis, neurogenesis, and molecular growth signals in the surrounding tissue elements. This cellular environment constitutes a niche in which regeneration of new blood vessels and new neurons leads to partial tissue repair after stroke. Cancer metastasis has similar proliferative cellular events in the brain and other organs. Do cancer and CNS tissue repair share similar cellular processes? In this study, we identify a novel role of the regenerative neurovascular niche induced by stroke in promoting brain melanoma metastasis through enhancing cellular interactions with surrounding niche components. Repair-mediated neurovascular signaling induces metastatic cells to express genes crucial to metastasis. Mimicking stroke-like conditions in vitro displays an enhancement of metastatic migration potential and allows for the determination of cell-specific signals produced by the regenerative neurovascular niche. Comparative analysis of both in vitro and in vivo expression profiles reveals a major contribution of endothelial cells in mediating melanoma metastasis. These results point to a previously undiscovered role of the regenerative neurovascular niche in shaping the tumor microenvironment and brain metastatic landscape.
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Affiliation(s)
- Roshini Prakash
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sivan Izraely
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nikita S Thareja
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Rex H Lee
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Maya Rappaport
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Riki Kawaguchi
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, United States
| | - Orit Sagi-Assif
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shlomit Ben-Menachem
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tsipi Meshel
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michal Machnicki
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Shuichi Ohe
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, United States
| | - Dave S Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, United States
| | - Giovanni Coppola
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, United States
| | - Isaac P Witz
- Department of Cell Research and Immunology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - S Thomas Carmichael
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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7
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Buga AM, Docea AO, Albu C, Malin RD, Branisteanu DE, Ianosi G, Ianosi SL, Iordache A, Calina D. Molecular and cellular stratagem of brain metastases associated with melanoma. Oncol Lett 2019; 17:4170-4175. [PMID: 30944612 DOI: 10.3892/ol.2019.9933] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/17/2018] [Indexed: 12/24/2022] Open
Abstract
Tumors of the central nervous system are the most prevalent complications of melanoma, especially in the late stage of disease. Melanoma, lung and breast cancer are the leading cause of secondary tumors in the brain, the majority of them having a poor outcome. Brain dissemination is developed in half of stage IV melanomas and these cases can increase up to 75%, having a major impact on the quality of life. This review will focus on recent findings that provide new ways to potentially prevent brain metastases in malignant melanoma. The key of these findings is based on the heterogeneity of the melanoma and of the brain metastases at genetic levels. This new era of technologies provides new tools in understanding the dissemination mechanisms of malignant cells. The cellular and molecular changes, the immune status of the patient and the blood-brain barrier permeability are key regulators of cancer cell dissemination. Understanding these mechanisms can render new hope in preventing brain metastases by focusing on melanoma and new pharmacologic approaches.
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Affiliation(s)
- Ana-Maria Buga
- Department of Functional Science, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania.,Department of Toxicology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Anca Oana Docea
- Department of Toxicology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Carmen Albu
- Department of Neurology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Ramona Denise Malin
- Department of Neurology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | | | - Gabriel Ianosi
- Department of Surgery, Dermatopharmacy and Cosmetology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Simona Laura Ianosi
- Department of Dermatology, Dermatopharmacy and Cosmetology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Andrei Iordache
- Department of Clinical Pharmacy, Dermatopharmacy and Cosmetology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Daniela Calina
- Department of Clinical Pharmacy, Dermatopharmacy and Cosmetology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
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8
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Global DNA demethylation as an epigenetic marker of human brain metastases. Biosci Rep 2018; 38:BSR20180731. [PMID: 30254100 PMCID: PMC6200709 DOI: 10.1042/bsr20180731] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/20/2018] [Accepted: 08/24/2018] [Indexed: 12/29/2022] Open
Abstract
Brain metastases are the most common intracranial tumors in adults. They usually originate from: lung, breast, renal cell and gastrointestinal cancers, as well as melanoma. Prognosis for brain metastases is still poor and classical treatment combining surgery and radiation therapy should be strongly supported with molecular approaches. However, their successful application depends on a deep understanding of not only genetic, but also epigenetic background of the disease. That will result in an earlier and more precise diagnosis, successful treatment, as well as individualized estimation of clinical outcomes and prognosis. It has already been shown that the epigenetic machinery plays a crucial role in cancer biology, development, and progression. Therefore, we decided to look for metastasis through changes in the most studied epigenetic mark, 5-methylcytosine (m5C) in DNA. We performed global analysis of the m5C contents in DNA isolated from the brain metastatic tumor tissue and peripheral blood samples of the same patients, using thin layer chromatography separation of radioactively labeled nucleotides. We found that the m5C level in DNA from brain metastases: changes in the broad range, overlaps with that of blood, and negatively correlates with the increasing tumor grade. Because the amount of m5C in tumor tissue and blood is almost identical, the genomic DNA methylation can be a useful marker for brain metastases detection and differentiation. Our research creates a scope for future studies on epigenetic mechanisms in neuro-oncology and can lead to development of new diagnostic methods in clinical practice.
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Graff-Baker AN, Orozco JIJ, Marzese DM, Salomon MP, Hoon DSB, Goldfarb M. Epigenomic and Transcriptomic Characterization of Secondary Breast Cancers. Ann Surg Oncol 2018; 25:3082-3087. [PMID: 29956094 DOI: 10.1245/s10434-018-6582-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Molecular alterations impact tumor prognosis and response to treatment. This study was designed to identify transcriptomic and epigenomic signatures of breast cancer (BC) tumors from patients with any prior malignancy. METHODS RNA-sequencing and genome-wide DNA methylation profiles from BCs were generated in the Cancer Genome Atlas project. Patients with secondary breast cancer (SBC) were separated by histological subtype and matched to primary breast cancer controls to create two independent cohorts of invasive ductal (IDC, n = 36) and invasive lobular (ILC, n = 40) carcinoma. Differentially expressed genes, as well as differentially methylated genomic regions, were integrated to identify epigenetically regulated abnormal gene pathways in SBCs. RESULTS Differentially expressed genes were identified in IDC SBCs (n = 727) and in ILC SBCs (n = 261; Wilcoxon's test; P < 0.05). In IDC SBCs, 105 genes were upregulated and hypomethylated, including an estrogen receptor gene, and 73 genes were downregulated and hypermethylated, including genes involved in antigen presentation and interferon response pathways (HLA-E, IRF8, and RELA). In ILC SBCs, however, only 17 genes were synchronously hypomethylated and upregulated, whereas 46 genes hypermethylated and downregulated. Interestingly, the SBC gene expression signatures closely corresponded with each histological subtype with only 1.51% of genes overlapping between the two histological subtypes. CONCLUSIONS Differential gene expression and DNA methylation signatures are seen in both IDC and ILC SBCs, including genes that are relevant to tumor growth and proliferation. Differences in gene expression signatures corresponding with each histological subtype emphasize the importance of disease subtype-specific evaluations of molecular alterations.
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Affiliation(s)
- Amanda N Graff-Baker
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Javier I J Orozco
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Diego M Marzese
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Matthew P Salomon
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Dave S B Hoon
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Melanie Goldfarb
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.
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10
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Moshe A, Izraely S, Sagi-Assif O, Prakash R, Telerman A, Meshel T, Carmichael T, Witz IP. Cystatin C takes part in melanoma-microglia cross-talk: possible implications for brain metastasis. Clin Exp Metastasis 2018; 35:369-378. [PMID: 29722001 PMCID: PMC6208992 DOI: 10.1007/s10585-018-9891-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/16/2018] [Indexed: 12/20/2022]
Abstract
The development of melanoma brain metastasis is largely dependent on mutual interactions between the melanoma cells and cells in the brain microenvironment. Here, we report that the extracellular cysteine protease inhibitor cystatin C (CysC) is involved in these interactions. Microglia-derived factors upregulated CysC secretion by melanoma. Similarly, melanoma-derived factors upregulated CysC secretion by microglia. Whereas CysC enhanced melanoma cell migration through a layer of brain endothelial cells, it inhibited the migration of microglia cells toward melanoma cells. CysC was also found to promote the formation of melanoma three-dimensional structures in matrigel. IHC analysis revealed increased expression levels of CysC in the brain of immune-deficient mice bearing xenografted human melanoma brain metastasis compared to the brain of control mice. Based on these in vitro and in vivo experiments we hypothesize that CysC promotes melanoma brain metastasis. Increased expression levels of CysC were detected in the regenerating brain of mice after stroke. Post-stroke brain with melanoma brain metastasis showed an even stronger expression of CysC. The in vitro induction of stroke-like conditions in brain microenvironmental cells increased the levels of CysC in the secretome of microglia cells, but not in the secretome of brain endothelial cells. The similarities between melanoma brain metastasis and stroke with respect to CysC expression by and secretion from microglia cells suggest that CysC may be involved in shared pathways between brain metastasis and post-stroke regeneration. This manifests the tendency of tumor cells to highjack physiological molecular pathways in their progression.
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Affiliation(s)
- Adi Moshe
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Sivan Izraely
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Orit Sagi-Assif
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Roshini Prakash
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Alona Telerman
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Tsipi Meshel
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Thomas Carmichael
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Isaac P Witz
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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11
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Bustos MA, Ono S, Marzese DM, Oyama T, Iida Y, Cheung G, Nelson N, Hsu SC, Yu Q, Hoon DSB. MiR-200a Regulates CDK4/6 Inhibitor Effect by Targeting CDK6 in Metastatic Melanoma. J Invest Dermatol 2017; 137:1955-1964. [PMID: 28526299 DOI: 10.1016/j.jid.2017.03.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 03/03/2017] [Accepted: 03/19/2017] [Indexed: 12/29/2022]
Abstract
The CDK4/6 pathway is frequently dysregulated in cutaneous melanoma. Recently, CDK4/6 inhibitors have shown promising clinical activity against several cancer types, including melanoma. Here, we show that microRNA-200a decreases CDK6 expression and thus reduces the response of CDK4/6 inhibitor in highly proliferative metastatic melanoma. Down-regulation of microRNA-200a expression in melanoma cells is associated with disease progression and a higher number of lymph node metastases. Furthermore, microRNA-200a expression is epigenetically modulated by both DNA methylation at the promoter region and chromatin accessibility of an upstream genomic region with enhancer activity. Mechanistically, overexpression of miR-200a in metastatic melanoma cells induces cell cycle arrest by targeting CDK6 and decreases the levels of phosphorylated-Rb1 and E2F-downstream targets, diminishing cell proliferation; these effects are recovered by CDK6 overexpression. Conversely, low microRNA-200a expression in metastatic melanoma cells results in higher levels of CDK6 and a more significant response to CDK4/6 inhibitors. We propose that microRNA-200a functions as a "cell cycle brake" that is lost during melanoma progression to metastasis and provides the ability to identify melanomas that are highly proliferative and more prompted to respond to CDK4/6 inhibitors.
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Affiliation(s)
- Matias A Bustos
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Shigeshi Ono
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Diego M Marzese
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Takashi Oyama
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Yuuki Iida
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Garrett Cheung
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Nellie Nelson
- Sequencing Center, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Sandy C Hsu
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA; Sequencing Center, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Qiang Yu
- Cancer Biology and Pharmacology, Genome Institute of Singapore, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Division of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA; Sequencing Center, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA.
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12
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Izraely S, Ben-Menachem S, Sagi-Assif O, Meshel T, Marzese DM, Ohe S, Zubrilov I, Pasmanik-Chor M, Hoon DSB, Witz IP. ANGPTL4 promotes the progression of cutaneous melanoma to brain metastasis. Oncotarget 2017; 8:75778-75796. [PMID: 29100268 PMCID: PMC5652662 DOI: 10.18632/oncotarget.19018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/10/2017] [Indexed: 01/16/2023] Open
Abstract
In an ongoing effort to identify molecular determinants regulating melanoma brain metastasis, we previously identified Angiopoietin-like 4 (ANGPTL4) as a component of the molecular signature of such metastases. The aim of this study was to determine the functional significance of ANGPTL4 in the shaping of melanoma malignancy phenotype, especially in the establishment of brain metastasis. We confirmed that ANGPTL4 expression is significantly higher in cells metastasizing to the brain than in cells from the cutaneous (local) tumor from the same melanoma in a nude mouse xenograft model, and also in paired clinical specimens of melanoma metastases than in primary melanomas from the same patients. In vitro experiments indicated that brain-derived soluble factors and transforming growth factor β1 (TGFβ1) up-regulated ANGPTL4 expression by melanoma cells. Forced over-expression of ANGPTL4 in cutaneous melanoma cells promoted their ability to adhere and transmigrate brain endothelial cells. Over-expressing ANGPTL4 in cells derived from brain metastases resulted in the opposite effects. In vivo data indicated that forced overexpression of ANGPTL4 promoted the tumorigenicity of cutaneous melanoma cells but did not increase their ability to form brain metastasis. This finding can be explained by inhibitory activities of brain-derived soluble factors. Taken together these findings indicate that ANGPTL4 promotes the malignancy phenotype of primary melanomas of risk to metastasize to the brain.
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Affiliation(s)
- Sivan Izraely
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shlomit Ben-Menachem
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Orit Sagi-Assif
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tsipi Meshel
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Diego M Marzese
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Shuichi Ohe
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Inna Zubrilov
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Isaac P Witz
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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Abstract
The past decade has witnessed impressive advances in cancer treatment ushered in by targeted and immunotherapies. However, with significantly prolonged survival, upon recurrence, more patients become inflicted by brain metastasis, which is mostly refractory to all currently available therapeutic regimens. Historically, brain metastasis is an understudied area in cancer research, partly due to the dearth of appropriate experimental models that closely simulate the special biological features of metastasis in the unique brain environment and to the sophistication of techniques required to perform in-depth studies of the extremely complex and challenging brain metastasis. Yet, with increasing clinical demand for more effective treatment options, brain metastasis research has rapidly advanced in recent years. The present review spotlights the recent major progresses in basic and translational studies of brain metastasis with focuses on new animal models, novel imaging technologies, omics "big data" resources, and some new and exciting biological insights on brain metastasis.
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