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Kaur P, Nazeer N, Gurjar V, Tiwari R, Mishra PK. Nanophotonic waveguide-based sensing of circulating cell-free mitochondrial DNA: implications for personalized medicine. Drug Discov Today 2024; 29:104086. [PMID: 38960132 DOI: 10.1016/j.drudis.2024.104086] [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: 11/30/2023] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
Circulating cell-free mitochondrial DNA (ccf-mtDNA) has emerged as a promising biomarker, with potential implications for disease diagnosis. Changes in mtDNA, such as deletions, mutations or variations in the number of copies, have been associated with mitochondrial disorders, heart diseases, cancer and age-related non-communicable diseases. Previous methods, such as polymerase chain reaction-based approaches, next-generation sequencing and imaging-based techniques, have shown improved accuracy in identifying rare mtDNA variants or mutations, but they have limitations. This article explains the basic principles and benefits of using planar optical waveguide-based detection devices, which represent an advanced approach in the field of sensing.
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Affiliation(s)
- Prasan Kaur
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Nazim Nazeer
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Vikas Gurjar
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Rajnarayan Tiwari
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Pradyumna Kumar Mishra
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India.
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2
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Phillips D, Noble D. Reply from Daniel Phillips and Denis Noble. J Physiol 2024; 602:2669-2672. [PMID: 38305416 DOI: 10.1113/jp286224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Affiliation(s)
- Daniel Phillips
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Denis Noble
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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3
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Filatova AA, Alekseeva LA, Sen’kova AV, Savin IA, Sounbuli K, Zenkova MA, Mironova NL. Tumor- and Fibroblast-Derived Cell-Free DNAs Differently Affect the Progression of B16 Melanoma In Vitro and In Vivo. Int J Mol Sci 2024; 25:5304. [PMID: 38791341 PMCID: PMC11120878 DOI: 10.3390/ijms25105304] [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: 03/28/2024] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
It is widely postulated that the majority of pathologically elevated extracellular or cell-free DNA (cfDNA) in cancer originates from tumor cells; however, evidence has emerged regarding the significant contributions of other cells from the tumor microenvironment. Here, the effect of cfDNA originating from murine B16 melanoma cells and L929 fibroblasts on B16 cells was investigated. It was found that cfDNAL929 increased the viability and migration properties of B16 cells in vitro and their invasiveness in vivo. In contrast, cfDNAB16 exhibited a negative effect on B16 cells, reducing their viability and migration in vitro, which in vivo led to decreased tumor size and metastasis number. It was shown that cell treatment with both cfDNAs resulted in an increase in the expression of genes encoding DNases and the oncogenes Braf, Kras, and Myc. cfDNAL929-treated cells were shown to experience oxidative stress. Gene expression changes in the case of cfDNAB16 treatment are well correlated with the observed decrease in proliferation and migration of B16 cells. The obtained data may indicate the possible involvement of fibroblast DNA in the tumor microenvironment in tumor progression and, potentially, in the formation of new tumor foci due to the transformation of normal cells.
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Affiliation(s)
- Alina A. Filatova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ludmila A. Alekseeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Aleksandra V. Sen’kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Innokenty A. Savin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Khetam Sounbuli
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Marina A. Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
| | - Nadezhda L. Mironova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Ave., 8, Novosibirsk 630090, Russia; (A.A.F.); (L.A.A.); (A.V.S.); (I.A.S.); (K.S.); (M.A.Z.)
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4
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Ebrahim T, Ebrahim AS, Kandouz M. Diversity of Intercellular Communication Modes: A Cancer Biology Perspective. Cells 2024; 13:495. [PMID: 38534339 DOI: 10.3390/cells13060495] [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: 01/05/2024] [Revised: 02/27/2024] [Accepted: 03/10/2024] [Indexed: 03/28/2024] Open
Abstract
From the moment a cell is on the path to malignant transformation, its interaction with other cells from the microenvironment becomes altered. The flow of molecular information is at the heart of the cellular and systemic fate in tumors, and various processes participate in conveying key molecular information from or to certain cancer cells. For instance, the loss of tight junction molecules is part of the signal sent to cancer cells so that they are no longer bound to the primary tumors and are thus free to travel and metastasize. Upon the targeting of a single cell by a therapeutic drug, gap junctions are able to communicate death information to by-standing cells. The discovery of the importance of novel modes of cell-cell communication such as different types of extracellular vesicles or tunneling nanotubes is changing the way scientists look at these processes. However, are they all actively involved in different contexts at the same time or are they recruited to fulfill specific tasks? What does the multiplicity of modes mean for the overall progression of the disease? Here, we extend an open invitation to think about the overall significance of these questions, rather than engage in an elusive attempt at a systematic repertory of the mechanisms at play.
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Affiliation(s)
- Thanzeela Ebrahim
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Abdul Shukkur Ebrahim
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Mustapha Kandouz
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48202, USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48202, USA
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5
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Mittra I. Exploiting the damaging effects of ROS for therapeutic use by deactivating cell-free chromatin: the alchemy of resveratrol and copper. Front Pharmacol 2024; 15:1345786. [PMID: 38455966 PMCID: PMC10917901 DOI: 10.3389/fphar.2024.1345786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024] Open
Abstract
Cell-free chromatin particles (cfChPs) that circulate in blood, or those that are released locally from dying cells, have myriad pathological effects. They can horizontally transfer themselves into healthy cells to induce DNA damage and activate inflammatory and apoptotic pathways. It has been proposed that repeated and lifelong assault on healthy cells by cfChPs may be the underlying cause of ageing and multiple age related disorders including cancer. The damaging effects of cfChPs can be minimized by deactivating them via the medium of ROS generated by admixing the nutraceuticals resveratrol (R) and copper (Cu). The antioxidant R acts as a pro-oxidant in the presence of Cu by its ability to catalyse the reduction of Cu(II) to Cu(I) with the generation of ROS via a Fenton-like reaction which can deactivate extra-cellular cfChPs. This perspective article explores the possibility of using the damaging potential of ROS for therapeutic purposes. It discusses the ability of ROS generating nutraceuticals R-Cu to deactivate the extracellular cfChPs without damaging effects on the genomic DNA. As cfChPs play a key role in activation of various disease associated pathways, R-Cu mediated deactivation of these pathways may open up multiple novel avenues for therapy. These findings have considerable translational implications which deserve further investigation by the way of well-designed randomised clinical trials.
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Affiliation(s)
- Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Navi Mumbai, India
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Raghuram GV, Pal K, Sriram G, Khan A, Joshi R, Jadhav V, Shinde S, Shaikh A, Rane B, Kangne H, Mittra I. Therapeutic interventions on human breast cancer xenografts promote systemic dissemination of oncogenes. PLoS One 2024; 19:e0298042. [PMID: 38346047 PMCID: PMC10861051 DOI: 10.1371/journal.pone.0298042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
Metastatic dissemination following successful treatment of the primary tumour remains a common cause of death. There is mounting evidence that therapeutic interventions themselves may promote development of metastatic disease. We earlier reported that cell-free chromatin particles (cfChPs) released from dying cancer cells are potentially oncogenic. Based on this observation we hypothesized that therapeutic interventions may lead to the release of cfChPs from therapy induced dying cancer cells which could be carried via the blood stream to distant organs to transform healthy cells into new cancers that would masquerade as metastasis. To test this hypothesis, we generated xenografts of MDA-MB-231 human breast cancer cells in severe combined immune-deficient mice, and using immuno-fluorescence and FISH analysis looked for cfChPs in their brain cells. We detected multiple human DNA signals representing cfChPs in nuclei of brain cells of mice which co-localized with eight human onco-proteins. No intact MDA-MB-231 cells were detected. The number of co-localizing human DNA and human c-Myc signals increased dramatically following treatment with chemotherapy, localized radiotherapy or surgery, which could be prevented by concurrent treatment with three different cfChPs deactivating agents. These results suggest that therapeutic interventions lead to the release cfChPs from therapy induced dying cancer cells carrying oncogenes and are transported via the blood stream to brain cells to potentially transform them to generate new cancers that would appear as metastases. cfChPs induced metastatic spread of cancer is preventable by concurrent treatment with agents that deactivate cfChPs.
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Affiliation(s)
- Gorantla V. Raghuram
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Kavita Pal
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Gaurav Sriram
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Afzal Khan
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Ruchi Joshi
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Vishalkumar Jadhav
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Sushma Shinde
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Alfina Shaikh
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Bhagyeshri Rane
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Harshada Kangne
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Indraneel Mittra
- Translational Research Laboratory, Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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7
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Witz A, Dardare J, Betz M, Gilson P, Merlin JL, Harlé A. Tumor-derived cell-free DNA and circulating tumor cells: partners or rivals in metastasis formation? Clin Exp Med 2024; 24:2. [PMID: 38231464 PMCID: PMC10794481 DOI: 10.1007/s10238-023-01278-9] [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: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The origin of metastases is a topic that has sparked controversy. Despite recent advancements, metastatic disease continues to pose challenges. The first admitted model of how metastases develop revolves around cells breaking away from the primary tumor, known as circulating tumor cells (CTCs). These cells survive while circulating through the bloodstream and subsequently establish themselves in secondary organs, a process often referred to as the "metastatic cascade". This intricate and dynamic process involves various steps, but all the mechanisms behind metastatic dissemination are not yet comprehensively elucidated. The "seed and soil" theory has shed light on the phenomenon of metastatic organotropism and the existence of pre-metastatic niches. It is now established that these niches can be primed by factors secreted by the primary tumor before the arrival of CTCs. In particular, exosomes have been identified as important contributors to this priming. Another concept then emerged, i.e. the "genometastasis" theory, which challenged all other postulates. It emphasizes the intriguing but promising role of cell-free DNA (cfDNA) in metastasis formation through oncogenic formation of recipient cells. However, it cannot be ruled out that all these theories are intertwined. This review outlines the primary theories regarding the metastases formation that involve CTCs, and depicts cfDNA, a potential second player in the metastasis formation. We discuss the potential interrelationships between CTCs and cfDNA, and propose both in vitro and in vivo experimental strategies to explore all plausible theories.
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Affiliation(s)
- Andréa Witz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France.
| | - Julie Dardare
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Margaux Betz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Pauline Gilson
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Jean-Louis Merlin
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Alexandre Harlé
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
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8
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Raghuram GV, Tripathy BK, Avadhani K, Shabrish S, Khare NK, Lopes R, Pal K, Mittra I. Cell-free chromatin particles released from dying cells inflict mitochondrial damage and ROS production in living cells. Cell Death Discov 2024; 10:30. [PMID: 38225229 PMCID: PMC10789803 DOI: 10.1038/s41420-023-01728-z] [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: 09/20/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 01/17/2024] Open
Abstract
Mitochondrial damage and the resultant oxidative stress are associated with neurodegenerative diseases, ageing, and cancer. However, the triggers of mitochondrial damage remain unclear. We previously reported that cell-free chromatin particles (cfChPs) released from the billions of cells that die in the body every day can readily enter healthy cells and damage their DNA. Here, we show that cfChPs isolated from the sera of healthy individuals, when applied to NIH3T3 mouse fibroblast cells, cause physical damage to mitochondrial DNA (mtDNA). cfChPs also induce ultrastructural changes, increase mitochondrial mass, alter mitochondrial shape, upregulate mitochondrial outer membrane protein translocase of the outer membrane 20, and change mitochondrial membrane potential. Furthermore, a marked increase was observed in mitochondrial superoxide (ROS) production, as detected by MitoSOX Red, and intracellular superoxide dismutase-1 activation. ROS production was also activated when a conditioned medium containing cfChPs released from hypoxia-induced dying NIH3T3 cells was applied to healthy NIH3T3 cells. ROS activation was significantly reduced when the conditioned medium was pre-treated with three different cfChP-deactivating agents: anti-histone antibody-complexed nanoparticles, DNase I, and the novel pro-oxidant combination of the nutraceuticals resveratrol and copper. Given that 1 × 109-1 × 1012 cells die in the body every day, we hypothesise that cfChPs from dying cells are the major physiological triggers for mtDNA damage and ROS production. Deactivation of cfChPs may provide a novel therapeutic approach to retard ageing and associated degenerative conditions linked to oxidative stress.
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Affiliation(s)
- Gorantla V Raghuram
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Bhabesh Kumar Tripathy
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Kartikeya Avadhani
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Snehal Shabrish
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Naveen Kumar Khare
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Relestina Lopes
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Kavita Pal
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Indraneel Mittra
- Translational Research Laboratory Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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Shabrish S, Pal K, Khare NK, Satsangi D, Pilankar A, Jadhav V, Shinde S, Raphael N, Sriram G, Lopes R, Raghuram GV, Tandel H, Mittra I. Cell-free chromatin particles released from dying cancer cells activate immune checkpoints in human lymphocytes: implications for cancer therapy. Front Immunol 2024; 14:1331491. [PMID: 38274821 PMCID: PMC10808321 DOI: 10.3389/fimmu.2023.1331491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Immune checkpoint blockade is the exciting breakthrough in cancer, but how immune checkpoints are activated is unknown. We have earlier reported that cell-free chromatin particles (cfChPs) that circulate in blood of cancer patients, or those that are released locally from dying cancer cells, are readily internalized by healthy cells with biological consequences. Here we report that treatment of human lymphocytes with cfChPs isolated from sera of cancer patients led to marked activation of the immune checkpoints PD-1, CTLA-4, LAG-3, NKG2A, and TIM-3. This finding was corroborated in vivo in splenocytes of mice when cfChPs were injected intravenously. Significant upregulation of immune checkpoint was also observed when isolated lymphocytes were exposed to conditioned medium containing cfChPs released from hypoxia-induced dying HeLa cells. Immune checkpoint activation could be down-regulated by pre-treating the conditioned media with three different cfChPs deactivating agents. Down-regulation of immune checkpoints by cfChPs deactivating agents may herald a novel form of immunotherapy of cancer.
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Affiliation(s)
- Snehal Shabrish
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Kavita Pal
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Naveen Kumar Khare
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Dharana Satsangi
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Aishwarya Pilankar
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Vishalkumar Jadhav
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Sushma Shinde
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Nimisha Raphael
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Gaurav Sriram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Relestina Lopes
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Gorantla V. Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Harshali Tandel
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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10
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Filatova AA, Alekseeva LA, Savin IA, Sen'kova AV, Zenkova MA, Mironova NL. The Effect of Cell-Free DNA from Blood Serum of Mice with Metastatic Melanoma on Enhancement of Oncogenic Properties of Melanoma Cells. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:995-1007. [PMID: 37751869 DOI: 10.1134/s0006297923070118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 09/28/2023]
Abstract
Currently, a significant increase in the levels of circulating cell-free DNA (cfDNA) in the blood of patients is considered as a generally recognized marker of the development of oncological diseases. Although the tumor-associated cfDNA has been well studied, its biological functions remain unclear. In this work, we investigated the effect of cfDNA isolated from the blood serum of the mice with B16-F10 metastatic melanoma on the properties of the B16-F10 melanoma cells in vitro. It was found that the profile of cfDNA isolated from the blood serum of mice with melanoma differs significantly from the cfDNA isolated from the blood serum of healthy mice, and is similar to the genomic DNA of B16 cells with regards to abundance of oncogenes and mobile genetic elements (MGE). It was shown that the cfDNA of mice with melanoma penetrated into B16 cells, resulting in the increase in abundance of oncogenes and MGE fragments, and caused 5-fold increase of the mRNA level of the secreted DNase Dnase1l3 and a slight increase of the mRNA level of the Jun, Fos, Ras, and Myc oncogenes. cfDNA of the healthy mice caused increase of the mRNA level of intracellular regulatory DNase EndoG and 4-fold increase of the mRNA level of Fos and Ras oncogenes, which are well-known triggers of a large number of signal cascades, from apoptosis inhibition to increased tumor cell proliferation. Thus, it is obvious that the circulating cfDNA of tumor origin is able to penetrate into the cells and, despite the fact that no changes were found in the level of viability and migration activity of the tumor cells, cfDNA, even with a single exposure, can cause changes at the cellular level that increase oncogenicity of the recipient cells.
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Affiliation(s)
- Alina A Filatova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Ludmila A Alekseeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Innokenty A Savin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Aleksandra V Sen'kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Nadezhda L Mironova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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11
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Gaitsch H, Franklin RJM, Reich DS. Cell-free DNA-based liquid biopsies in neurology. Brain 2023; 146:1758-1774. [PMID: 36408894 PMCID: PMC10151188 DOI: 10.1093/brain/awac438] [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: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
This article reviews recent developments in the application of cell-free DNA-based liquid biopsies to neurological diseases. Over the past few decades, an explosion of interest in the use of accessible biofluids to identify and track molecular disease has revolutionized the fields of oncology, prenatal medicine and others. More recently, technological advances in signal detection have allowed for informative analysis of biofluids that are typically sparse in cells and other circulating components, such as CSF. In parallel, advancements in epigenetic profiling have allowed for novel applications of liquid biopsies to diseases without characteristic mutational profiles, including many degenerative, autoimmune, inflammatory, ischaemic and infectious disorders. These events have paved the way for a wide array of neurological conditions to benefit from enhanced diagnostic, prognostic, and treatment abilities through the use of liquid biomarkers: a 'liquid biopsy' approach. This review includes an overview of types of liquid biopsy targets with a focus on circulating cell-free DNA, methods used to identify and probe potential liquid biomarkers, and recent applications of such biomarkers to a variety of complex neurological conditions including CNS tumours, stroke, traumatic brain injury, Alzheimer's disease, epilepsy, multiple sclerosis and neuroinfectious disease. Finally, the challenges of translating liquid biopsies to use in clinical neurology settings-and the opportunities for improvement in disease management that such translation may provide-are discussed.
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Affiliation(s)
- Hallie Gaitsch
- NIH-Oxford-Cambridge Scholars Program, Wellcome-MRC Cambridge Stem Cell Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 1TN, UK
| | | | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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郑 适, 孟 琳, 任 飞, 任 春, 李 杏, 王 丹, 孙 宏. [Oral Squamous Cell Carcinoma-Derived Cell-Free DNA Modulates Stemness and Migration of Oral Squamous Cell Carcinoma Cell Line by Inducing M2 Macrophage Polarization]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:510-516. [PMID: 37248576 PMCID: PMC10475408 DOI: 10.12182/20230560206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Indexed: 05/31/2023]
Abstract
Objective To investigate the effect of oral squamous cell carcinoma (OSCC)-derived cell-free DNA (cfDNA) on the polarization of macrophages and the regulatory effect of polarized macrophages on the stemness and migration of OSCC cells. Methods A total of 30 OSCC tissue samples, 10 dysplastic oral tissue samples, and 10 normal oral tissue samples were collected. The status of all tissue samples was confirmed by pathology analysis. Immunohistochemical (IHC) staining and immunofluorescence (IF) staining were performed to examine the cell count and location of M2 macrophages in different types of oral tissue samples. The conditioned medium (CM) of OSCC cell line CAL-27 from the human tongue was collected and the cfDNA was concentrated and isolated for identification. The macrophages were treated by cfDNA and their morphological characteristics were observed under microscope. The expression levels of polarization-related indicators were determined by RT-qPCR. CAL-27 cell line was treated with macrophage CM induced by cfDNA and the expression levels of stemness-related genes were determined by RT-qPCR. Scratch-wound assay was conducted to verify that the migration ability of CAL-27 was modulated by macrophages induced by cfDNA. Results There were more M2 macrophages in the deep connective tissue of dysplastic oral epithelium and the stroma of OSCC compared with those in the normal oral tissues ( P<0.05). OSCC cell line CAL-27 could secret cfDNA of 10000-15000 bp in length. cfDNA secreted by CAL-27 could induced in macrophages significantly higher expression of M2-macrophage-related genes ( P<0.05). cfDNA-treated macrophages induced significantly increased expression of stemness-related genes in CAL-27 cell line ( P<0.05) and promoted the migration ability of CAL-27 cell line ( P<0.05). Conclusion OSCC-derived cfDNA promotes stemness and migration of OSCC cell line by inducing M2 macrophage polarization.
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Affiliation(s)
- 适泽 郑
- 吉林大学口腔医院 病理科 (长春 130021)Department of Pathology, Hospital of Stomatology, Jilin University, Changchun 130021, China
- 吉林省牙发育及颌骨重塑与再生重点实验室 (长春 130021)Jilin Provincial Key Laboratory of Tooth Development, Jaw Bone Remodeling and Regeneration, Changchun 130021, China
| | - 琳 孟
- 吉林大学口腔医院 病理科 (长春 130021)Department of Pathology, Hospital of Stomatology, Jilin University, Changchun 130021, China
- 吉林省牙发育及颌骨重塑与再生重点实验室 (长春 130021)Jilin Provincial Key Laboratory of Tooth Development, Jaw Bone Remodeling and Regeneration, Changchun 130021, China
| | - 飞龙 任
- 吉林大学口腔医院 病理科 (长春 130021)Department of Pathology, Hospital of Stomatology, Jilin University, Changchun 130021, China
- 吉林省牙发育及颌骨重塑与再生重点实验室 (长春 130021)Jilin Provincial Key Laboratory of Tooth Development, Jaw Bone Remodeling and Regeneration, Changchun 130021, China
| | - 春霞 任
- 吉林大学口腔医院 病理科 (长春 130021)Department of Pathology, Hospital of Stomatology, Jilin University, Changchun 130021, China
- 吉林省牙发育及颌骨重塑与再生重点实验室 (长春 130021)Jilin Provincial Key Laboratory of Tooth Development, Jaw Bone Remodeling and Regeneration, Changchun 130021, China
| | - 杏 李
- 吉林大学口腔医院 病理科 (长春 130021)Department of Pathology, Hospital of Stomatology, Jilin University, Changchun 130021, China
- 吉林省牙发育及颌骨重塑与再生重点实验室 (长春 130021)Jilin Provincial Key Laboratory of Tooth Development, Jaw Bone Remodeling and Regeneration, Changchun 130021, China
| | - 丹丹 王
- 吉林大学口腔医院 病理科 (长春 130021)Department of Pathology, Hospital of Stomatology, Jilin University, Changchun 130021, China
- 吉林省牙发育及颌骨重塑与再生重点实验室 (长春 130021)Jilin Provincial Key Laboratory of Tooth Development, Jaw Bone Remodeling and Regeneration, Changchun 130021, China
| | - 宏晨 孙
- 吉林大学口腔医院 病理科 (长春 130021)Department of Pathology, Hospital of Stomatology, Jilin University, Changchun 130021, China
- 吉林省牙发育及颌骨重塑与再生重点实验室 (长春 130021)Jilin Provincial Key Laboratory of Tooth Development, Jaw Bone Remodeling and Regeneration, Changchun 130021, China
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Abramson DH, Mandelker DL, Brannon AR, Dunkel IJ, Benayed R, Berger MF, Arcila ME, Ladanyi M, Friedman DN, Jayakumaran G, Diosdado MS, Robbins MA, Haggag-Lindgren D, Shukla N, Walsh MF, Kothari P, Tsui DWY, Francis JH. Mutant-RB1 circulating tumor DNA in the blood of unilateral retinoblastoma patients: What happens during enucleation surgery: A pilot study. PLoS One 2023; 18:e0271505. [PMID: 36735656 PMCID: PMC9897525 DOI: 10.1371/journal.pone.0271505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/04/2022] [Indexed: 02/04/2023] Open
Abstract
Cell free DNA (cfDNA) and circulating tumor cell free DNA (ctDNA) from blood (plasma) are increasingly being used in oncology for diagnosis, monitoring response, identifying cancer causing mutations and detecting recurrences. Circulating tumor RB1 DNA (ctDNA) is found in the blood (plasma) of retinoblastoma patients at diagnosis before instituting treatment (naïve). We investigated ctDNA in naïve unilateral patients before enucleation and during enucleation (6 patients/ 8 mutations with specimens collected 5-40 minutes from severing the optic nerve) In our cohort, following transection the optic nerve, ctDNA RB1 VAF was measurably lower than pre-enucleation levels within five minutes, 50% less within 15 minutes and 90% less by 40 minutes.
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Affiliation(s)
- David H. Abramson
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Ophthalmology, Weill Cornell Medical Center, New York, New York, United States of America
- * E-mail:
| | - Diana L. Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - A. Rose Brannon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ira J. Dunkel
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Pediatrics, Weill Cornell Medical Center, New York, New York, United States of America
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Danielle Novetsky Friedman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Monica S. Diosdado
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Melissa A. Robbins
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Dianna Haggag-Lindgren
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Michael F. Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Prachi Kothari
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Dana W. Y. Tsui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Jasmine H. Francis
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Ophthalmology, Weill Cornell Medical Center, New York, New York, United States of America
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14
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The Overview of Perspectives of Clinical Application of Liquid Biopsy in Non-Small-Cell Lung Cancer. Life (Basel) 2022; 12:life12101640. [PMID: 36295075 PMCID: PMC9604747 DOI: 10.3390/life12101640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 01/19/2023] Open
Abstract
The standard diagnostics procedure for non-small-cell lung cancer (NSCLC) requires a pathological evaluation of tissue samples obtained by surgery or biopsy, which are considered invasive sampling procedures. Due to this fact, re-sampling of the primary tumor at the moment of progression is limited and depends on the patient’s condition, even if it could reveal a mechanism of resistance to applied therapy. Recently, many studies have indicated that liquid biopsy could be provided for the noninvasive management of NSCLC patients who receive molecularly targeted therapies or immunotherapy. The liquid biopsy of neoplastic patients harbors small fragments of circulating-free DNA (cfDNA) and cell-free RNA (cfRNA) secreted to the circulation from normal cells, as well as a subset of tumor-derived circulating tumor cells (CTCs) or circulating tumor DNA (ctDNA). In NSCLC patients, a longitudinal assessment of genetic alterations in “druggable” genes in liquid biopsy might improve the follow-up of treatment efficacy and allow for the detection of an early progression before it is detectable in computed tomography or a clinical image. However, a liquid biopsy may be used to determine a variety of relevant molecular or genetic information for understanding tumor biology and its evolutionary trajectories. Thus, liquid biopsy is currently associated with greater hope for common diagnostic and clinical applications. In this review, we would like to highlight diagnostic challenges in the application of liquid biopsy into the clinical routine and indicate its implications on the metastatic spread of NSCLC or monitoring of personalized treatment regimens.
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15
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A pro-oxidant combination of resveratrol and copper down-regulates multiple biological hallmarks of ageing and neurodegeneration in mice. Sci Rep 2022; 12:17209. [PMID: 36241685 PMCID: PMC9568542 DOI: 10.1038/s41598-022-21388-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/27/2022] [Indexed: 01/06/2023] Open
Abstract
Billions of cells die in the body every day, and cell-free chromatin particles (cfChPs) which are released from them enter into the extracellular compartments of the body, including into the circulation. cfChPs are known to readily enter into healthy cells to damage their DNA and activate apoptotic and inflammatory pathways. We have hypothesized that lifelong assault on healthy cells by cfChPs is the underlying cause of ageing, and that ageing could be retarded by deactivating extra-cellular cfChPs. The latter can be effected by oxygen radicals that are generated upon admixing the nutraceuticals resveratrol and copper (R-Cu). The present study investigated whether prolonged administration of R-Cu would retard biological hallmarks of ageing. C57Bl/6 mice were divided into 3 equal groups; one group was sacrificed at age 3 months, and which acted as young controls. The remaining mice were allowed to age, and at age 10 months the experimental ageing group was given R-Cu by oral gavage twice daily for further 12 months at a dose of 1 mg/kg of R and 0.1 μg/kg of Cu. The control ageing group was given water by oral gavage twice daily for 12 months. Animals of both groups were sacrificed at age 22 months. R-Cu treatment led to reduction of several biological hallmarks of ageing in brain cells which included telomere attrition, amyloid deposition, DNA damage, apoptosis, inflammation, senescence, aneuploidy and mitochondrial dysfunction. R-Cu treatment also led to significant reduction in blood levels of glucose, cholesterol and C-reactive protein. These findings suggest that cfChPs may act as global instigators of ageing and neurodegeneration, and that therapeutic use of R-Cu may help to make healthy ageing an attainable goal.
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New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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17
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Agarwal A, Khandelwal A, Pal K, Khare NK, Jadhav V, Gurjar M, Punatar S, Gokarn A, Bonda A, Nayak L, Kannan S, Gota V, Khattry N, Mittra I. A novel pro-oxidant combination of resveratrol and copper reduces transplant related toxicities in patients receiving high dose melphalan for multiple myeloma (RESCU 001). PLoS One 2022; 17:e0262212. [PMID: 35120140 PMCID: PMC8815866 DOI: 10.1371/journal.pone.0262212] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/03/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Transplant related toxicity is a major therapeutic challenge. We have previously reported that the toxicity of chemotherapy is largely not directly because of the drugs themselves; rather it is mainly due to DNA damage, apoptosis and hyper-inflammation triggered by cell-free chromatin particles that are released because of drug-induced host cell death. Cell-free chromatin particles can be inactivated by free-radicals which are generated when the nutraceuticals resveratrol and copper are administered orally. We investigated if a combination of resveratrol and copper would reduce transplant related toxicities in an exploratory, prospective dose-escalation study. PATIENTS AND METHODS Twenty-five patients with multiple myeloma were enrolled between March 2017 to August 2019. Patients were divided into 3 groups: control (Group 1, N = 5) received vehicle alone; group 2 (N = 15) received resveratrol-copper at dose level I (resveratrol = 5.6 mg and copper = 560 ng); group 3 (N = 5) received resveratrol-copper at dose level II (resveratrol = 50 mg and copper = 5 μg). The dose was given twice daily with the first dose administered 48 hours before administering melphalan and continued until day +21 post-transplant. Common Terminology Criteria for Adverse Events version 4.02 was used to assess toxicities which included oral mucositis, nausea, vomiting and diarrhea. Measurement of inflammatory cytokines was done by ELISA. RESULTS All patients (100%) in the control group developed grade 3/4 oral mucositis compared to 8/20 (40%) in both resveratrol-copper group 2 plus group 3 combined (P = 0.039). Reduction in inflammatory cytokines: salivary TNF - α (p = 0.012) and IL-1β (p = 0.009) in dose level I but not in dose level II was observed. CONCLUSIONS A combination of resveratrol-copper reduced transplant related toxicities in patients with multiple myeloma receiving high dose melphalan. We conclude that relatively inexpensive nutraceuticals may be useful as adjuncts to chemotherapy to reduce its toxicity. REGISTRATION The trial was registered under Clinical Trial Registry of India (no.CTRI/2018/02/011905).
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Affiliation(s)
- Anshul Agarwal
- Bone Marrow Transplant Unit, Department of Medical Oncology, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Aakanksha Khandelwal
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Translational Research Laboratory, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Kavita Pal
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Translational Research Laboratory, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Naveen Kumar Khare
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Translational Research Laboratory, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Vishal Jadhav
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Translational Research Laboratory, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Murarilal Gurjar
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Clinical Pharmacology Laboratory, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Sachin Punatar
- Bone Marrow Transplant Unit, Department of Medical Oncology, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Anant Gokarn
- Bone Marrow Transplant Unit, Department of Medical Oncology, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Avinash Bonda
- Bone Marrow Transplant Unit, Department of Medical Oncology, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Lingaraj Nayak
- Bone Marrow Transplant Unit, Department of Medical Oncology, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Sadhana Kannan
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Department of Biostatistics, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Vikram Gota
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Clinical Pharmacology Laboratory, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
| | - Navin Khattry
- Bone Marrow Transplant Unit, Department of Medical Oncology, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Indraneel Mittra
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
- Translational Research Laboratory, Tata Memorial Centre, Advance Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
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Song HS, Kang DH, Kim H, Ahn TS, Kim TW, Baek MJ. Clinical relevance and prognostic role of preoperative cell-free single-stranded DNA concentrations in colorectal cancer patients. KOREAN JOURNAL OF CLINICAL ONCOLOGY 2021; 17:59-67. [PMID: 36945669 PMCID: PMC9942756 DOI: 10.14216/kjco.21010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/19/2021] [Indexed: 06/18/2023]
Abstract
PURPOSE Circulating cell-free single-stranded DNA (ccf-ssDNA) is extracellular DNA and it is a useful biomarker for the diagnosis of tumors and predicting the prognosis of tumors. However, the clinical usefulness of ccf-ssDNA in colorectal cancer (CRC) is not well known. Thus, the purpose of this study was to investigate the clinical usefulness of ccf-ssDNA in CRC. METHODS The study was conducted on 44 patients who had undergone surgery for CRC, and ccf-ssDNA level was measured before surgery and statistical analysis was performed on clinical factors. RESULTS The association between ccf-ssDNA level and clinicopathological factors was analyzed and compared, and these factors included age, sex, body mass index, diabetes mellitus, hypertension, tumor markers (carcinoembryonic antigen and carbohydrate antigen 19-9), tumor location, size, stage (TNM), recurrence, and death. The group with a ccf-ssDNA level of ≥7.5 ng/μL had a lower age (P=0.010), and was associated with diabetes mellitus (P=0.037) and lymph node metastasis (P=0.049). Multivariate analysis of disease-free survival showed that lymph node metastasis and ccf-ssDNA level (hazard ratio, 10.011; 95% confidence interval, 2.269-44.175; P=0.002) were independent prognostic factors for recurrence. In terms of overall survival, there were no statistically significant results except for vascular invasion. CONCLUSION This study showed that ccf-ssDNA level in plasma in CRC patients was an independent prognostic factor that could predict recurrence non-invasively. In this regard, further evaluation with a prospective, large sample size study will be needed to obtain additional results.
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Affiliation(s)
- Hyun Soo Song
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Dong Hyun Kang
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Hyunjung Kim
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Tae Sung Ahn
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Tae Wan Kim
- Department of Medical Life Science, Soonchunhyang University, Asan, Korea
| | - Moo-Jun Baek
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
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Fernández-Domínguez IJ, Manzo-Merino J, Taja-Chayeb L, Dueñas-González A, Pérez-Cárdenas E, Trejo-Becerril C. The role of extracellular DNA (exDNA) in cellular processes. Cancer Biol Ther 2021; 22:267-278. [PMID: 33858306 DOI: 10.1080/15384047.2021.1890319] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nowadays, extracellular DNA or circulating cell-free DNA is considered to be a molecule with clinical applications (diagnosis, prognosis, monitoring of treatment responses, or patient follow-up) in diverse pathologies, especially in cancer. Nevertheless, because of its molecular characteristics, it can have many other functions. This review focuses on the participation of extracellular DNA (exDNA) in fundamental processes such as cell signaling, coagulation, immunity, evolution through horizontal transfer of genetic information, and adaptive response to inflammatory processes. A deeper understanding of its role in each of these processes will allow development of better tools to monitor and control pathologies, as well as helping to generate new therapeutic options, beyond the applicability of DNA in liquid biopsy.
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Affiliation(s)
| | | | - Lucia Taja-Chayeb
- Division of Basic Research, Instituto Nacional de Cancerología, México City
| | - Alfonso Dueñas-González
- Division of Basic Research, Instituto Nacional de Cancerología, México City.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Shabrish S, Mittra I. Cytokine Storm as a Cellular Response to dsDNA Breaks: A New Proposal. Front Immunol 2021; 12:622738. [PMID: 33597956 PMCID: PMC7882731 DOI: 10.3389/fimmu.2021.622738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/07/2021] [Indexed: 12/20/2022] Open
Abstract
Pathogenesis of cytokine storm is poorly understood. In this article we propose a new mechanism and suggest innovative therapeutic avenues for its prevention. We have reported that particles of cell-free chromatin (cfCh) that are released from the billions of cells that die in the body everyday can illegitimately integrate into genomes of healthy cells to trigger dsDNA breaks. The latter leads to apoptosis and/or intense activation of inflammatory cytokines in the affected cells. We hypothesise that a similar phenomenon of dsDNA breaks and inflammation is involved in cytokine storm. The abundant cfCh particles that are released from dying host cells following viral/microbial invasion initiate a cascading effect of more cell death resulting in a vicious cycle of further DNA damage, apoptosis and hyper-inflammation which culminate in cytokine storm. We propose that this unrelenting vicious cycle of cellular DNA damage and cytokine storm may be the underlying cause of high mortality from severe COVID-19. We discuss results of our preclinical studies wherein we have shown that endotoxin induced cytokine storm in mice can be reversed by three different agents that have the ability to inactivate cfCh. These agents may be worthy of investigation in clinical trials to reduce mortality from COVID-19.
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Affiliation(s)
- Snehal Shabrish
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, and Homi Bhabha National Institute, Mumbai, India
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, and Homi Bhabha National Institute, Mumbai, India
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21
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A New Perspective on the Origin of DNA Double-Strand Breaks and Its Implications for Ageing. Genes (Basel) 2021; 12:genes12020163. [PMID: 33530310 PMCID: PMC7912064 DOI: 10.3390/genes12020163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
It is estimated that 10-50 DNA double-strand breaks (DSBs) occur in a nucleated human cell per cell cycle. We reviewed the present state of knowledge and hypothesized that the currently accepted mechanisms cannot explain such high frequency of DSBs occurring daily under normal physiological conditions. We propose an alternative model that implicates illegitimate genomic integration into healthy cells of cell-free chromatin (cfCh) particles released from the billions of cells that die in the body every day. Repeated genomic integration of cfCh may have catastrophic consequences for the cell, such as DSBs, their faulty repair by nonhomologous end joining (NHEJ) followed by apoptosis with release of more cfCh which would integrate into genomes of surrounding cells. This can creates a vicious cycle of cfCh integration, DSBs, NHEJ, and more apoptosis, thereby providing a potential explanation as to why so many billions of cells die in the body on a daily basis. We also recount the recent observation that cfCh integration and the resulting DSBs activate inflammatory cytokines. This leads us to propose that concurrent DSBs and induction of inflammation occurring throughout life may be the underlying cause of ageing, degenerative disorders, and cancer. Finally, we discuss the prospect that agents that can inactivate/degrade cfCh may hold the key to making healthy ageing a realizable goal.
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22
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Koçana CÇ, Toprak SF, Sözer S. Extracellular genetic materials and their application in clinical practice. Cancer Genet 2020; 252-253:48-63. [PMID: 33387935 DOI: 10.1016/j.cancergen.2020.12.006] [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: 06/11/2020] [Revised: 11/12/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.
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Affiliation(s)
- Cemal Çağıl Koçana
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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23
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Souza AGD, Bastos VAF, Fujimura PT, Ferreira ICC, Leal LF, da Silva LS, Laus AC, Reis RM, Martins MM, Santos PS, Corrêa NCR, Marangoni K, Thomé CH, Colli LM, Goulart LR, Goulart VA. Cell-free DNA promotes malignant transformation in non-tumor cells. Sci Rep 2020; 10:21674. [PMID: 33303880 PMCID: PMC7728762 DOI: 10.1038/s41598-020-78766-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free DNA is present in different biological fluids and when released by tumor cells may contribute to pro-tumor events such as malignant transformation of cells adjacent to the tumor and metastasis. Thus, this study analyzed the effect of tumor cell-free DNA, isolated from the blood of prostate cancer patients, on non-tumor prostate cell lines (RWPE-1 and PNT-2). To achieve this, we performed cell-free DNA quantification and characterization assays, evaluation of gene and miRNA expression profiling focused on cancer progression and EMT, and metabolomics by mass spectrometry and cellular migration. The results showed that tumor-free cell DNA was able to alter the gene expression of MMP9 and CD44, alter the expression profile of nine miRNAs, and increased the tryptophan consumption and cell migration rates in non-tumor cells. Therefore, tumor cell-free DNA was capable of altering the receptor cell phenotype, triggering events related to malignant transformation in these cells, and can thus be considered a potential target for cancer diagnosis and therapy.
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Affiliation(s)
- Aline Gomes de Souza
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil.
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil.
| | - Victor Alexandre F Bastos
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Patricia Tieme Fujimura
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Izabella Cristina C Ferreira
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Letícia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
- 3ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Mario Machado Martins
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Paula Souza Santos
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Natássia C Resende Corrêa
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Karina Marangoni
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Carolina Hassibe Thomé
- Center for Cell Based Therapy, Hemotherapy Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Leandro Machado Colli
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz Ricardo Goulart
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
- Department of Medical Microbiology and Immunology, University of California-Davis, Davis, USA
| | - Vivian Alonso Goulart
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, MG, Brazil
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24
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The Influence of a Stressful Microenvironment on Tumor Exosomes: A Focus on the DNA Cargo. Int J Mol Sci 2020; 21:ijms21228728. [PMID: 33227947 PMCID: PMC7699188 DOI: 10.3390/ijms21228728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 11/30/2022] Open
Abstract
Exosomes secreted by tumor cells, through the transport of bioactive molecules, reprogram the surroundings, building a microenvironment to support the development of the tumor. The discovery that exosomes carry genomic DNA reflecting that of the tumor cell of origin has encouraged studies to use them as non-invasive biomarkers. The exosome-mediated transfer of oncogenes suggested a new mechanism of malignant transformation that could play a role in the formation of metastases. Several studies have examined the role of tumor exosomes on the modulation of the tumor microenvironment, but relatively few have been directed to assess how stressful stimuli can influence their production and cargo. Understanding the changes in exosome loads and the production pattern of the stressed tumor cell may uncover actionable mechanisms responsible for tumor progression.
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25
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Putative Origins of Cell-Free DNA in Humans: A Review of Active and Passive Nucleic Acid Release Mechanisms. Int J Mol Sci 2020; 21:ijms21218062. [PMID: 33137955 PMCID: PMC7662960 DOI: 10.3390/ijms21218062] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Through various pathways of cell death, degradation, and regulated extrusion, partial or complete genomes of various origins (e.g., host cells, fetal cells, and infiltrating viruses and microbes) are continuously shed into human body fluids in the form of segmented cell-free DNA (cfDNA) molecules. While the genetic complexity of total cfDNA is vast, the development of progressively efficient extraction, high-throughput sequencing, characterization via bioinformatics procedures, and detection have resulted in increasingly accurate partitioning and profiling of cfDNA subtypes. Not surprisingly, cfDNA analysis is emerging as a powerful clinical tool in many branches of medicine. In addition, the low invasiveness of longitudinal cfDNA sampling provides unprecedented access to study temporal genomic changes in a variety of contexts. However, the genetic diversity of cfDNA is also a great source of ambiguity and poses significant experimental and analytical challenges. For example, the cfDNA population in the bloodstream is heterogeneous and also fluctuates dynamically, differs between individuals, and exhibits numerous overlapping features despite often originating from different sources and processes. Therefore, a deeper understanding of the determining variables that impact the properties of cfDNA is crucial, however, thus far, is largely lacking. In this work we review recent and historical research on active vs. passive release mechanisms and estimate the significance and extent of their contribution to the composition of cfDNA.
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26
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Origin of Genome Instability and Determinants of Mutational Landscape in Cancer Cells. Genes (Basel) 2020; 11:genes11091101. [PMID: 32967144 PMCID: PMC7563369 DOI: 10.3390/genes11091101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/12/2020] [Accepted: 09/18/2020] [Indexed: 12/31/2022] Open
Abstract
Genome instability is a crucial and early event associated with an increased predisposition to tumor formation. In the absence of any exogenous agent, a single human cell is subjected to about 70,000 DNA lesions each day. It has now been shown that physiological cellular processes including DNA transactions during DNA replication and transcription contribute to DNA damage and induce DNA damage responses in the cell. These processes are also influenced by the three dimensional-chromatin architecture and epigenetic regulation which are altered during the malignant transformation of cells. In this review, we have discussed recent insights about how replication stress, oncogene activation, chromatin dynamics, and the illegitimate recombination of cell-free chromatin particles deregulate cellular processes in cancer cells and contribute to their evolution. The characterization of such endogenous sources of genome instability in cancer cells can be exploited for the development of new biomarkers and more effective therapies for cancer treatment.
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27
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Garcia-Gisbert N, Fernández-Ibarrondo L, Fernández-Rodríguez C, Gibert J, Andrade-Campos M, Arenillas L, Camacho L, Angona A, Longarón R, Salar A, Calvo X, Besses C, Bellosillo B. Circulating cell-free DNA improves the molecular characterisation of Ph-negative myeloproliferative neoplasms. Br J Haematol 2020; 192:300-309. [PMID: 32945548 DOI: 10.1111/bjh.17087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022]
Abstract
Genetic studies in patients with Philadelphia-negative myeloproliferative neoplasms (MPNs) are essential to establish the correct diagnosis and to optimise their management. Recently, it has been demonstrated that it is possible to detect molecular alterations analysing cell-free DNA (cfDNA) in plasma samples, which is known as liquid biopsy. We have assessed the molecular profile of a cohort of 107 MPN patients [33 polycythaemia vera (PV), 56 essential thrombocythaemia (ET), 14 primary myelofibrosis (PMF) and 4 unclassifiable MPN] by next-generation sequencing (NGS) using cfDNA and paired granulocyte DNA. A high concentration of cfDNA in plasma was observed in patients with high molecular complexity, in MPL-mutated cases, and in PMF patients. Targeted sequencing of cfDNA showed a comparable mutational profile (100% accuracy) to the one obtained in granulocytic DNA and a strong correlation was observed between the variant allele frequency (VAF) of gene mutations in both DNA sources. The median VAF detected in cfDNA (29·0%; range: 0·95-91·73%) was significantly higher than the VAF detected in granulocytes (median 25·2%; range: 0·10-95·5%), especially for MPL mutations (44·3% vs. 22·5%). In conclusion, our data support the use of cfDNA as a fast, sensitive and accurate strategy for performing molecular characterisation of MPN patients.
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Affiliation(s)
- Nieves Garcia-Gisbert
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Pompeu Fabra University, Barcelona, Spain
| | - Lierni Fernández-Ibarrondo
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Pompeu Fabra University, Barcelona, Spain
| | - Concepcion Fernández-Rodríguez
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Joan Gibert
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Marcio Andrade-Campos
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Haematology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Leonor Arenillas
- Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Laura Camacho
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Anna Angona
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Haematology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Raquel Longarón
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Antonio Salar
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Haematology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Xavier Calvo
- Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Carlos Besses
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Haematology, Hospital del Mar-IMIM, Barcelona, Spain
| | - Beatriz Bellosillo
- Group of Applied Clinical Research in Haematology, Cancer Research Program-IMIM (Hospital del Mar Medical Research Institute, Barcelona, Spain.,Pompeu Fabra University, Barcelona, Spain.,Department of Pathology, Hospital del Mar-IMIM, Barcelona, Spain
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28
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Hasan S. An Overview of Promising Biomarkers in Cancer Screening and Detection. Curr Cancer Drug Targets 2020; 20:831-852. [PMID: 32838718 DOI: 10.2174/1568009620666200824102418] [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: 05/13/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 11/22/2022]
Abstract
Applications of biomarkers have been proved in oncology screening, diagnosis, predicting response to treatment as well as monitoring the progress of the disease. Considering the crucial role played by them during different disease stages, it is extremely important to evaluate, validate, and assess them to incorporate them into routine clinical care. In this review, the role of few most promising and successfully used biomarkers in cancer detection, i.e. PD-L1, E-Cadherin, TP53, Exosomes, cfDNA, EGFR, mTOR with regard to their structure, mode of action, and reports signifying their pathological significance, are addressed. Also, an overview of some successfully used biomarkers for cancer medicine has been presented. The study also summarizes biomarker-driven personalized cancer therapy i.e., approved targets and indications, as per the US FDA. The review also highlights the increasingly prominent role of biomarkers in drug development at all stages, with particular reference to clinical trials. The increasing utility of biomarkers in clinical trials is clearly evident from the trend shown, wherein ~55 percent of all oncology clinical trials in 2019 were seen to involve biomarkers, as opposed to ~ 15 percent in 2001, which clearly proves the essence and applicability of biomarkers for synergizing clinical information with tumor progression. Still, there are significant challenges in the implementation of these possibilities with strong evidence in cost-- effective manner.
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Affiliation(s)
- Saba Hasan
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Lucknow, India
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29
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Elzanowska J, Semira C, Costa-Silva B. DNA in extracellular vesicles: biological and clinical aspects. Mol Oncol 2020; 15:1701-1714. [PMID: 32767659 PMCID: PMC8169445 DOI: 10.1002/1878-0261.12777] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
The study of extracellular vesicles (EVs), especially in the liquid biopsy field, has rapidly evolved in recent years. However, most EV studies have focused on RNA or protein content and DNA in EVs (EV‐DNA) has largely been unnoticed. In this review, we compile current evidence regarding EV‐DNA and provide an extensive discussion on EV‐DNA biology. We look into EV‐DNA biogenesis and mechanisms of DNA loading into EVs, as well as describe the particularly significant function of DNA‐carrying EVs in the maintenance of cellular homeostasis, intracellular communication, and immune response modulation. We also examine the current role of EV‐DNA in the clinical setting, specifically in cancer, infections, pregnancy, and prenatal diagnosis.
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Affiliation(s)
- Julia Elzanowska
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Christine Semira
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Bruno Costa-Silva
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
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30
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Shemetun OV, Pilinska MA. RADIATION-INDUCED BYSTANDER EFFECT - MODELING, MANIFESTATION, MECHANISMS, PERSISTENCE, CANCER RISKS (literature review). PROBLEMY RADIAT︠S︡IĬNOÏ MEDYT︠S︡YNY TA RADIOBIOLOHIÏ 2020; 24:65-92. [PMID: 31841459 DOI: 10.33145/2304-8336-2019-24-65-92] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Indexed: 01/02/2023]
Abstract
The review summarizes and analyzes the data of world scientific literature and the results of the own research con- cerning one of the main non-targeted effects of ionizing radiation - the radiation induced bystander effect (RIBE) - the ability of irradiated target cells to induce secondary biological changes in non-irradiated receptor cells. The his- tory of studies of this phenomenon is presented - it described under various names since 1905, began to study from the end of the twentieth century when named as RIBE and caused particular interest in the scientific community during recent decades. It is shown that the development of biological science and the improvement of research methods allowed to get new in-depth data on the development of RIBE not only at the level of the whole organism, but even at the genome level. The review highlights the key points of numerous RIBE investigations including mod- eling; methodological approaches to studying; classification; features of interaction between irradiated and intact cells; the role of the immune system, oxidative stress, cytogenetic disorders, changes in gene expression in the mechanism of development of RIBE; rescue effect, abscopal effect, persistence, modification, medical effects. It is emphasized that despite the considerable amount of research concerning the bystander response as the universal phenomenon and RIBE as one of its manifestations, there are still enough «white spots» in determining the mech- anisms of the RIBE formation and assessing the possible consequences of its development for human health.
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Affiliation(s)
- O V Shemetun
- State Institution «National Research Center for Radiation Medicine of the National Academy of MedicalSciences of Ukraine», 53 Yuriia Illienka St., Kyiv, 04050, Ukraine
| | - M A Pilinska
- State Institution «National Research Center for Radiation Medicine of the National Academy of MedicalSciences of Ukraine», 53 Yuriia Illienka St., Kyiv, 04050, Ukraine
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31
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Grabuschnig S, Soh J, Heidinger P, Bachler T, Hirschböck E, Rosales Rodriguez I, Schwendenwein D, Sensen CW. Circulating cell-free DNA is predominantly composed of retrotransposable elements and non-telomeric satellite DNA. J Biotechnol 2020; 313:48-56. [DOI: 10.1016/j.jbiotec.2020.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 12/19/2022]
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32
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Mittra I, Pal K, Pancholi N, Tidke P, Siddiqui S, Rane B, D’souza J, Shaikh A, Parab S, Shinde S, Jadhav V, Shende S, Raghuram GV. Cell-free chromatin particles released from dying host cells are global instigators of endotoxin sepsis in mice. PLoS One 2020; 15:e0229017. [PMID: 32130239 PMCID: PMC7055819 DOI: 10.1371/journal.pone.0229017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/28/2020] [Indexed: 12/29/2022] Open
Abstract
We have earlier reported that cell-free chromatin (cfCh) particles that are released from dying cells, or those that circulate blood, can readily enter into healthy cells, illegitimately integrate into their genomes and induce dsDNA breaks, apoptosis and intense activation of inflammatory cytokines. We hypothesized that sepsis is caused by cfCh released from dying host cells following microbial infection leading to bystander host cell apoptosis and inflammation which are perpetuated in a vicious cycle with release of more cfCh from dying host cells. To test this hypothesis we used three cfCh inactivating agents namely 1) anti-histone antibody complexed nanoparticles which inactivate cfCh by binding to histones; 2) DNase I which inactivates cfCh by degrading its DNA component, and 3) a novel pro-oxidant combination of Resveratrol and Copper which, like DNase I, inactivates cfCh by degrading its DNA component. Female C57 BL/6 mice, 6–8 weeks old, were administered a single i.p. injection of LPS at a dose of 10 mg/Kg or 20 mg/Kg with or without concurrent treatment with the above cfCh inactivating agents. Administration of cfCh inactivating agents concurrently with LPS resulted in prevention of following pathological parameters: 1) release of cfCh in extra-cellular spaces of brain, lung and heart and in circulation; 2) release of inflammatory cytokines in circulation; 3) activation of DNA damage, apoptosis and inflammation in cells of thymus, spleen and in PBMCs; 4) DNA damage, apoptosis and inflammation in cells of lung, liver, heart, brain, kidney and small intestine; 5) liver and kidney dysfunction and elevation of serum lactate; 6) coagulopathy, fibrinolysis and thrombocytopenia; 7) lethality. We conclude that cfCh that are released from dying host cells in response to bacterial endotoxin represents a global instigator of sepsis. cfCh inactivation may provide a novel approach to management of sepsis in humans.
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Affiliation(s)
- Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
- * E-mail:
| | - Kavita Pal
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Namrata Pancholi
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Pritishkumar Tidke
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Sophiya Siddiqui
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Bhagyeshri Rane
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Jenevieve D’souza
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Alfina Shaikh
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Saili Parab
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Sushma Shinde
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Vishal Jadhav
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Soniya Shende
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Gorantla V. Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
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Su Y, Wang L, Jiang C, Yue Z, Fan H, Hong H, Duan C, Jin M, Zhang D, Qiu L, Cheng X, Xu Z, Ma X. Increased plasma concentration of cell-free DNA precedes disease recurrence in children with high-risk neuroblastoma. BMC Cancer 2020; 20:102. [PMID: 32028911 PMCID: PMC7006086 DOI: 10.1186/s12885-020-6562-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/20/2020] [Indexed: 02/06/2023] Open
Abstract
Background Neuroblastoma is the most common extracranial solid tumor of childhood. The high rate of recurrence is associated with a low survival rate for patients with high-risk neuroblastoma. There is thus an urgent need to identify effective predictive biomarkers of disease recurrence. Methods A total of 116 patients with high-risk neuroblastoma were recruited at Beijing Children’s Hospital between February 2015 and December 2017. All patients received multidisciplinary treatment, were evaluated for the therapeutic response, and then initiated on maintenance treatment. Blood samples were collected at the beginning of maintenance treatment, every 3 months thereafter, and at the time of disease recurrence. Plasma levels of cell-free DNA (cfDNA) were quantified by qPCR. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the ability of plasma cfDNA concentration to predict recurrence. Results Of the 116 patients, 36 (31.0%) developed recurrence during maintenance treatment. The median time to recurrence was 19.00, 9.00, and 8.00 months for patients who had achieved complete response (n = 6), partial response (n = 25), and stable disease (n = 5), respectively, after multidisciplinary treatment. The median plasma cfDNA concentration at the time of recurrence was significantly higher than the concentration in recurrence-free patients throughout maintenance treatment (29.34 ng/mL vs 10.32 ng/mL). Patients recorded a plasma cfDNA level ≥ 29 ng/mL an average of 0.55 months before diagnosis of disease recurrence. ROC analysis of the power of plasma cfDNA to distinguish between patients with or without recurrence yielded an area under the curve of 0.825, with optimal sensitivity and specificity of 80.6 and 71.3%, respectively, at a cfDNA level of 12.93 ng/mL. Conclusions High plasma cfDNA concentration is a potential molecular marker to signal disease recurrence in patients with high-risk neuroblastoma.
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Affiliation(s)
- Yan Su
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Lijun Wang
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, Eastern Block of Jianwai SOHO, Chaoyang District, Beijing, 100022, China
| | - Chiyi Jiang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Zhixia Yue
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Hongjun Fan
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Huimin Hong
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Chao Duan
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Mei Jin
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Dawei Zhang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Lihua Qiu
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, Eastern Block of Jianwai SOHO, Chaoyang District, Beijing, 100022, China
| | - Xianfeng Cheng
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, Eastern Block of Jianwai SOHO, Chaoyang District, Beijing, 100022, China
| | - Zhong Xu
- Beijing Keyin Technology Company Limited, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, Eastern Block of Jianwai SOHO, Chaoyang District, Beijing, 100022, China.
| | - Xiaoli Ma
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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Novel Epigenetic Biomarkers in Pregnancy-Related Disorders and Cancers. Cells 2019; 8:cells8111459. [PMID: 31752198 PMCID: PMC6912400 DOI: 10.3390/cells8111459] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/08/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
As the majority of cancers and gestational diseases are prognostically stage- and grade-dependent, the ultimate goal of ongoing studies in precision medicine is to provide early and timely diagnosis of such disorders. These studies have enabled the development of various new diagnostic biomarkers, such as free circulating nucleic acids, and detection of their epigenetic changes. Recently, extracellular vesicles including exosomes, microvesicles, oncosomes, and apoptotic bodies have been recognized as powerful diagnostic tools. Extracellular vesicles carry specific proteins, lipids, DNAs, mRNAs, and miRNAs of the cells that produced them, thus reflecting the function of these cells. It is believed that exosomes, in particular, may be the optimal biomarkers of pathological pregnancies and cancers, especially those that are frequently diagnosed at an advanced stage, such as ovarian cancer. In the present review, we survey and critically appraise novel epigenetic biomarkers related to free circulating nucleic acids and extracellular vesicles, focusing especially on their status in trophoblasts (pregnancy) and neoplastic cells (cancers).
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Oxidized Cell-Free DNA Is a Factor of Stress Signaling in Radiation-Induced Bystander Effects in Different Types of Human Cells. Int J Genomics 2019; 2019:9467029. [PMID: 31531341 PMCID: PMC6721096 DOI: 10.1155/2019/9467029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/05/2019] [Accepted: 08/01/2019] [Indexed: 11/21/2022] Open
Abstract
In pathology or under damaging conditions, the properties of cell-free DNA (cfDNA) change. An example of such change is GC enrichment, which drastically alters the biological properties of cfDNA. GC-rich cfDNA is a factor of stress signaling, whereas genomic cfDNA is biologically inactive. GC-rich cfDNA stimulates TLR9-MyD88-NF-κB signaling cascade, leading to an increase in proinflammatory cytokine levels in the organism. In addition, GC-rich DNA is prone to oxidation and oxidized cfDNA can stimulate secondary oxidative stress. This article is a review of works dedicated to the investigation of a low-dose ionizing radiation effect, a bystander effect, and the role of cfDNA in both of these processes.
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Fujihara J, Takinami Y, Ueki M, Kimura-Kataoka K, Yasuda T, Takeshita H. Circulating cell-free DNA fragment analysis by microchip electrophoresis and its relationship with DNase I in cardiac diseases. Clin Chim Acta 2019; 497:61-66. [PMID: 31302100 DOI: 10.1016/j.cca.2019.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 11/29/2022]
Abstract
Circulating cell-free DNA (cfDNA) has been directly related to cancer, diabetes, stroke, systemic lupus erythematosus, trauma, rheumatoid arthritis, inflammation, infection, and myocardial infarction (MI). In this study, plasma cfDNA was extracted from the plasma of cardiac disease patients and the cfDNA fragment distribution as well as the relationships between cfDNA concentration and deoxyribonuclease I (DNase I) activity enzyme implicated in double-stranded DNA processing were examined. Results revealed that the cfDNA concentrations in patients with MI and cardiac angina were significantly higher than that in healthy control subjects. Microchip electrophoresis of plasma cfDNA revealed a single fragment (150-200 bp) in some healthy control subjects and three fragments (150-200 bp, 300-400 bp, and 500-600 bp) in all cardiac patient samples. Moreover, a cfDNA ratio of 150-200 bp/500-600 bp was significantly more prevalent in MI patients than in patients with other cardiac diseases (chest pain, cardiac angina, atrial fibrillation and cardiac failure). In addition, a positive correlation between DNase I activity and cfDNA concentration was observed. These results suggest that the plasma cfDNA in cardiac disease patients may originate from apoptosis and that the 150-200 bp/500-600 bp ratio for cfDNA may be a novel diagnostic indicator for MI.
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Affiliation(s)
- Junko Fujihara
- Department of Legal Medicine, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane 693-8501, Japan.
| | - Yoshikazu Takinami
- Department of Emergency and Critical Care Medicine, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane 693-8501, Japan
| | - Misuzu Ueki
- Division of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Kaori Kimura-Kataoka
- Department of Legal Medicine, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane 693-8501, Japan
| | - Toshihiro Yasuda
- Organization for Life Science Advancement Programs, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Haruo Takeshita
- Department of Legal Medicine, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane 693-8501, Japan
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Cell-Free DNA Plasma Levels Differ in Age-Specific Pattern in Healthy Rats and Castrates with Testosterone-Induced Benign Prostatic Hyperplasia. Int J Genomics 2019; 2019:8173630. [PMID: 31281830 PMCID: PMC6589250 DOI: 10.1155/2019/8173630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
The purpose of this work was to study changes in the level of cell-free DNA (cfDNA) in the blood of young and old rats in the normal state and with induced benign prostatic hyperplasia (BPH). Male Wistar rats were divided into 4 groups-young (3 months), old (20 months), intact, or with testosterone-induced BPH. Groups with BPH were subjected to surgical castration and administration of testosterone esters at a dose of 25 mg/kg for a total of 7 injections for 20 days. In intact animals, the level of cfDNA in old rats (2.00 ± 0.14 ng/μl) was significantly higher than that in the young (1.02 ± 0.30 ng/μl). The body and the prostate weights of old rats were 1.6 and 1.4 times larger than those of the young, without an increase in the prostate index (PI). The testosterone level in the blood of young rats was 1.6 times higher than that of old (6.20 ± 0.93 nmol/l vs. 3.77 ± 0.55 nmol/l; NS). In animals with BPH, the level of cfDNA in old rats (3.14 ± 0.76 ng/μl) was significantly higher than that in young rats (0.80 ± 0.14 ng/μl). The body and the prostate weights in old rats were 1.8 and 2.3 times larger, than those in young rats, with an increase in the PI. The level of testosterone in the blood of young (15.76 ± 0.51 nmol/l) and old (16.99 ± 1.1 nmol/l) rats was not significantly different. Morphological signs of BPH were observed in the prostate of both young and old rats. During the induction of BPH in the experiment, according to the level of cfDNA, cell death processes have not changed significantly in young rats but significantly increased in old rats. A similar trend was observed in the group of intact animals. The obtained data indicate that apoptosis processes are enhanced during the development of BPH despite the growth of tissues in the prostate itself.
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Chaudhary S, Mittra I. Cell-free chromatin: A newly described mediator of systemic inflammation. J Biosci 2019; 44:32. [PMID: 31180045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent research has shown that cell-free chromatin (cfCh) particles that are released from the billions of cells that die in the body everyday can enter into healthy cells, integrate into their genomes and induce dsDNA breaks and apoptotic responses. Genomic integration of cfCh activates NF κ B suggesting a novel mechanism of induction of systemic inflammation. Since DNA damage and inflammation are underlying pathologies in multiple devastating acute and chronic disease conditions, the discovery of agents that can inactivate cfCh may provide therapeutic possibilities.
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Affiliation(s)
- Shahid Chaudhary
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410 210, India
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Raghuram GV, Chaudhary S, Johari S, Mittra I. Illegitimate and Repeated Genomic Integration of Cell-Free Chromatin in the Aetiology of Somatic Mosaicism, Ageing, Chronic Diseases and Cancer. Genes (Basel) 2019; 10:genes10060407. [PMID: 31142004 PMCID: PMC6628102 DOI: 10.3390/genes10060407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence suggests that an individual is a complex mosaic of genetically divergent cells. Post-zygotic genomes of the same individual can differ from one another in the form of single nucleotide variations, copy number variations, insertions, deletions, inversions, translocations, other structural and chromosomal variations and footprints of transposable elements. High-throughput sequencing has led to increasing detection of mosaicism in healthy individuals which is related to ageing, neuro-degenerative disorders, diabetes mellitus, cardiovascular diseases and cancer. These age-related disorders are also known to be associated with significant increase in DNA damage and inflammation. Herein, we discuss a newly described phenomenon wherein the genome is under constant assault by illegitimate integration of cell-free chromatin (cfCh) particles that are released from the billions of cells that die in the body every day. We propose that such repeated genomic integration of cfCh followed by dsDNA breaks and repair by non-homologous-end-joining as well as physical damage to chromosomes occurring throughout life may lead to somatic/chromosomal mosaicism which would increase with age. We also discuss the recent finding that genomic integration of cfCh and the accompanying DNA damage is associated with marked activation of inflammatory cytokines. Thus, the triple pathologies of somatic mosaicism, DNA/chromosomal damage and inflammation brought about by a common mechanism of genomic integration of cfCh may help to provide an unifying model for the understanding of aetiologies of the inter-related conditions of ageing, degenerative disorders and cancer.
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Affiliation(s)
- Gorantla V Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Shahid Chaudhary
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Shweta Johari
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
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Kustanovich A, Schwartz R, Peretz T, Grinshpun A. Life and death of circulating cell-free DNA. Cancer Biol Ther 2019; 20:1057-1067. [PMID: 30990132 PMCID: PMC6606043 DOI: 10.1080/15384047.2019.1598759] [Citation(s) in RCA: 305] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/24/2019] [Accepted: 03/12/2019] [Indexed: 12/18/2022] Open
Abstract
Tumor-specific, circulating cell-free DNA in liquid biopsies is a promising source of biomarkers for minimally invasive serial monitoring of treatment responses in cancer management. We will review the current understanding of the origin of circulating cell-free DNA and different forms of DNA release (including various types of cell death and active secretion processes) and clearance routes. The dynamics of extracellular DNA in blood during therapy and the role of circulating DNA in pathophysiological processes (tumor-associated inflammation, NETosis, and pre-metastatic niche development) provide insights into the mechanisms that contribute to tumor development and metastases formation. Better knowledge of circulating tumor-specific cell-free DNA could facilitate the development of new therapeutic and diagnostic options for cancer management.
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Affiliation(s)
- Anatoli Kustanovich
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ruth Schwartz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Peretz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Albert Grinshpun
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100087. [PMID: 30923679 PMCID: PMC6425120 DOI: 10.1016/j.bdq.2019.100087] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
An increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, physical properties, and dynamics in circulation. The latter knowledge is crucial for interpreting the associations between changes in the baseline characteristics of cfDNA and the clinical manifestations of cancer. In this review we explore recent advancements and highlight the current gaps in our knowledge concerning each point of contact between cfDNA analysis and the different stages of cancer management.
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Affiliation(s)
| | | | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße. 36, D-80636, Munich, Germany
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Farhood B, Goradel NH, Mortezaee K, Khanlarkhani N, Salehi E, Nashtaei MS, Shabeeb D, Musa AE, Fallah H, Najafi M. Intercellular communications-redox interactions in radiation toxicity; potential targets for radiation mitigation. J Cell Commun Signal 2019; 13:3-16. [PMID: 29911259 PMCID: PMC6381372 DOI: 10.1007/s12079-018-0473-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/12/2018] [Indexed: 12/20/2022] Open
Abstract
Nowadays, using ionizing radiation (IR) is necessary for clinical, agricultural, nuclear energy or industrial applications. Accidental exposure to IR after a radiation terror or disaster poses a threat to human. In contrast to the old dogma of radiation toxicity, several experiments during the last two recent decades have revealed that intercellular signaling and communications play a key role in this procedure. Elevated level of cytokines and other intercellular signals increase oxidative damage and inflammatory responses via reduction/oxidation interactions (redox system). Intercellular signals induce production of free radicals and inflammatory mediators by some intermediate enzymes such as cyclooxygenase-2 (COX-2), nitric oxide synthase (NOS), NADPH oxidase, and also via triggering mitochondrial ROS. Furthermore, these signals facilitate cell to cell contact and increasing cell toxicity via cohort effect. Nitric oxide is a free radical with ability to act as an intercellular signal that induce DNA damage and changes in some signaling pathways in irradiated as well as non-irradiated adjacent cells. Targeting of these mediators by some anti-inflammatory agents or via antioxidants such as mitochondrial ROS scavengers opens a window to mitigate radiation toxicity after an accidental exposure. Experiments which have been done so far suggests that some cytokines such as IL-1β, TNF-α, TGF-β, IL-4 and IL-13 are some interesting targets that depend on irradiated organs and may help mitigate radiation toxicity. Moreover, animal experiments in recent years indicated that targeting of toll like receptors (TLRs) may be more useful for radioprotection and mitigation. In this review, we aimed to describe the role of intercellular interactions in oxidative injury, inflammation, cell death and killing effects of IR. Moreover, we described evidence on potential mitigation of radiation injury via targeting of these mediators.
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Affiliation(s)
- Bagher Farhood
- Department of Medical Physics and Radiology, Faculty of Paramedical Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Nasser Hashemi Goradel
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Keywan Mortezaee
- Department of Anatomy, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Neda Khanlarkhani
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ensieh Salehi
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Shabani Nashtaei
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Infertility Department, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Dheyauldeen Shabeeb
- Department of Medical Physics & Biomedical Engineering, School of Medicine, Tehran University of Medical Sciences, International Campus, Tehran, Iran
- Department of Physiology, College of Medicine, University of Misan, Misan, Iraq
| | - Ahmed Eleojo Musa
- Department of Medical Physics & Biomedical Engineering, School of Medicine, Tehran University of Medical Sciences, International Campus, Tehran, Iran
- Research Center for Molecular and Cellular Imaging, Tehran University of Medical Sciences, Tehran, Iran
| | - Hengameh Fallah
- Department of Chemistry, Faculty of Science, Islamic Azad University, Arak, Iran
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Laine VN, Gossmann TI, van Oers K, Visser ME, Groenen MAM. Exploring the unmapped DNA and RNA reads in a songbird genome. BMC Genomics 2019; 20:19. [PMID: 30621573 PMCID: PMC6323668 DOI: 10.1186/s12864-018-5378-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 12/16/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND A widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. Despite methodological and hardware improvements which have enhanced the efficiency and accuracy of alignments, a significant percentage of reads frequently remain unmapped. Usually, unmapped reads are discarded from the analysis process, but significant biological information and insights can be uncovered from these data. We explored the unmapped DNA (normal and bisulfite treated) and RNA sequence reads of the great tit (Parus major) reference genome individual. From the unmapped reads we generated de novo assemblies, after which the generated sequence contigs were aligned to the NCBI non-redundant nucleotide database using BLAST, identifying the closest known matching sequence. RESULTS Many of the aligned contigs showed sequence similarity to different bird species and genes that were absent in the great tit reference assembly. Furthermore, there were also contigs that represented known P. major pathogenic species. Most interesting were several species of blood parasites such as Plasmodium and Trypanosoma. CONCLUSIONS Our analyses revealed that meaningful biological information can be found when further exploring unmapped reads. For instance, it is possible to discover sequences that are either absent or misassembled in the reference genome, and sequences that indicate infection or sample contamination. In this study we also propose strategies to aid the capture and interpretation of this information from unmapped reads.
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Affiliation(s)
- Veronika N Laine
- Department of Animal Ecology, NIOO-KNAW, Wageningen, The Netherlands.
| | - Toni I Gossmann
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, UK
| | - Kees van Oers
- Department of Animal Ecology, NIOO-KNAW, Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, NIOO-KNAW, Wageningen, The Netherlands.,Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Martien A M Groenen
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
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Kirolikar S, Prasannan P, Raghuram GV, Pancholi N, Saha T, Tidke P, Chaudhari P, Shaikh A, Rane B, Pandey R, Wani H, Khare NK, Siddiqui S, D'souza J, Prasad R, Shinde S, Parab S, Nair NK, Pal K, Mittra I. Prevention of radiation-induced bystander effects by agents that inactivate cell-free chromatin released from irradiated dying cells. Cell Death Dis 2018; 9:1142. [PMID: 30442925 PMCID: PMC6238009 DOI: 10.1038/s41419-018-1181-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/15/2022]
Abstract
Radiation-induced bystander effect (RIBE) is a poorly understood phenomenon wherein non-targeted cells exhibit effects of radiation. We have reported that cell-free chromatin (cfCh) particles that are released from dying cells can integrate into genomes of surrounding healthy cells to induce DNA damage and inflammation. This raised the possibility that RIBE might be induced by cfCh released from irradiated dying cells. When conditioned media from BrdU-labeled irradiated cells were passed through filters of pore size 0.22 µm and incubated with unexposed cells, BrdU-labeled cfCh particles could be seen to readily enter their nuclei to activate H2AX, active Caspase-3, NFκB, and IL-6. A direct relationship was observed with respect to activation of RIBE biomarkers and radiation dose in the range of 0.1-0 Gy. We confirmed by FISH and cytogenetic analysis that cfCh had stably integrated into chromosomes of bystander cells and had led to extensive chromosomal instability. The above RIBE effects could be abrogated when conditioned media were pre-treated with agents that inactivate cfCh, namely, anti-histone antibody complexed nanoparticles (CNPs), DNase I and a novel DNA degrading agent Resveratrol-copper (R-Cu). Lower hemi-body irradiation with γ-rays (0.1-50 Gy) led to activation of H2AX, active Caspase-3, NFκB, and IL-6 in brain cells in a dose-dependent manner. Activation of these RIBE biomarkers could be abrogated by concurrent treatment with CNPs, DNase I and R-Cu indicating that activation of RIBE was not due to radiation scatter to the brain. RIBE activation was seen even when mini-beam radiation was delivered to the umbilical region of mice wherein radiation scatter to brain was negligible and could be abrogated by cfCh inactivating agents. These results indicate that cfCh released from radiation-induced dying cells are activators of RIBE and that it can be prevented by treatment with appropriate cfCh inactivating agents.
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Affiliation(s)
- Saurabh Kirolikar
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Preeti Prasannan
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Gorantla V Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Namrata Pancholi
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Tannishtha Saha
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Pritishkumar Tidke
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Pradip Chaudhari
- Comparative Oncology Program and Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Alfina Shaikh
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Bhagyeshri Rane
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Richa Pandey
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Harshada Wani
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Naveen K Khare
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Sophiya Siddiqui
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Jenevieve D'souza
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Ratnam Prasad
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Sushma Shinde
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Sailee Parab
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Naveen K Nair
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Kavita Pal
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India.
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Vymetalkova V, Cervena K, Bartu L, Vodicka P. Circulating Cell-Free DNA and Colorectal Cancer: A Systematic Review. Int J Mol Sci 2018; 19:ijms19113356. [PMID: 30373199 PMCID: PMC6274807 DOI: 10.3390/ijms19113356] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 02/06/2023] Open
Abstract
There is a strong demand for the identification of new biomarkers in colorectal cancer (CRC) diagnosis. Among all liquid biopsy analysts, cell-free circulating DNA (cfDNA) is probably the most promising tool with respect to the identification of minimal residual diseases, assessment of treatment response and prognosis, and identification of resistance mechanisms. Circulating cell-free tumor DNA (ctDNA) maintains the same genomic signatures that are present in the matching tumor tissue allowing for the quantitative and qualitative evaluation of mutation burdens in body fluids. Thus, ctDNA-based research represents a non-invasive method for cancer detection. Among the numerous possible applications, the diagnostic, predictive, and/or prognostic utility of ctDNA in CRC has attracted intense research during the last few years. In the present review, we will describe the different aspects related to cfDNA research and evidence from studies supporting its potential use in CRC diagnoses and the improvement of therapy efficacy. We believe that ctDNA-based research should be considered as key towards the introduction of personalized medicine and patient benefits.
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Affiliation(s)
- Veronika Vymetalkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
| | - Klara Cervena
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
| | - Linda Bartu
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
| | - Pavel Vodicka
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
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Wu J, Tang W, Huang L, Hou N, Wu J, Cheng X, Ma D, Qian P, Shen Q, Guo W, Peng W, Liu Y, Jiang C, Feng J. The analysis of cell-free DNA concentrations and integrity in serum of initial and treated of lymphoma patients. Clin Biochem 2018; 63:59-65. [PMID: 30292543 DOI: 10.1016/j.clinbiochem.2018.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 09/13/2018] [Accepted: 10/03/2018] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To evaluate cell-free DNA (cfDNA) in plasma as a promising biomarker for lymphoma, altered levels of cfDNA and its association with clinical parameters are investigated in patients suffered from lymphomas. METHODS Peripheral blood specimens were collected from 60 patients with lymphoma during initial diagnosis and those of another 107 patients with lymphoma during treated stage were also collected, 93 healthy volunteers were selected as control group. Quantitative PCR was used to detect cfDNA level in each group, cfDNA level in different groups was analyzed to understand its relationship with lymphoma patients' clinical features. After correlation analysis between cfDNA and clinical characteristics, Receiver operator characteristic curve was performed to analyze sensitivity and specificity of cfDNA and LDH. RESULTS cfDNA concentration and integrity in initial stage of lymphoma patients were significantly higher than those in treated stage, and cfDNA concentration in treated phase was significantly higher than cfDNA concentration in control group. There was no significant difference in cfDNA integrity at treated stage compared with control group. There was no significant correlation between patient's age, gender, extranodal invasion and lymphoma pathological type and cfDNA concentration and integrity; In contrast, there was a significant correlation between ECOG score, LDH content, Ann Arbor stage, IPI, B-symptoms, Ki-67 expression and radiotherapy and cfDNA concentration and integrity, both at the time of initial diagnosis and treated stage. cfDNA concentration detection is an optimal diagnostic indicator, followed by cfDNA integrity detection, the sensitivity and specificity of both are superior to the traditional LDH detection. CONCLUSION cfDNA level is significantly increased in lymphomas patient plasma and may help lymphoma screening. cfDNA level may serve as a potential indicator of lymphomas treatment efficacy.
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Affiliation(s)
- Jianqiu Wu
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Weiyan Tang
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Laiquan Huang
- Department of Hematology, The First Affiliated Hospital of Wannan Medical College, No.2, Zheshan West Road, Wuhu City 241001, Anhui Province, China
| | - Ning Hou
- Department of Pathology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Jing Wu
- Soochow University, No.1, Shizi Street, Suzhou city 215006, Jiangsu Province, China
| | - Xianfeng Cheng
- Clinic laboratory of Institute of Dermatology and Hospital for Skin Diseases, Chinese Academy of Medical Sciences, No.12, Jiangwangmiao Street, Xuanwu District, Nanjing City 210042, Jiangsu Province, China
| | - Dawei Ma
- Department of Pathology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Pudong Qian
- Department of Radiotherapy, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Qian Shen
- Department of Medical Oncology, Nantong Tumor Hospital, No.48, Qingnian West Road, Nantong city 226000, Jiangsu Province, China
| | - Wenjie Guo
- Department of Radiotherapy, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Wei Peng
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Yufei Liu
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China
| | - Cunshun Jiang
- Department of Medical Oncology, Lanxi County People's Hospital. No.65, North Street of Langxi County, 242100, Anhui Province, China
| | - Jifeng Feng
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, No.42, Baiziting, Nanjing City 210009, Jiangsu Province, China.
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Wang X, Wang L, Su Y, Yue Z, Xing T, Zhao W, Zhao Q, Duan C, Huang C, Zhang D, Jin M, Cheng X, Chen S, Liu Y, Ma X. Plasma cell-free DNA quantification is highly correlated to tumor burden in children with neuroblastoma. Cancer Med 2018; 7:3022-3030. [PMID: 29905010 PMCID: PMC6051223 DOI: 10.1002/cam4.1586] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/13/2022] Open
Abstract
To evaluate plasma cell-free DNA (cfDNA) as a promising biomarker for neuroblastoma (NB) tumor burden. Seventy-nine eligible patients with newly diagnosed NB were recruited from Beijing Children's Hospital between April 2016 and April 2017. Additionally, from September 2011 to June 2017, 79 patients with stable NB were evaluated with a median follow-up time of 21 months. Approximately 2 mL of peripheral blood was drawn upon enrollment, and plasma cfDNA levels were measured via quantitative polymerase chain reaction (qPCR). Total cfDNA analysis was performed using the long interspersed nuclear element 1 (LINE-1) 79 bp fragment, and DNA integrity was calculated by the ratio of the LINE-1 300 bp fragment to the LINE-1 79 bp fragment. A total of 79 NB patients with a median age of 36 months comprised the group of newly diagnosed NB patients. The main primary tumor site was the retroperitoneal and adrenal region (81%). Three or more metastatic sites were found in 17.7% of patients. Stable NB patients older than 18 months comprised 98.7% of the stable NB patients. Neuron-specific enolase (NSE), lactate dehydrogenase (LDH), and cfDNA levels were dramatically increased in the newly diagnosed NB patients and significantly different from those in the stable NB patients. Moreover, the concentration of cfDNA was much higher in patients with larger tumors. By analyzing the area under the receiver operator characteristic (ROC) curve (AUC), the areas of total cfDNA, NSE, and LDH levels were 0.953, 0.929, and 0.906, respectively. The sensitivity and specificity data clarified that the level of circulating cfDNA in plasma can be considered as a reliable biomarker for describing tumor load in NB. The plasma cfDNA concentration was as good as the levels of LDH and NSE to discriminate the tumor burden in children with NB.
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Affiliation(s)
- Xisi Wang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Lijun Wang
- Beijing Keyin Technology Company, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, Chaoyang District, Beijing, China
| | - Yan Su
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Zhixia Yue
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Tianyu Xing
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Wen Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Qian Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Chao Duan
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Cheng Huang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Dawei Zhang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Mei Jin
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Xianfeng Cheng
- Beijing Keyin Technology Company, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, Chaoyang District, Beijing, China
| | - Shenglan Chen
- Taizhou Genewill Medical Laboratory Company Limited, Pharmaceutics City of China, Taizhou, Jiangsu, China
| | - Yi Liu
- Beijing Keyin Technology Company, Beijing Keyin Evergreen Institutes for Medical Research Company Limited, Chaoyang District, Beijing, China
| | - Xiaoli Ma
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Discipline of Pediatrics, Ministry of Education, MOE Key Laboratory of Major Diseases in Children, Hematology Oncology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
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Podgornaya OI, Ostromyshenskii DI, Enukashvily NI. Who Needs This Junk, or Genomic Dark Matter. BIOCHEMISTRY (MOSCOW) 2018; 83:450-466. [PMID: 29626931 DOI: 10.1134/s0006297918040156] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Centromeres (CEN), pericentromeric regions (periCEN), and subtelomeric regions (subTel) comprise the areas of constitutive heterochromatin (HChr). Tandem repeats (TRs or satellite DNA) are the main components of HChr forming no less than 10% of the mouse and human genome. HChr is assembled within distinct structures in the interphase nuclei of many species - chromocenters. In this review, the main classes of HChr repeat sequences are considered in the order of their number increase in the sequencing reads of the mouse chromocenters (ChrmC). TRs comprise ~70% of ChrmC occupying the first place. Non-LTR (-long terminal repeat) retroposons (mainly LINE, long interspersed nuclear element) are the next (~11%), and endogenous retroviruses (ERV; LTR-containing) are in the third position (~9%). HChr is not enriched with ERV in comparison with the whole genome, but there are differences in distribution of certain elements: while MaLR-like elements (ERV3) are dominant in the whole genome, intracisternal A-particles and corresponding LTR (ERV2) are prevalent in HChr. Most of LINE in ChrmC is represented by the 2-kb fragment at the end of the 2nd open reading frame and its flanking regions. Almost all tandem repeats classified as CEN or periCEN are contained in ChrmC. Our previous classification revealed 60 new mouse TR families with 29 of them being absent in ChrmC, which indicates their location on chromosome arms. TR transcription is necessary for maintenance of heterochromatic status of the HChr genome part. A burst of TR transcription is especially important in embryogenesis and other cases of radical changes in the cell program, including carcinogenesis. The recently discovered mechanism of epigenetic regulation with noncoding sequences transcripts, long noncoding RNA, and its role in embryogenesis and pluripotency maintenance is discussed.
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Affiliation(s)
- O I Podgornaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
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Bansal S, Sharma M, R R, Mohanakumar T. The role of exosomes in allograft immunity. Cell Immunol 2018; 331:85-92. [PMID: 29907298 DOI: 10.1016/j.cellimm.2018.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/17/2018] [Accepted: 06/06/2018] [Indexed: 12/15/2022]
Abstract
Extracellular vesicles are emerging as potent vehicles of intercellular communication. In this review, we focus on a subclass of extracellular vesicles called exosomes. Previously considered an unimportant catch-all, exosomes have recently been recognized for their role in various diseases and their potential for therapeutic use. We have examined the role of exosomes after human lung transplantation and have delineated the composition of circulating exosomes isolated from lung transplant recipients diagnosed with acute and chronic rejection, primary graft dysfunction, and respiratory viral infection. The presence of lung-associated self-antigens (K-alpha 1 Tubulin and collagen V) and mismatched donor HLA in exosomes isolated from lung transplant recipients signifies that these exosomes originated in the transplanted lungs, and therefore dramatically affect transplant biology and immune pathways. Exosomes released from transplanted organs also carry other proteins, costimulatory molecules, and nucleic acids. Therefore, these molecules may be used as biomarkers for allograft rejection and immunity.
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