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Mangrum DS, Finley SD. Modeling the heterogeneous apoptotic response of caspase-mediated signaling in tumor cells. J Theor Biol 2024; 590:111857. [PMID: 38797470 DOI: 10.1016/j.jtbi.2024.111857] [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: 10/31/2023] [Revised: 02/01/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
Resisting apoptosis is a hallmark of cancer. For this reason, it may be possible to force cancer cells to die by targeting components along the apoptotic signaling pathway. However, apoptosis signaling is challenging to understand due to dynamic and complex behaviors of ligands, receptors, and intracellular signaling components in response to cancer therapy. In this work, we forecast the apoptotic response based on the combined impact of these features. We expanded a previously established mathematical model of caspase-mediated apoptosis to include extracellular activation and receptor dynamics. In addition, three potential threshold values of caspase-3 necessary for the activation of apoptosis were selected to forecast which cells become apoptotic over time. We first vary ligand and receptor levels with the number of intracellular signaling proteins remaining consistent. Then, we vary the intracellular protein molecules in each simulated tumor cell to forecast the response of a heterogeneous population. By leveraging the benefits of computational modeling, we investigate the combined effect of several factors on the onset of apoptosis. This work provides quantitative insights for how the apoptotic signaling response can be forecasted, and precisely triggered, amongst heterogeneous cells via extracellular activation.
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Affiliation(s)
- Diamond S Mangrum
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Stacey D Finley
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA.
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Kalra J, Baker J, Song J, Kyle A, Minchinton A, Bally M. Inter-Metastatic Heterogeneity of Tumor Marker Expression and Microenvironment Architecture in a Preclinical Cancer Model. Int J Mol Sci 2021; 22:6336. [PMID: 34199298 PMCID: PMC8231937 DOI: 10.3390/ijms22126336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/25/2021] [Accepted: 06/09/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Preclinical drug development studies rarely consider the impact of a candidate drug on established metastatic disease. This may explain why agents that are successful in subcutaneous and even orthotopic preclinical models often fail to demonstrate efficacy in clinical trials. It is reasonable to anticipate that sites of metastasis will be phenotypically unique, as each tumor will have evolved heterogeneously with respect to gene expression as well as the associated phenotypic outcome of that expression. The objective for the studies described here was to gain an understanding of the tumor heterogeneity that exists in established metastatic disease and use this information to define a preclinical model that is more predictive of treatment outcome when testing novel drug candidates clinically. METHODS Female NCr nude mice were inoculated with fluorescent (mKate), Her2/neu-positive human breast cancer cells (JIMT-mKate), either in the mammary fat pad (orthotopic; OT) to replicate a primary tumor, or directly into the left ventricle (intracardiac; IC), where cells eventually localize in multiple sites to create a model of established metastasis. Tumor development was monitored by in vivo fluorescence imaging (IVFI). Subsequently, animals were sacrificed, and tumor tissues were isolated and imaged ex vivo. Tumors within organ tissues were further analyzed via multiplex immunohistochemistry (mIHC) for Her2/neu expression, blood vessels (CD31), as well as a nuclear marker (Hoechst) and fluorescence (mKate) expressed by the tumor cells. RESULTS Following IC injection, JIMT-1mKate cells consistently formed tumors in the lung, liver, brain, kidney, ovaries, and adrenal glands. Disseminated tumors were highly variable when assessing vessel density (CD31) and tumor marker expression (mkate, Her2/neu). Interestingly, tumors which developed within an organ did not adopt a vessel microarchitecture that mimicked the organ where growth occurred, nor did the vessel microarchitecture appear comparable to the primary tumor. Rather, metastatic lesions showed considerable variability, suggesting that each secondary tumor is a distinct disease entity from a microenvironmental perspective. CONCLUSIONS The data indicate that more phenotypic heterogeneity in the tumor microenvironment exists in models of metastatic disease than has been previously appreciated, and this heterogeneity may better reflect the metastatic cancer in patients typically enrolled in early-stage Phase I/II clinical trials. Similar to the suggestion of others in the past, the use of models of established metastasis preclinically should be required as part of the anticancer drug candidate development process, and this may be particularly important for targeted therapeutics and/or nanotherapeutics.
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Affiliation(s)
- Jessica Kalra
- Experimental Therapeutics, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada;
- Applied Research Centre, Langara, Vancouver, BC V5Y 2Z6, Canada
- Department Anesthesia Pharmacology and Therapeutics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Jennifer Baker
- Integrative Oncology, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; (J.B.); (A.K.)
| | - Justin Song
- Chemical and Biomolecular Engineering Department, Vanderbilt University, Nashville, TN 37235, USA;
| | - Alastair Kyle
- Integrative Oncology, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; (J.B.); (A.K.)
| | - Andrew Minchinton
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Integrative Oncology, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; (J.B.); (A.K.)
| | - Marcel Bally
- Experimental Therapeutics, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada;
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Nanomedicine Innovation Network, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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3
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Heng J, Heng HH. Genome chaos: Creating new genomic information essential for cancer macroevolution. Semin Cancer Biol 2020; 81:160-175. [PMID: 33189848 DOI: 10.1016/j.semcancer.2020.11.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/26/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022]
Abstract
Cancer research has traditionally focused on the characterization of individual molecular mechanisms that can contribute to cancer. Due to the multiple levels of genomic and non-genomic heterogeneity, however, overwhelming molecular mechanisms have been identified, most with low clinical predictability. It is thus necessary to search for new concepts to unify these diverse mechanisms and develop better strategies to understand and treat cancer. In recent years, two-phased cancer evolution (comprised of the genome reorganization-mediated punctuated phase and gene mutation-mediated stepwise phase), initially described by tracing karyotype evolution, was confirmed by the Cancer Genome Project. In particular, genome chaos, the process of rapid and massive genome reorganization, has been commonly detected in various cancers-especially during key phase transitions, including cellular transformation, metastasis, and drug resistance-suggesting the importance of genome-level changes in cancer evolution. In this Perspective, genome chaos is used as a discussion point to illustrate new genome-mediated somatic evolutionary frameworks. By rephrasing cancer as a new system emergent from normal tissue, we present the multiple levels (or scales) of genomic and non-genomic information. Of these levels, evolutionary studies at the chromosomal level are determined to be of ultimate importance, since altered genomes change the karyotype coding and karyotype change is the key event for punctuated cellular macroevolution. Using this lens, we differentiate and analyze developmental processes and cancer evolution, as well as compare the informational relationship between genome chaos and its various subtypes in the context of macroevolution under crisis. Furthermore, the process of deterministic genome chaos is discussed to interpret apparently random events (including stressors, chromosomal variation subtypes, surviving cells with new karyotypes, and emergent stable cellular populations) as nonrandom patterns, which supports the new cancer evolutionary model that unifies genome and gene contributions during different phases of cancer evolution. Finally, the new perspective of using cancer as a model for organismal evolution is briefly addressed, emphasizing the Genome Theory as a new and necessary conceptual framework for future research and its practical implications, not only in cancer but evolutionary biology as a whole.
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Affiliation(s)
- Julie Heng
- Harvard College, 86 Brattle Street Cambridge, MA, 02138, USA
| | - Henry H Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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4
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Ye CJ, Sharpe Z, Heng HH. Origins and Consequences of Chromosomal Instability: From Cellular Adaptation to Genome Chaos-Mediated System Survival. Genes (Basel) 2020; 11:E1162. [PMID: 33008067 PMCID: PMC7601827 DOI: 10.3390/genes11101162] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
When discussing chromosomal instability, most of the literature focuses on the characterization of individual molecular mechanisms. These studies search for genomic and environmental causes and consequences of chromosomal instability in cancer, aiming to identify key triggering factors useful to control chromosomal instability and apply this knowledge in the clinic. Since cancer is a phenomenon of new system emergence from normal tissue driven by somatic evolution, such studies should be done in the context of new genome system emergence during evolution. In this perspective, both the origin and key outcome of chromosomal instability are examined using the genome theory of cancer evolution. Specifically, chromosomal instability was linked to a spectrum of genomic and non-genomic variants, from epigenetic alterations to drastic genome chaos. These highly diverse factors were then unified by the evolutionary mechanism of cancer. Following identification of the hidden link between cellular adaptation (positive and essential) and its trade-off (unavoidable and negative) of chromosomal instability, why chromosomal instability is the main player in the macro-cellular evolution of cancer is briefly discussed. Finally, new research directions are suggested, including searching for a common mechanism of evolutionary phase transition, establishing chromosomal instability as an evolutionary biomarker, validating the new two-phase evolutionary model of cancer, and applying such a model to improve clinical outcomes and to understand the genome-defined mechanism of organismal evolution.
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Affiliation(s)
- Christine J. Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zachary Sharpe
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
| | - Henry H. Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Ravel JM, Monraz Gomez LC, Sompairac N, Calzone L, Zhivotovsky B, Kroemer G, Barillot E, Zinovyev A, Kuperstein I. Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases. Cancers (Basel) 2020; 12:E990. [PMID: 32316560 PMCID: PMC7226067 DOI: 10.3390/cancers12040990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 12/25/2022] Open
Abstract
The processes leading to, or avoiding cell death are widely studied, because of their frequent perturbation in various diseases. Cell death occurs in three highly interconnected steps: Initiation, signaling and execution. We used a systems biology approach to gather information about all known modes of regulated cell death (RCD). Based on the experimental data retrieved from literature by manual curation, we graphically depicted the biological processes involved in RCD in the form of a seamless comprehensive signaling network map. The molecular mechanisms of each RCD mode are represented in detail. The RCD network map is divided into 26 functional modules that can be visualized contextually in the whole seamless network, as well as in individual diagrams. The resource is freely available and accessible via several web platforms for map navigation, data integration, and analysis. The RCD network map was employed for interpreting the functional differences in cell death regulation between Alzheimer's disease and non-small cell lung cancer based on gene expression data that allowed emphasizing the molecular mechanisms underlying the inverse comorbidity between the two pathologies. In addition, the map was used for the analysis of genomic and transcriptomic data from ovarian cancer patients that provided RCD map-based signatures of four distinct tumor subtypes and highlighted the difference in regulations of cell death molecular mechanisms.
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Affiliation(s)
- Jean-Marie Ravel
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
- Laboratoire de génétique médicale, CHRU-Nancy, F-54000 Nancy, France
- Inserm, NGERE, Université de Lorraine, F-54000 Nancy, France
| | - L. Cristobal Monraz Gomez
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Nicolas Sompairac
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
- Centre de Recherches Interdisciplinaires, Université Paris Descartes, 75006 Paris, France
| | - Laurence Calzone
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Boris Zhivotovsky
- Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006 Paris, France;
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou 215163, China
- Karolinska Institute, Department of Women’s and Children’s Health, Karolinska University Hospital, 171 77 Stockholm, Sweden
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Inna Kuperstein
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
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Ye CJ, Sharpe Z, Alemara S, Mackenzie S, Liu G, Abdallah B, Horne S, Regan S, Heng HH. Micronuclei and Genome Chaos: Changing the System Inheritance. Genes (Basel) 2019; 10:genes10050366. [PMID: 31086101 PMCID: PMC6562739 DOI: 10.3390/genes10050366] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 12/18/2022] Open
Abstract
Micronuclei research has regained its popularity due to the realization that genome chaos, a rapid and massive genome re-organization under stress, represents a major common mechanism for punctuated cancer evolution. The molecular link between micronuclei and chromothripsis (one subtype of genome chaos which has a selection advantage due to the limited local scales of chromosome re-organization), has recently become a hot topic, especially since the link between micronuclei and immune activation has been identified. Many diverse molecular mechanisms have been illustrated to explain the causative relationship between micronuclei and genome chaos. However, the newly revealed complexity also causes confusion regarding the common mechanisms of micronuclei and their impact on genomic systems. To make sense of these diverse and even conflicting observations, the genome theory is applied in order to explain a stress mediated common mechanism of the generation of micronuclei and their contribution to somatic evolution by altering the original set of information and system inheritance in which cellular selection functions. To achieve this goal, a history and a current new trend of micronuclei research is briefly reviewed, followed by a review of arising key issues essential in advancing the field, including the re-classification of micronuclei and how to unify diverse molecular characterizations. The mechanistic understanding of micronuclei and their biological function is re-examined based on the genome theory. Specifically, such analyses propose that micronuclei represent an effective way in changing the system inheritance by altering the coding of chromosomes, which belongs to the common evolutionary mechanism of cellular adaptation and its trade-off. Further studies of the role of micronuclei in disease need to be focused on the behavior of the adaptive system rather than specific molecular mechanisms that generate micronuclei. This new model can clarify issues important to stress induced micronuclei and genome instability, the formation and maintenance of genomic information, and cellular evolution essential in many common and complex diseases such as cancer.
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Affiliation(s)
- Christine J Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Zachary Sharpe
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Sarah Alemara
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Stephanie Mackenzie
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Guo Liu
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Batoul Abdallah
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Steve Horne
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Sarah Regan
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Henry H Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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Voices from the dead: The complex vocabulary and intricate grammar of dead cells. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 116:1-90. [PMID: 31036289 DOI: 10.1016/bs.apcsb.2019.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Of the roughly one million cells per second dying throughout the body, the vast majority dies by apoptosis, the predominant form of regulated cell death in higher organisms. Long regarded as mere waste, apoptotic cells are now recognized as playing a prominent and active role in homeostatic maintenance, especially resolution of inflammation, and in the sculpting of tissues during development. The activities associated with apoptotic cells are continually expanding, with more recent studies demonstrating their ability to modulate such vital functions as proliferation, survival, differentiation, metabolism, migration, and angiogenesis. In each case, the role of apoptotic cells is active, exerting their effects via new activities acquired during the apoptotic program. Moreover, the capacity to recognize and respond to apoptotic cells is not limited to professional phagocytes. Most, if not all, cells receive and integrate an array of signals from cells dying in their vicinity. These signals comprise a form of biochemical communication. As reviewed in this chapter, this communication is remarkably sophisticated; each of its three critical steps-encoding, transmission, and decoding of the apoptotic cell's "message"-is endowed with exquisite robustness. Together, the abundance and intricacy of the variables at each step comprise the vocabulary and grammar of the language by which dead cells achieve their post-mortem voice. The combinatorial complexity of the resulting communication network permits dying cells, through the signals they emit and the responses those signals elicit, to partake of an expanded role in homeostasis, acting as both sentinels of environmental change and agents of adaptation.
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Anticancer chemotherapy and radiotherapy trigger both non-cell-autonomous and cell-autonomous death. Cell Death Dis 2018; 9:716. [PMID: 29915308 PMCID: PMC6006149 DOI: 10.1038/s41419-018-0747-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/11/2018] [Accepted: 05/24/2018] [Indexed: 12/26/2022]
Abstract
Even though cell death modalities elicited by anticancer chemotherapy and radiotherapy have been extensively studied, the ability of anticancer treatments to induce non-cell-autonomous death has never been investigated. By means of multispectral imaging flow-cytometry-based technology, we analyzed the lethal fate of cancer cells that were treated with conventional anticancer agents and co-cultured with untreated cells, observing that anticancer agents can simultaneously trigger cell-autonomous and non-cell-autonomous death in treated and untreated cells. After ionizing radiation, oxaliplatin, or cisplatin treatment, fractions of treated cancer cell populations were eliminated through cell-autonomous death mechanisms, while other fractions of the treated cancer cells engulfed and killed neighboring cells through non-cell-autonomous processes, including cellular cannibalism. Under conditions of treatment with paclitaxel, non-cell-autonomous and cell-autonomous death were both detected in the treated cell population, while untreated neighboring cells exhibited features of apoptotic demise. The transcriptional activity of p53 tumor-suppressor protein contributed to the execution of cell-autonomous death, yet failed to affect the non-cell-autonomous death by cannibalism for the majority of tested anticancer agents, indicating that the induction of non-cell-autonomous death can occur under conditions in which cell-autonomous death was impaired. Altogether, these results reveal that chemotherapy and radiotherapy can induce both non-cell-autonomous and cell-autonomous death of cancer cells, highlighting the heterogeneity of cell death responses to anticancer treatments and the unsuspected potential contribution of non-cell-autonomous death to the global effects of anticancer treatment.
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Heng HH, Horne SD, Chaudhry S, Regan SM, Liu G, Abdallah BY, Ye CJ. A Postgenomic Perspective on Molecular Cytogenetics. Curr Genomics 2018; 19:227-239. [PMID: 29606910 PMCID: PMC5850511 DOI: 10.2174/1389202918666170717145716] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/29/2017] [Accepted: 02/03/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The postgenomic era is featured by massive data collection and analyses from various large scale-omics studies. Despite the promising capability of systems biology and bioinformatics to handle large data sets, data interpretation, especially the translation of -omics data into clinical implications, has been challenging. DISCUSSION In this perspective, some important conceptual and technological limitations of current systems biology are discussed in the context of the ultimate importance of the genome beyond the collection of all genes. Following a brief summary of the contributions of molecular cytogenetics/cytogenomics in the pre- and post-genomic eras, new challenges for postgenomic research are discussed. Such discussion leads to a call to search for a new conceptual framework and holistic methodologies. CONCLUSION Throughout this synthesis, the genome theory of somatic cell evolution is highlighted in contrast to gene theory, which ignores the karyotype-mediated higher level of genetic information. Since "system inheritance" is defined by the genome context (gene content and genomic topology) while "parts inheritance" is defined by genes/epigenes, molecular cytogenetics and cytogenomics (which directly study genome structure, function, alteration and evolution) will play important roles in this postgenomic era.
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Affiliation(s)
- Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Steven D. Horne
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sophia Chaudhry
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sarah M. Regan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Guo Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Batoul Y. Abdallah
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Christine J. Ye
- The Division of Hematology/Oncology, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI, USA
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Inde Z, Dixon SJ. The impact of non-genetic heterogeneity on cancer cell death. Crit Rev Biochem Mol Biol 2018; 53:99-114. [PMID: 29250983 PMCID: PMC6089072 DOI: 10.1080/10409238.2017.1412395] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 12/22/2022]
Abstract
The goal of cancer chemotherapy is to induce homogeneous cell death within the population of targeted cancer cells. However, no two cells are exactly alike at the molecular level, and sensitivity to drug-induced cell death, therefore, varies within a population. Genetic alterations can contribute to this variability and lead to selection for drug resistant clones. However, there is a growing appreciation for the role of non-genetic variation in producing drug-tolerant cellular states that exhibit reduced sensitivity to cell death for extended periods of time, from hours to weeks. These cellular states may result from individual variation in epigenetics, gene expression, metabolism, and other processes that impact drug mechanism of action or the execution of cell death. Such population-level non-genetic heterogeneity may contribute to treatment failure and provide a cellular "substrate" for the emergence of genetic alterations that confer frank drug resistance.
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Affiliation(s)
- Zintis Inde
- a Cancer Biology Program , Stanford University School of Medicine , Stanford , CA , USA
| | - Scott J Dixon
- a Cancer Biology Program , Stanford University School of Medicine , Stanford , CA , USA
- b Department of Biology , Stanford University , Stanford , CA , USA
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Liu X, Yang W, Guan Z, Yu W, Fan B, Xu N, Liao DJ. There are only four basic modes of cell death, although there are many ad-hoc variants adapted to different situations. Cell Biosci 2018; 8:6. [PMID: 29435221 PMCID: PMC5796572 DOI: 10.1186/s13578-018-0206-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/19/2018] [Indexed: 02/06/2023] Open
Abstract
There have been enough cell death modes delineated in the biomedical literature to befuddle all cell death researchers. Mulling over cell death from the viewpoints of the host tissue or organ and of the host animal, we construe that there should be only two physiological cell death modes, i.e. apoptosis and senescent death (SD), as well as two pathological modes, i.e. necrosis and stress-induced cell death (SICD). Other death modes described in the literature are ad-hoc variants or coalescences of some of these four basic ones in different physiological or pathological situations. SD, SICD and necrosis kill useful cells and will thus trigger regeneration, wound healing and probably also scar formation. SICD and necrosis will likely instigate inflammation as well. Apoptosis occurs as a mechanism to purge no-longer useful cells from a tissue via phagocytosis by cells with phagocytic ability that are collectively tagged by us as scavengers, including macrophages; therefore apoptosis is not followed by regeneration and inflammation. The answer for the question of “who dies” clearly differentiates apoptosis from SD, SICD and necrosis, despite other similarities and disparities among the four demise modes. Apoptosis cannot occur in cell lines in vitro, because cell lines are immortalized by reprogramming the death program of the parental cells, because in culture there lack scavengers and complex communications among different cell types, and because culture condition is a stress to the cells. Several issues of cell death that remain enigmatic to us are also described for peers to deliberate and debate.
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Affiliation(s)
- Xingde Liu
- 1Department of Cardiology, Guizhou Medical University Hospital, Guiyang, 550004 Guizhou People's Republic of China
| | - Wenxiu Yang
- 2Department of Pathology, Guizhou Medical University Hospital, Guiyang, 550004 Guizhou People's Republic of China
| | - Zhizhong Guan
- 3Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang, 550004 People's Republic of China
| | - Wenfeng Yu
- 3Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang, 550004 People's Republic of China
| | - Bin Fan
- 2Department of Pathology, Guizhou Medical University Hospital, Guiyang, 550004 Guizhou People's Republic of China
| | - Ningzhi Xu
- 4Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - D Joshua Liao
- 2Department of Pathology, Guizhou Medical University Hospital, Guiyang, 550004 Guizhou People's Republic of China.,3Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang, 550004 People's Republic of China.,4Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
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12
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Abstract
Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.
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Affiliation(s)
- Christine J Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Guo Liu
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Henry H Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, USA.
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA.
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13
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Zhong H, Chetty I. A note on modeling of tumor regression for estimation of radiobiological parameters. Med Phys 2015; 41:081702. [PMID: 25086512 DOI: 10.1118/1.4884019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Accurate calculation of radiobiological parameters is crucial to predicting radiation treatment response. Modeling differences may have a significant impact on derived parameters. In this study, the authors have integrated two existing models with kinetic differential equations to formulate a new tumor regression model for estimation of radiobiological parameters for individual patients. METHODS A system of differential equations that characterizes the birth-and-death process of tumor cells in radiation treatment was analytically solved. The solution of this system was used to construct an iterative model (Z-model). The model consists of three parameters: tumor doubling time Td, half-life of dead cells Tr, and cell survival fraction SFD under dose D. The Jacobian determinant of this model was proposed as a constraint to optimize the three parameters for six head and neck cancer patients. The derived parameters were compared with those generated from the two existing models: Chvetsov's model (C-model) and Lim's model (L-model). The C-model and L-model were optimized with the parameter Td fixed. RESULTS With the Jacobian-constrained Z-model, the mean of the optimized cell survival fractions is 0.43 ± 0.08, and the half-life of dead cells averaged over the six patients is 17.5 ± 3.2 days. The parameters Tr and SFD optimized with the Z-model differ by 1.2% and 20.3% from those optimized with the Td-fixed C-model, and by 32.1% and 112.3% from those optimized with the Td-fixed L-model, respectively. CONCLUSIONS The Z-model was analytically constructed from the differential equations of cell populations that describe changes in the number of different tumor cells during the course of radiation treatment. The Jacobian constraints were proposed to optimize the three radiobiological parameters. The generated model and its optimization method may help develop high-quality treatment regimens for individual patients.
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Affiliation(s)
- Hualiang Zhong
- Department of Radiation Oncology, Henry Ford Health System, Detroit, Michigan 48202
| | - Indrin Chetty
- Department of Radiation Oncology, Henry Ford Health System, Detroit, Michigan 48202
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14
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Kuo YJ, Yang JS, Lu CC, Chiang SY, Lin JG, Chung JG. Ethanol extract of Hedyotis diffusa willd upregulates G0/G1 phase arrest and induces apoptosis in human leukemia cells by modulating caspase cascade signaling and altering associated genes expression was assayed by cDNA microarray. ENVIRONMENTAL TOXICOLOGY 2015; 30:1162-1177. [PMID: 24677778 DOI: 10.1002/tox.21989] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/11/2014] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
The authors' previous study has shown that water extract of Hedyotis diffusa Willd (HDW) promoted immune response and exhibited anti-leukemic activity in BALB/c leukemic mice in vivo. In this study, the anti-proliferation effects of ethanol extract of H. diffusa Willd (EEHDW) on lung cancer cell lines (A549, H1355, and LLC), leukemia cell lines (HL-60, WEHI-3), and a mouse melanoma cell line (B16F10) in vitro were investigated. The results demonstrated that EEHDW suppressed the cell proliferation of A549, H1355, HL-60, WEHI-3, and B16F10 cells as well as reduced cell viability in a concentration-dependent manner. We found that EEHDW inhibited the cell proliferation of HL-60 cells in concentration-dependent manner. In addition, EEHDW triggered an arrest of HL-60 cells at G0/G1 phase and sub-G1 population (apoptotic cells). EEHDW provoked DNA condensation and DNA damage in HL-60 cells. The activities of caspase-3, caspase-8, and caspase-9 were elevated in EEHDW-treated HL-60 cells. DNA microarray to investigate and display the gene levels related to cell growth, signal transduction, apoptosis, cell adhesion, cell cycle, DNA damage and repair, transcription and translation was also used. These findings suggest that EEHDW may be a potential herbal medicine and therapeutic agent for the treatment of leukemia.
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Affiliation(s)
- Yu-Jui Kuo
- Graduate Institute of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Jai-Sing Yang
- Department of Pharmacology, China Medical University, Taichung, Taiwan
| | - Chi-Cheng Lu
- Department of Life Sciences, National Chung Hsing University, 250, Kuo-Kuang Road, Taichung, 402, Taiwan
| | - Su-Yin Chiang
- Graduate Institute of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Jaung-Geng Lin
- Graduate Institute of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Jing-Gung Chung
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
- Department of Biotechnology, Asia University, Taichung 413, Taiwan, People's Republic of China
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15
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Expression of cell cycle and apoptosis regulators in thymus and thymic epithelial tumors. Clin Exp Med 2015; 16:147-59. [PMID: 25794494 DOI: 10.1007/s10238-015-0344-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/05/2015] [Indexed: 12/15/2022]
Abstract
The human thymus supports the production of self-tolerant T cells with competent and regulatory functions. Various cellular components of the thymic microenvironment such as thymic epithelial cells (TEC) and dendritic cells play essential roles in thymic T cell differentiation. The multiple cellular events occurring during thymic T cell and TEC differentiation involve proteins regulating cell cycle and apoptosis. Dysregulation of the cell cycle and apoptosis networks is involved in the pathogenesis of thymic epithelial tumors (TET) which are divided into two broad categories, thymomas and thymic carcinomas. The present review focuses on the usefulness of the analysis of the expression patterns of major cell cycle and apoptosis regulators in order to gain insight in the histophysiology of thymus and the histopathology, the clinical behavior and the biology of TET.
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16
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Conde de la Rosa L, Vrenken TE, Buist-Homan M, Faber KN, Moshage H. Metformin protects primary rat hepatocytes against oxidative stress-induced apoptosis. Pharmacol Res Perspect 2015; 3:e00125. [PMID: 26038701 PMCID: PMC4448984 DOI: 10.1002/prp2.125] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/05/2015] [Accepted: 01/14/2015] [Indexed: 12/21/2022] Open
Abstract
The majority of chronic liver diseases are accompanied by oxidative stress, which induces apoptosis in hepatocytes and liver injury. Recent studies suggest that oxidative stress and insulin resistance are important in the pathogenesis of nonalcoholic fatty liver disease (NAFLD) and the pathophysiology of diabetes complications. Metformin has been shown to be hepatoprotective in the insulin-resistant and leptin-deficient ob/ob mouse model of NAFLD. However, the mechanism involved in the protective effects of metformin has not been elucidated yet. Therefore, we investigated the protective effect of metformin against oxidative stress-induced apoptosis. Primary rat hepatocytes were exposed to the oxidative stress-generating compound menadione in the presence and absence of metformin. Apoptosis was determined by measuring caspase activity and poly(ADP-ribose) polymerase (PARP)-cleavage, and necrosis was measured by Sytox Green nuclear staining. We demonstrate that (1) Metformin inhibits menadione-induced caspase-9,-6,-3 activation and PARP-cleavage in a concentration-dependent manner. (2) Metformin increases menadione-induced heme oxygenase-1 (HO-1) expression and inhibits c-Jun N-terminal kinase (JNK)-phosphorylation. (3) Metformin does not induce necrosis in primary hepatocytes. Metformin protects hepatocytes against oxidative stress-induced caspase activation, PARP-cleavage and apoptosis. The anti-apoptotic effect of metformin is in part dependent on HO-1 and bcl-xl induction and inhibition of JNK activation and independent of insulin signaling. Our results elucidate novel protective mechanisms of metformin and indicate that metformin could be investigated as a novel therapeutic agent for the treatment of oxidative stress-related liver diseases.
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Affiliation(s)
- Laura Conde de la Rosa
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen Groningen, The Netherlands
| | - Titia E Vrenken
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen Groningen, The Netherlands
| | - Manon Buist-Homan
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen Groningen, The Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen Groningen, The Netherlands
| | - Han Moshage
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen Groningen, The Netherlands
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17
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Dahlman JE, Barnes C, Khan O, Thiriot A, Jhunjunwala S, Shaw TE, Xing Y, Sager HB, Sahay G, Speciner L, Bader A, Bogorad RL, Yin H, Racie T, Dong Y, Jiang S, Seedorf D, Dave A, Sandu KS, Webber MJ, Novobrantseva T, Ruda VM, Lytton-Jean AKR, Levins CG, Kalish B, Mudge DK, Perez M, Abezgauz L, Dutta P, Smith L, Charisse K, Kieran MW, Fitzgerald K, Nahrendorf M, Danino D, Tuder RM, von Andrian UH, Akinc A, Schroeder A, Panigrahy D, Kotelianski V, Langer R, Anderson DG. In vivo endothelial siRNA delivery using polymeric nanoparticles with low molecular weight. NATURE NANOTECHNOLOGY 2014; 9:648-655. [PMID: 24813696 PMCID: PMC4207430 DOI: 10.1038/nnano.2014.84] [Citation(s) in RCA: 429] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 03/25/2014] [Indexed: 05/03/2023]
Abstract
Dysfunctional endothelium contributes to more diseases than any other tissue in the body. Small interfering RNAs (siRNAs) can help in the study and treatment of endothelial cells in vivo by durably silencing multiple genes simultaneously, but efficient siRNA delivery has so far remained challenging. Here, we show that polymeric nanoparticles made of low-molecular-weight polyamines and lipids can deliver siRNA to endothelial cells with high efficiency, thereby facilitating the simultaneous silencing of multiple endothelial genes in vivo. Unlike lipid or lipid-like nanoparticles, this formulation does not significantly reduce gene expression in hepatocytes or immune cells even at the dosage necessary for endothelial gene silencing. These nanoparticles mediate the most durable non-liver silencing reported so far and facilitate the delivery of siRNAs that modify endothelial function in mouse models of vascular permeability, emphysema, primary tumour growth and metastasis.
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Affiliation(s)
- James E Dahlman
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Carmen Barnes
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | - Omar Khan
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Aude Thiriot
- Department of Microbiology and Immunology, Harvard Medical School, Boston 02115, USA
| | - Siddharth Jhunjunwala
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Taylor E Shaw
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yiping Xing
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Hendrik B Sager
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston 02114, USA
| | - Gaurav Sahay
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Lauren Speciner
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | - Andrew Bader
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Hao Yin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tim Racie
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | - Yizhou Dong
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shan Jiang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Danielle Seedorf
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Apeksha Dave
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Kamaljeet S Sandu
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Matthew J Webber
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Vera M Ruda
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Abigail K R Lytton-Jean
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Christopher G Levins
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Brian Kalish
- Vascular Biology Program, Children's Hospital Boston, and Division of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston 02115, USA
| | - Dayna K Mudge
- Vascular Biology Program, Children's Hospital Boston, and Division of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston 02115, USA
| | - Mario Perez
- Program in Translational Lung Research, Division of Pulmonary Sciences and Critical Care Program, Department of Medicine, University of Colorado School of Medicine, Aurora, USA
| | - Ludmila Abezgauz
- Deparment of Biotechnology and Food Engineering, and The Russell Berrie Nanotechnology Institute, Technion Israel Institute of Technology, Haifa 3200, Israel
| | - Partha Dutta
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston 02114, USA
| | - Lynelle Smith
- Program in Translational Lung Research, Division of Pulmonary Sciences and Critical Care Program, Department of Medicine, University of Colorado School of Medicine, Aurora, USA
| | - Klaus Charisse
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | - Mark W Kieran
- Department of Microbiology and Immunology, Harvard Medical School, Boston 02115, USA
| | | | - Matthias Nahrendorf
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston 02114, USA
| | - Dganit Danino
- Deparment of Biotechnology and Food Engineering, and The Russell Berrie Nanotechnology Institute, Technion Israel Institute of Technology, Haifa 3200, Israel
| | - Rubin M Tuder
- Program in Translational Lung Research, Division of Pulmonary Sciences and Critical Care Program, Department of Medicine, University of Colorado School of Medicine, Aurora, USA
| | - Ulrich H von Andrian
- Department of Microbiology and Immunology, Harvard Medical School, Boston 02115, USA
| | - Akin Akinc
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | - Avi Schroeder
- Department of Chemical Engineering, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Dipak Panigrahy
- Department of Microbiology and Immunology, Harvard Medical School, Boston 02115, USA
| | - Victor Kotelianski
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Robert Langer
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Daniel G Anderson
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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18
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Horne SD, Pollick SA, Heng HHQ. Evolutionary mechanism unifies the hallmarks of cancer. Int J Cancer 2014; 136:2012-21. [PMID: 24957955 DOI: 10.1002/ijc.29031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/13/2014] [Indexed: 12/15/2022]
Abstract
The basis for the gene mutation theory of cancer that dominates current molecular cancer research consists of: the belief that gene-level aberrations such as mutations are the main cause of cancers, the concept that stepwise gene mutation accumulation drives cancer progression, and the hallmarks of cancer. The research community swiftly embraced the hallmarks of cancer, as such synthesis has supported the notions that common cancer genes are responsible for the majority of cancers and the complexity of cancer can be dissected into simplified molecular principles. The gene/pathway classification based on individual hallmarks provides explanation for the large number of diverse gene mutations, which is in contrast to the original estimation that only a handful of gene mutations would be discovered. Further, these hallmarks have been highly influential as they also provide the rationale and research direction for continued gene-based cancer research. While the molecular knowledge of these hallmarks is drastically increasing, the clinical implication remains limited, as cancer dynamics cannot be summarized by a few isolated/fixed molecular principles. Furthermore, the highly heterogeneous genetic signature of cancers, including massive stochastic genome alterations, challenges the utility of continuously studying each individual gene mutation under the framework of these hallmarks. It is therefore necessary to re-evaluate the concept of cancer hallmarks through the lens of cancer evolution. In this analysis, the evolutionary basis for the hallmarks of cancer will be discussed and the evolutionary mechanism of cancer suggested by the genome theory will be employed to unify the diverse molecular mechanisms of cancer.
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Affiliation(s)
- Steven D Horne
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI
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19
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Horne SD, Chowdhury SK, Heng HHQ. Stress, genomic adaptation, and the evolutionary trade-off. Front Genet 2014; 5:92. [PMID: 24795754 PMCID: PMC4005935 DOI: 10.3389/fgene.2014.00092] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/03/2014] [Indexed: 12/27/2022] Open
Abstract
Cells are constantly exposed to various internal and external stresses. The importance of cellular stress and its implication to disease conditions have become popular research topics. Many ongoing investigations focus on the sources of stress, their specific molecular mechanisms and interactions, especially regarding their contributions to many common and complex diseases through defined molecular pathways. Numerous molecular mechanisms have been linked to endoplasmic reticulum stress along with many unexpected findings, drastically increasing the complexity of our molecular understanding and challenging how to apply individual mechanism-based knowledge in the clinic. A newly emergent genome theory searches for the synthesis of a general evolutionary mechanism that unifies different types of stress and functional relationships from a genome-defined system point of view. Herein, we discuss the evolutionary relationship between stress and somatic cell adaptation under physiological, pathological, and somatic cell survival conditions, the multiple meanings to achieve adaptation and its potential trade-off. In particular, we purposely defocus from specific stresses and mechanisms by redirecting attention toward studying underlying general mechanisms.
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Affiliation(s)
- Steven D Horne
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University Detroit, MI, USA
| | | | - Henry H Q Heng
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University Detroit, MI, USA ; Department of Pathology, School of Medicine, Wayne State University Detroit, MI, USA
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20
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Stevens JB, Liu G, Abdallah BY, Horne SD, Ye KJ, Bremer SW, Ye CJ, Krawetz SA, Heng HH. Unstable genomes elevate transcriptome dynamics. Int J Cancer 2014; 134:2074-87. [PMID: 24122714 DOI: 10.1002/ijc.28531] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/10/2013] [Accepted: 09/26/2013] [Indexed: 01/15/2023]
Abstract
The challenge of identifying common expression signatures in cancer is well known, however the reason behind this is largely unclear. Traditionally variation in expression signatures has been attributed to technological problems, however recent evidence suggests that chromosome instability (CIN) and resultant karyotypic heterogeneity may be a large contributing factor. Using a well-defined model of immortalization, we systematically compared the pattern of genome alteration and expression dynamics during somatic evolution. Co-measurement of global gene expression and karyotypic alteration throughout the immortalization process reveals that karyotype changes influence gene expression as major structural and numerical karyotypic alterations result in large gene expression deviation. Replicate samples from stages with stable genomes are more similar to each other than are replicate samples with karyotypic heterogeneity. Karyotypic and gene expression change during immortalization is dynamic as each stage of progression has a unique expression pattern. This was further verified by comparing global expression in two replicates grown in one flask with known karyotypes. Replicates with higher karyotypic instability were found to be less similar than replicates with stable karyotypes. This data illustrates the karyotype, transcriptome, and transcriptome determined pathways are in constant flux during somatic cellular evolution (particularly during the macroevolutionary phase) and this flux is an inextricable feature of CIN and essential for cancer formation. The findings presented here underscore the importance of understanding the evolutionary process of cancer in order to design improved treatment modalities.
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21
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Plumbagin induces apoptotic and autophagic cell death through inhibition of the PI3K/Akt/mTOR pathway in human non-small cell lung cancer cells. Cancer Lett 2013; 344:239-59. [PMID: 24280585 DOI: 10.1016/j.canlet.2013.11.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/30/2013] [Accepted: 11/07/2013] [Indexed: 12/22/2022]
Abstract
Plumbagin (PLB) has shown anti-cancer activity but the mechanism is unclear. This study has found that PLB has a potent pro-apoptotic and pro-autophagic effect on A549 and H23 cells. PLB arrests cells in G2/M phase, and increases the intracellular level of reactive oxygen species in both cell lines. PLB dose-dependently induces autophagy through inhibition of PI3K/Akt/mTOR pathway as indicated by reduced phosphorylation of Akt and mTOR. Inhibition or induction of autophagy enhances PLB-induced apoptosis. There is crosstalk between PLB-induced apoptosis and autophagy. These findings indicate that PLB initiates both apoptosis and autophagy in NSCLC cells through coordinated pathways.
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22
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Heng HHQ, Liu G, Stevens JB, Abdallah BY, Horne SD, Ye KJ, Bremer SW, Chowdhury SK, Ye CJ. Karyotype heterogeneity and unclassified chromosomal abnormalities. Cytogenet Genome Res 2013; 139:144-57. [PMID: 23571381 DOI: 10.1159/000348682] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In a departure from traditional gene-centric thinking with regard to cytogenetics and cytogenomics, the recently introduced genome theory calls upon a re-focusing of our attention on karyotype analyses of disease conditions. Karyotype heterogeneity has been demonstrated to be directly involved in the somatic cell evolution process which is the basis of many common and complex diseases such as cancer. To correctly use karyotype heterogeneity and apply it to monitor system instability, we need to include many seemingly unimportant non-specific chromosomal aberrations into our analysis. Traditionally, cytogenetic analysis has been focused on identifying recurrent types of abnormalities, particularly those that have been linked to specific diseases. In this perspective, drawing on the new framework of 4D-genomics, we will briefly review the importance of studying karyotype heterogeneity. We have also listed a number of overlooked chromosomal aberrations including defective mitotic figures, chromosome fragmentation as well as genome chaos. Finally, we call for the systematic discovery/characterization and classification of karyotype abnormalities in human diseases, as karyotype heterogeneity is the common factor that is essential for somatic cell evolution.
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Affiliation(s)
- H H Q Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Mich. 48201, USA.
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23
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Horne SD, Stevens JB, Abdallah BY, Liu G, Bremer SW, Ye CJ, Heng HH. Why imatinib remains an exception of cancer research. J Cell Physiol 2012; 228:665-70. [DOI: 10.1002/jcp.24233] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 09/27/2012] [Indexed: 12/26/2022]
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