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Paromov V, Uversky VN, Cooley A, Liburd LE, Mukherjee S, Na I, Dayhoff GW, Pratap S. The Proteomic Analysis of Cancer-Related Alterations in the Human Unfoldome. Int J Mol Sci 2024; 25:1552. [PMID: 38338831 PMCID: PMC10855131 DOI: 10.3390/ijms25031552] [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: 12/01/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/12/2024] Open
Abstract
Many proteins lack stable 3D structures. These intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains with intrinsically disordered protein regions (IDPRs) often carry out regulatory functions related to molecular recognition and signal transduction. IDPs/IDPRs constitute a substantial portion of the human proteome and are termed "the unfoldome". Herein, we probe the human breast cancer unfoldome and investigate relations between IDPs and key disease genes and pathways. We utilized bottom-up proteomics, MudPIT (Multidimensional Protein Identification Technology), to profile differentially expressed IDPs in human normal (MCF-10A) and breast cancer (BT-549) cell lines. Overall, we identified 2271 protein groups in the unfoldome of normal and cancer proteomes, with 148 IDPs found to be significantly differentially expressed in cancer cells. Further analysis produced annotations of 140 IDPs, which were then classified to GO (Gene Ontology) categories and pathways. In total, 65% (91 of 140) IDPs were related to various diseases, and 20% (28 of 140) mapped to cancer terms. A substantial portion of the differentially expressed IDPs contained disordered regions, confirmed by in silico characterization. Overall, our analyses suggest high levels of interactivity in the human cancer unfoldome and a prevalence of moderately and highly disordered proteins in the network.
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Affiliation(s)
- Victor Paromov
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA; (V.N.U.); (I.N.)
| | - Ayorinde Cooley
- Meharry Bioinformatics Core, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Lincoln E. Liburd
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA (S.M.)
| | - Shyamali Mukherjee
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA (S.M.)
| | - Insung Na
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA; (V.N.U.); (I.N.)
| | - Guy W. Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL 33613, USA;
| | - Siddharth Pratap
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
- Meharry Bioinformatics Core, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
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2
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García de Herreros A. Dual role of Snail1 as transcriptional repressor and activator. Biochim Biophys Acta Rev Cancer 2024; 1879:189037. [PMID: 38043804 DOI: 10.1016/j.bbcan.2023.189037] [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: 10/24/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Snail1 transcriptional factor plays a key role in the control of epithelial to mesenchymal transition, a process that remodels tumor cells increasing their invasion and chemo-resistance as well as reprograms their metabolism and provides stemness properties. During this transition, Snail1 acts as a transcriptional repressor and, as growing evidences have demonstrated, also as a direct activator of mesenchymal genes. In this review, I describe the different proteins that interact with Snail1 and are responsible for these two different functions on gene expression; I focus on the transcriptional factors that associate to Snail1 in their target promoters, both activated and repressed. I also present working models for Snail1 action both as repressor and activator and raise some issues that still need to be investigated.
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Affiliation(s)
- Antonio García de Herreros
- Programa de Recerca en Càncer, Hospital del Mar Research Institute (IMIM), Unidad Asociada al CSIC, Barcelona, Spain; Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain.
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3
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Kulkarni P, Salgia R, Rangarajan G. Intrinsically disordered proteins and conformational noise: The hypothesis a decade later. iScience 2023; 26:107109. [PMID: 37408690 PMCID: PMC10319216 DOI: 10.1016/j.isci.2023.107109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
Phenotypic plasticity is the ability of individual genotypes to produce different phenotypes in response to environmental perturbations. We previously postulated how conformational noise emanating from conformational dynamics of intrinsically disordered proteins (IDPs) which is distinct from transcriptional noise, can contribute to phenotypic switching by rewiring the cellular protein interaction network. Since most transcription factors are IDPs, we posited that conformational noise is an integral component of transcriptional noise implying that IDPs may amplify total noise in the system either stochastically or in response to environmental changes. Here, we review progress in elucidating the details of the hypothesis. We highlight empirical evidence supporting the hypothesis, discuss conceptual advances that underscore its fundamental importance and implications, and identify areas for future investigations.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
- Department of Systems Biology, City of Hope National Medical Center, Duarte, CA, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
- Center for Neuroscience, Indian Institute of Science, Bangalore 560012, India
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4
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Grody EI, Abraham A, Shukla V, Goyal Y. Toward a systems-level probing of tumor clonality. iScience 2023; 26:106574. [PMID: 37192968 PMCID: PMC10182304 DOI: 10.1016/j.isci.2023.106574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023] Open
Abstract
Cancer has been described as a genetic disease that clonally evolves in the face of selective pressures imposed by cell-intrinsic and extrinsic factors. Although classical models based on genetic data predominantly propose Darwinian mechanisms of cancer evolution, recent single-cell profiling of cancers has described unprecedented heterogeneity in tumors providing support for alternative models of branched and neutral evolution through both genetic and non-genetic mechanisms. Emerging evidence points to a complex interplay between genetic, non-genetic, and extrinsic environmental factors in shaping the evolution of tumors. In this perspective, we briefly discuss the role of cell-intrinsic and extrinsic factors that shape clonal behaviors during tumor progression, metastasis, and drug resistance. Taking examples of pre-malignant states associated with hematological malignancies and esophageal cancer, we discuss recent paradigms of tumor evolution and prospective approaches to further enhance our understanding of this spatiotemporally regulated process.
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Affiliation(s)
- Emanuelle I. Grody
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ajay Abraham
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Vipul Shukla
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Corresponding author
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Corresponding author
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5
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Pillai M, Hojel E, Jolly MK, Goyal Y. Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools. NATURE COMPUTATIONAL SCIENCE 2023; 3:301-313. [PMID: 38177938 DOI: 10.1038/s43588-023-00427-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/03/2023] [Indexed: 01/06/2024]
Abstract
Individual cells within an otherwise genetically homogenous population constantly undergo fluctuations in their molecular state, giving rise to non-genetic heterogeneity. Such diversity is being increasingly implicated in cancer therapy resistance and metastasis. Identifying the origins of non-genetic heterogeneity is therefore crucial for making clinical breakthroughs. We discuss with examples how dynamical models and computational tools have provided critical multiscale insights into the nature and consequences of non-genetic heterogeneity in cancer. We demonstrate how mechanistic modeling has been pivotal in establishing key concepts underlying non-genetic diversity at various biological scales, from population dynamics to gene regulatory networks. We discuss advances in single-cell longitudinal profiling techniques to reveal patterns of non-genetic heterogeneity, highlighting the ongoing efforts and challenges in statistical frameworks to robustly interpret such multimodal datasets. Moving forward, we stress the need for data-driven statistical and mechanistically motivated dynamical frameworks to come together to develop predictive cancer models and inform therapeutic strategies.
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Affiliation(s)
- Maalavika Pillai
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Emilia Hojel
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India.
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL, USA.
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6
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Jindal R, Nanda A, Pillai M, Ware KE, Singh D, Sehgal M, Armstrong AJ, Somarelli JA, Jolly MK. Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer. Comput Struct Biotechnol J 2023; 21:1498-1509. [PMID: 36851919 PMCID: PMC9957767 DOI: 10.1016/j.csbj.2023.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
Advanced prostate cancer patients initially respond to hormone therapy, be it in the form of androgen deprivation therapy or second-generation hormone therapies, such as abiraterone acetate or enzalutamide. However, most men with prostate cancer eventually develop hormone therapy resistance. This resistance can arise through multiple mechanisms, such as through genetic mutations, epigenetic mechanisms, or through non-genetic pathways, such as lineage plasticity along epithelial-mesenchymal or neuroendocrine-like axes. These mechanisms of hormone therapy resistance often co-exist within a single patient's tumor and can overlap within a single cell. There exists a growing need to better understand how phenotypic heterogeneity and plasticity results from emergent dynamics of the regulatory networks governing androgen independence. Here, we investigated the dynamics of a regulatory network connecting the drivers of androgen receptor (AR) splice variant-mediated androgen independence and those of epithelial-mesenchymal transition. Model simulations for this network revealed four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR) and mesenchymal-sensitive (MS), with the latter phenotype occurring rarely. We observed that well-coordinated "teams" of regulators working antagonistically within the network enable these phenotypes. These model predictions are supported by multiple transcriptomic datasets both at single-cell and bulk levels, including in vitro EMT induction models and clinical samples. Further, our simulations reveal spontaneous stochastic switching between the ES and MR states. Addition of the immune checkpoint molecule, PD-L1, to the network was able to capture the interactions between AR, PD-L1, and the mesenchymal marker SNAIL, which was also confirmed through quantitative experiments. This systems-level understanding of the driver of androgen independence and EMT could aid in understanding non-genetic transitions and progression of such cancers and help in identifying novel therapeutic strategies or targets.
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Affiliation(s)
- Rashi Jindal
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.,Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Abheepsa Nanda
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.,Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Maalavika Pillai
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.,Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Kathryn E Ware
- Department of Medicine, Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC 27710, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.,Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Manas Sehgal
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Andrew J Armstrong
- Department of Medicine, Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC 27710, USA.,Department of Surgery, Duke University, Durham, NC 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Jason A Somarelli
- Department of Medicine, Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC 27710, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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7
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Carvalho Leão MH, Costa ML, Mermelstein C. Epithelial-to-mesenchymal transition as a learning paradigm of cell biology. Cell Biol Int 2023; 47:352-366. [PMID: 36411367 DOI: 10.1002/cbin.11967] [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: 08/25/2022] [Revised: 10/17/2022] [Accepted: 11/09/2022] [Indexed: 11/23/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a complex biological process that occurs during normal embryogenesis and in certain pathological conditions, particularly in cancer. EMT can be viewed as a cell biology-based process, since it involves all the cellular components, including the plasma membrane, cytoskeleton and extracellular matrix, endoplasmic reticulum, Golgi apparatus, lysosomes, and mitochondria, as well as cellular processes, such as regulation of gene expression and cell cycle, adhesion, migration, signaling, differentiation, and death. Therefore, we propose that EMT could be used to motivate undergraduate medical students to learn and understand cell biology. Here, we describe and discuss the involvement of each cellular component and process during EMT. To investigate the density with which different cell biology concepts are used in EMT research, we apply a bibliometric approach. The most frequent cell biology topics in EMT studies were regulation of gene expression, cell signaling, cell cycle, cell adhesion, cell death, cell differentiation, and cell migration. Finally, we suggest that the study of EMT could be incorporated into undergraduate disciplines to improve cell biology understanding among premedical, medical and biomedical students.
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Affiliation(s)
| | - Manoel Luis Costa
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claudia Mermelstein
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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8
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Functional Resilience of Mutually Repressing Motifs Embedded in Larger Networks. Biomolecules 2022; 12:biom12121842. [PMID: 36551270 PMCID: PMC9775907 DOI: 10.3390/biom12121842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Elucidating the design principles of regulatory networks driving cellular decision-making has important implications for understanding cell differentiation and guiding the design of synthetic circuits. Mutually repressing feedback loops between 'master regulators' of cell fates can exhibit multistable dynamics enabling "single-positive" phenotypes: (high A, low B) and (low A, high B) for a toggle switch, and (high A, low B, low C), (low A, high B, low C) and (low A, low B, high C) for a toggle triad. However, the dynamics of these two motifs have been interrogated in isolation in silico, but in vitro and in vivo, they often operate while embedded in larger regulatory networks. Here, we embed these motifs in complex larger networks of varying sizes and connectivity to identify hallmarks under which these motifs maintain their canonical dynamical behavior. We show that an increased number of incoming edges onto a motif leads to a decay in their canonical stand-alone behaviors. We also show that this decay can be exacerbated by adding self-inhibition but not self-activation loops on the 'master regulators'. These observations offer insights into the design principles of biological networks containing these motifs and can help devise optimal strategies for the integration of these motifs into larger synthetic networks.
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9
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Deritei D, Kunšič N, Csermely P. Probabilistic edge weights fine-tune Boolean network dynamics. PLoS Comput Biol 2022; 18:e1010536. [PMID: 36215324 PMCID: PMC9584532 DOI: 10.1371/journal.pcbi.1010536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 10/20/2022] [Accepted: 09/02/2022] [Indexed: 11/04/2022] Open
Abstract
Biological systems are noisy by nature. This aspect is reflected in our experimental measurements and should be reflected in the models we build to better understand these systems. Noise can be especially consequential when trying to interpret specific regulatory interactions, i.e. regulatory network edges. In this paper, we propose a method to explicitly encode edge-noise in Boolean dynamical systems by probabilistic edge-weight (PEW) operators. PEW operators have two important features: first, they introduce a form of edge-weight into Boolean models through the noise, second, the noise is dependent on the dynamical state of the system, which enables more biologically meaningful modeling choices. Moreover, we offer a simple-to-use implementation in the already well-established BooleanNet framework. In two application cases, we show how the introduction of just a few PEW operators in Boolean models can fine-tune the emergent dynamics and increase the accuracy of qualitative predictions. This includes fine-tuning interactions which cause non-biological behaviors when switching between asynchronous and synchronous update schemes in dynamical simulations. Moreover, PEW operators also open the way to encode more exotic cellular dynamics, such as cellular learning, and to implementing edge-weights for regulatory networks inferred from omics data.
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Affiliation(s)
- Dávid Deritei
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, United States of America
- * E-mail:
| | - Nina Kunšič
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Péter Csermely
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
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10
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Cancer: More than a geneticist’s Pandora’s box. J Biosci 2022. [DOI: 10.1007/s12038-022-00254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Kulkarni P, Bhattacharya S, Achuthan S, Behal A, Jolly MK, Kotnala S, Mohanty A, Rangarajan G, Salgia R, Uversky V. Intrinsically Disordered Proteins: Critical Components of the Wetware. Chem Rev 2022; 122:6614-6633. [PMID: 35170314 PMCID: PMC9250291 DOI: 10.1021/acs.chemrev.1c00848] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite the wealth of knowledge gained about intrinsically disordered proteins (IDPs) since their discovery, there are several aspects that remain unexplored and, hence, poorly understood. A living cell is a complex adaptive system that can be described as a wetware─a metaphor used to describe the cell as a computer comprising both hardware and software and attuned to logic gates─capable of "making" decisions. In this focused Review, we discuss how IDPs, as critical components of the wetware, influence cell-fate decisions by wiring protein interaction networks to keep them minimally frustrated. Because IDPs lie between order and chaos, we explore the possibility that they can be modeled as attractors. Further, we discuss how the conformational dynamics of IDPs manifests itself as conformational noise, which can potentially amplify transcriptional noise to stochastically switch cellular phenotypes. Finally, we explore the potential role of IDPs in prebiotic evolution, in forming proteinaceous membrane-less organelles, in the origin of multicellularity, and in protein conformation-based transgenerational inheritance of acquired characteristics. Together, these ideas provide a new conceptual framework to discern how IDPs may perform critical biological functions despite their lack of structure.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
- Address for correspondence: Prakash Kulkarni, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, , Vladimir N. Uversky, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612,
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, USA
| | - Srisairam Achuthan
- Division of Research Informatics, Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Amita Behal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sourabh Kotnala
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
- Center for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow region 141700, Russia
- Address for correspondence: Prakash Kulkarni, Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, , Vladimir N. Uversky, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612,
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12
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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13
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Uversky VN. Protein folding, misfolding, and un/non-folding: overview of the SP16 Session at the 20 th IUPAB congress, 45 th Annual Meeting of SBBf, and 50 th Annual Meeting of SBBq. Biophys Rev 2022; 13:879-882. [PMID: 35059012 DOI: 10.1007/s12551-021-00885-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022] Open
Abstract
The classical and idealistic consideration of the protein universe as a set of well-ordered proteinaceous machines with unique spatial organizations conducting unique biological functions is changed because of the recognition that proteins can fold, misfold, or be disordered to different degree. Functional repertoires of intrinsically disordered proteins complement functions of ordered proteins, whereas protein misfolding and concomitant oligomerization, aggregation, and fibrillation are related to the pathogenesis of numerous human diseases. Flexible proteins can undergo liquid-liquid phase separation, which is at the heart of the biogenesis of numerous membrane-less organelles. Many of these aspects were highlighted in four talks delivered at the SP16 Session at the 20th IUPAB congress, 45th Annual Meeting of SBBf, and 50th Annual Meeting of SBBq.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL MDC07 USA
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14
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Dynamic Phenotypic Switching and Group Behavior Help Non-Small Cell Lung Cancer Cells Evade Chemotherapy. Biomolecules 2021; 12:biom12010008. [PMID: 35053156 PMCID: PMC8773639 DOI: 10.3390/biom12010008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022] Open
Abstract
Drug resistance, a major challenge in cancer therapy, is typically attributed to mutations and genetic heterogeneity. Emerging evidence suggests that dynamic cellular interactions and group behavior also contribute to drug resistance. However, the underlying mechanisms remain poorly understood. Here, we present a new mathematical approach with game theoretical underpinnings that we developed to model real-time growth data of non-small cell lung cancer (NSCLC) cells and discern patterns in response to treatment with cisplatin. We show that the cisplatin-sensitive and cisplatin-tolerant NSCLC cells, when co-cultured in the absence or presence of the drug, display dynamic group behavior strategies. Tolerant cells exhibit a 'persister-like' behavior and are attenuated by sensitive cells; they also appear to 'educate' sensitive cells to evade chemotherapy. Further, tolerant cells can switch phenotypes to become sensitive, especially at low cisplatin concentrations. Finally, switching treatment from continuous to an intermittent regimen can attenuate the emergence of tolerant cells, suggesting that intermittent chemotherapy may improve outcomes in lung cancer.
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15
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Fiandaca G, Bernardi S, Scianna M, Delitala ME. A phenotype-structured model to reproduce the avascular growth of a tumor and its interaction with the surrounding environment. J Theor Biol 2021; 535:110980. [PMID: 34915043 DOI: 10.1016/j.jtbi.2021.110980] [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: 04/07/2021] [Revised: 10/08/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022]
Abstract
We here propose a one-dimensional spatially explicit phenotype-structured model to analyze selected aspects of avascular tumor progression. In particular, our approach distinguishes viable and necrotic cell fractions. The metabolically active part of the disease is, in turn, differentiated according to a continuous trait, that identifies cell variants with different degrees of motility and proliferation potential. A parabolic partial differential equation (PDE) then governs the spatio-temporal evolution of the phenotypic distribution of active cells within the host tissue. In this respect, active tumor agents are allowed to duplicate, move upon haptotactic and pressure stimuli, and eventually undergo necrosis. The mutual influence between the emerging malignancy and its environment (in terms of molecular landscape) is implemented by coupling the evolution law of the viable tumor mass with a parabolic PDE for oxygen kinetics and a differential equation that accounts for local consumption of extracellular matrix (ECM) elements. The resulting numerical realizations reproduce tumor growth and invasion in a number scenarios that differ for cell properties (i.e., individual migratory behavior, duplication and mutation potential) and environmental conditions (i.e., level of tissue oxygenation and homogeneity in the initial matrix profile). In particular, our simulations show that, in all cases, more mobile cell variants occupy the front edge of the tumor, whereas more proliferative clones are selected at the more internal regions. A necrotic core constantly occupies the bulk of the mass due to nutrient deprivation. This work may eventually suggest some biomedical strategies to partially reduce tumor aggressiveness, i.e., to enhance necrosis of malignant tissue and to promote the presence of more proliferative cell phenotypes over more invasive ones.
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Affiliation(s)
- Giada Fiandaca
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
| | - Sara Bernardi
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
| | - Marco Scianna
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
| | - Marcello Edoardo Delitala
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
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16
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Protein conformational dynamics and phenotypic switching. Biophys Rev 2021; 13:1127-1138. [PMID: 35059032 PMCID: PMC8724335 DOI: 10.1007/s12551-021-00858-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/18/2021] [Indexed: 12/14/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure but exist as conformational ensembles. Because of their structural plasticity, they can interact with multiple partners. The protein interactions between IDPs and their partners form scale-free protein interaction networks (PINs) that facilitate information flow in the cell. Because of their plasticity, IDPs typically occupy hub positions in cellular PINs. Furthermore, their conformational dynamics and propensity for post-translational modifications contribute to "conformational" noise which is distinct from the well-recognized transcriptional noise. Therefore, upregulation of IDPs in response to a specific input, such as stress, contributes to increased noise and, hence, an increase in stochastic, "promiscuous" interactions. These interactions lead to activation of latent pathways or can induce "rewiring" of the PIN to yield an optimal output underscoring the critical role of IDPs in regulating information flow. We have used PAGE4, a highly intrinsically disordered stress-response protein as a paradigm. Employing a variety of experimental and computational techniques, we have elucidated the role of PAGE4 in phenotypic switching of prostate cancer cells at a systems level. These cumulative studies over the past decade provide a conceptual framework to better understand how IDP conformational dynamics and conformational noise might facilitate cellular decision-making.
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17
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Dasari K, Somarelli JA, Kumar S, Townsend JP. The somatic molecular evolution of cancer: Mutation, selection, and epistasis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 165:56-65. [PMID: 34364910 DOI: 10.1016/j.pbiomolbio.2021.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022]
Abstract
Cancer progression has been attributed to somatic changes in single-nucleotide variants, copy-number aberrations, loss of heterozygosity, chromosomal instability, epistatic interactions, and the tumor microenvironment. It is not entirely clear which of these changes are essential and which are ancillary to cancer. The dynamic nature of cancer evolution in a patient can be illuminated using several concepts and tools from classical evolutionary biology. Neutral mutation rates in cancer cells are calculable from genomic data such as synonymous mutations, and selective pressures are calculable from rates of fixation occurring beyond the expectation by neutral mutation and drift. However, these cancer effect sizes of mutations are complicated by epistatic interactions that can determine the likely sequence of gene mutations. In turn, longitudinal phylogenetic analyses of somatic cancer progression offer an opportunity to identify key moments in cancer evolution, relating the timing of driver mutations to corresponding landmarks in the clinical timeline. These analyses reveal temporal aspects of genetic and phenotypic change during tumorigenesis and across clinical timescales. Using a related framework, clonal deconvolution, physical locations of clones, and their phylogenetic relations can be used to infer tumor migration histories. Additionally, genetic interactions with the tumor microenvironment can be analyzed with longstanding approaches applied to organismal genotype-by-environment interactions. Fitness landscapes for cancer evolution relating to genotype, phenotype, and environment could enable more accurate, personalized therapeutic strategies. An understanding of the trajectories underlying the evolution of neoplasms, primary, and metastatic tumors promises fundamental advances toward accurate and personalized predictions of therapeutic response.
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Affiliation(s)
| | | | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, and Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Jeffrey P Townsend
- Yale College, New Haven, CT, USA; Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA; Yale Cancer Center, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
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18
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Li T, Tang C, Huang Z, Yang L, Dai H, Tang B, Xiao B, Li J, Lei X. miR-144-3p inhibited the growth, metastasis and epithelial-mesenchymal transition of colorectal adenocarcinoma by targeting ZEB1/2. Aging (Albany NY) 2021; 13:17349-17369. [PMID: 34226299 PMCID: PMC8312459 DOI: 10.18632/aging.203225] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/04/2021] [Indexed: 01/05/2023]
Abstract
miR-144-3p is aberrantly expressed in several types of human cancer and functions as a tumor suppressor by inhibiting metastasis. However, the clinical significance and biological function of miR-144-3p in colorectal adenocarcinoma (CRA) have yet to be elucidated. Here we reported that miR-144-3p expression level was significantly down-regulated in CRA tissues compared with matched noncancerous colorectal mucosae tissues. Low miR-144-3p expression was correlated with adverse clinicopathologic characteristics and poor prognosis of CRA patients. Cox regression analysis showed that low miR-144-3p expression was an independent risk factor for DFS and OS in CRA. In vitro and in vivo assays showed that miR-144-3p significantly inhibited proliferation, migration and invasion of CRA cells. In particular, miR-144-3p could suppress EMT process of CRA cells by regulating the cytoskeleton and EMT markers. Bioinformatics analysis indicated that EMT associated transcription factors ZEB1 and ZEB2 were potential targets of miR-144-3p, and miR-144-3p inhibited ZEB1 and ZEB2 expression and was negatively correlated with their expression in CRA. Finally, we confirmed that ZEB1 and ZEB2 down-regulation collaboratively mediated the inhibitory effect of miR-144-3p on proliferation, invasion and EMT of CRA cells. In conclusion, our study provided evidence that miR-144-3p could inhibit CRA cell proliferation, invasion and EMT by targeting ZEB1/2.
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Affiliation(s)
- Taiyuan Li
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Gastrointestinal Surgical Institute, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Cheng Tang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Zhixiang Huang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Lingling Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Hua Dai
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Bo Tang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Benping Xiao
- Department of General Surgery, Jiangxi Pingxiang People’s Hospital, Pingxiang 337000, Jiangxi, China
| | - Jianfeng Li
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Xiong Lei
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
- Gastrointestinal Surgical Institute, Nanchang University, Nanchang 330006, Jiangxi, China
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19
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Hati S, Duddu AS, Jolly MK. Operating principles of circular toggle polygons. Phys Biol 2021; 18. [PMID: 33730700 DOI: 10.1088/1478-3975/abef79] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/17/2021] [Indexed: 11/12/2022]
Abstract
Decoding the dynamics of cellular decision-making and cell differentiation is a central question in cell and developmental biology. A common network motif involved in many cell-fate decisions is a mutually inhibitory feedback loop between two self-activating 'master regulators' A and B, also called as toggle switch. Typically, it can allow for three stable states-(high A, low B), (low A, high B) and (medium A, medium B). A toggle triad-three mutually repressing regulators A, B and C, i.e. three toggle switches arranged circularly (between A and B, between B and C, and between A and C)-can allow for six stable states: three 'single positive' and three 'double positive' ones. However, the operating principles of larger toggle polygons, i.e. toggle switches arranged circularly to form a polygon, remain unclear. Here, we simulate using both discrete and continuous methods the dynamics of different sized toggle polygons. We observed a pattern in their steady state frequency depending on whether the polygon was an even or odd numbered one. The even-numbered toggle polygons result in two dominant states with consecutive components of the network expressing alternating high and low levels. The odd-numbered toggle polygons, on the other hand, enable more number of states, usually twice the number of components with the states that follow 'circular permutation' patterns in their composition. Incorporating self-activations preserved these trends while increasing the frequency of multistability in the corresponding network. Our results offer insights into design principles of circular arrangement of regulatory units involved in cell-fate decision making, and can offer design strategies for synthesizing genetic circuits.
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Affiliation(s)
- Souvadra Hati
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India.,Undergraduate Programme, Indian Institute of Science, Bangalore, India
| | - Atchuta Srinivas Duddu
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
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20
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Bhattacharya S, Mohanty A, Achuthan S, Kotnala S, Jolly MK, Kulkarni P, Salgia R. Group Behavior and Emergence of Cancer Drug Resistance. Trends Cancer 2021; 7:323-334. [PMID: 33622644 PMCID: PMC8500356 DOI: 10.1016/j.trecan.2021.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023]
Abstract
Drug resistance is a major impediment in cancer. Although it is generally thought that acquired drug resistance is due to genetic mutations, emerging evidence indicates that nongenetic mechanisms also play an important role. Resistance emerges through a complex interplay of clonal groups within a heterogeneous tumor and the surrounding microenvironment. Traits such as phenotypic plasticity, intercellular communication, and adaptive stress response, act in concert to ensure survival of intermediate reversible phenotypes, until permanent, resistant clones can emerge. Understanding the role of group behavior, and the underlying nongenetic mechanisms, can lead to more efficacious treatment designs and minimize or delay emergence of resistance.
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Affiliation(s)
- Supriyo Bhattacharya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Sourabh Kotnala
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA.
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21
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A Theoretical Approach to Coupling the Epithelial-Mesenchymal Transition (EMT) to Extracellular Matrix (ECM) Stiffness via LOXL2. Cancers (Basel) 2021; 13:cancers13071609. [PMID: 33807227 PMCID: PMC8037024 DOI: 10.3390/cancers13071609] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/12/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Epithelial-mesenchymal transition (EMT) is a key process in cancer progression through which cells weaken their cell-cell adhesion and gain mobility and invasive traits. Besides chemical signaling, recent studies have established the connection of EMT to mechanical microenvironment, such as the stiffness of extracellular matrix (ECM). LOXL2 is representative of a family of enzymes that promotes fiber cross-linking in ECM. With increased cross-linking comes increased stiffness, which induces EMT that can, in turn, elevate LOXL2 levels. As such, a positive feedback loop among EMT, LOXL2, and ECM stiffness can be formed. We built a mathematical model on a core biochemical reaction network featuring this feedback loop, and showed how strongly it drives EMT. We also illustrated mechanistically how cross-linking connects with stiffness, using a mechanical model of collagen (a major component of ECM). Using this theoretical framework, we demonstrated the heterogeneity of LOXL2/stiffness and its implications on migrating cancer cells that could seed metastasis, the growth of secondary malignant tumors. This framework can inspire experimental studies of more fine-grained mechanotransduction and biomechanical heterogeneity in cancers. Abstract The epithelial-mesenchymal transition (EMT) plays a critical role in cancer progression, being responsible in many cases for the onset of the metastatic cascade and being integral in the ability of cells to resist drug treatment. Most studies of EMT focus on its induction via chemical signals such as TGF-β or Notch ligands, but it has become increasingly clear that biomechanical features of the microenvironment such as extracellular matrix (ECM) stiffness can be equally important. Here, we introduce a coupled feedback loop connecting stiffness to the EMT transcription factor ZEB1, which acts via increasing the secretion of LOXL2 that leads to increased cross-linking of collagen fibers in the ECM. This increased cross-linking can effectively increase ECM stiffness and increase ZEB1 levels, thus setting a positive feedback loop between ZEB1 and ECM stiffness. To investigate the impact of this non-cell-autonomous effect, we introduce a computational approach capable of connecting LOXL2 concentration to increased stiffness and thereby to higher ZEB1 levels. Our results indicate that this positive feedback loop, once activated, can effectively lock the cells in a mesenchymal state. The spatial-temporal heterogeneity of the LOXL2 concentration and thus the mechanical stiffness also has direct implications for migrating cells that attempt to escape the primary tumor.
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22
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Singh D, Bocci F, Kulkarni P, Jolly MK. Coupled Feedback Loops Involving PAGE4, EMT and Notch Signaling Can Give Rise to Non-genetic Heterogeneity in Prostate Cancer Cells. ENTROPY (BASEL, SWITZERLAND) 2021; 23:288. [PMID: 33652914 PMCID: PMC7996788 DOI: 10.3390/e23030288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 12/12/2022]
Abstract
Non-genetic heterogeneity is emerging as a crucial factor underlying therapy resistance in multiple cancers. However, the design principles of regulatory networks underlying non-genetic heterogeneity in cancer remain poorly understood. Here, we investigate the coupled dynamics of feedback loops involving (a) oscillations in androgen receptor (AR) signaling mediated through an intrinsically disordered protein PAGE4, (b) multistability in epithelial-mesenchymal transition (EMT), and c) Notch-Delta-Jagged signaling mediated cell-cell communication, each of which can generate non-genetic heterogeneity through multistability and/or oscillations. Our results show how different coupling strengths between AR and EMT signaling can lead to monostability, bistability, or oscillations in the levels of AR, as well as propagation of oscillations to EMT dynamics. These results reveal the emergent dynamics of coupled oscillatory and multi-stable systems and unravel mechanisms by which non-genetic heterogeneity in AR levels can be generated, which can act as a barrier to most existing therapies for prostate cancer patients.
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Affiliation(s)
- Divyoj Singh
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
- Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Federico Bocci
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA;
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA
| | - Prakash Kulkarni
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
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23
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Subbalakshmi AR, Sahoo S, Biswas K, Jolly MK. A Computational Systems Biology Approach Identifies SLUG as a Mediator of Partial Epithelial-Mesenchymal Transition (EMT). Cells Tissues Organs 2021; 211:689-702. [PMID: 33567424 DOI: 10.1159/000512520] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/19/2020] [Indexed: 01/25/2023] Open
Abstract
Epithelial-mesenchymal plasticity comprises reversible transitions among epithelial, hybrid epithelial/mesenchymal (E/M) and mesenchymal phenotypes, and underlies various aspects of aggressive tumor progression such as metastasis, therapy resistance, and immune evasion. The process of cells attaining one or more hybrid E/M phenotypes is termed as partial epithelial mesenchymal transition (EMT). Cells in hybrid E/M phenotype(s) can be more aggressive than those in either fully epithelial or mesenchymal state. Thus, identifying regulators of hybrid E/M phenotypes is essential to decipher the rheostats of phenotypic plasticity and consequent accelerators of metastasis. Here, using a computational systems biology approach, we demonstrate that SLUG (SNAIL2) - an EMT-inducing transcription factor - can inhibit cells from undergoing a complete EMT and thus stabilize them in hybrid E/M phenotype(s). It expands the parametric range enabling the existence of a hybrid E/M phenotype, thereby behaving as a phenotypic stability factor. Our simulations suggest that this specific property of SLUG emerges from the topology of the regulatory network it forms with other key regulators of epithelial-mesenchymal plasticity. Clinical data suggest that SLUG associates with worse patient prognosis across multiple carcinomas. Together, our results indicate that SLUG can stabilize hybrid E/M phenotype(s).
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Affiliation(s)
- Ayalur R Subbalakshmi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Kuheli Biswas
- Department of Physical Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India,
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24
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Chedere A, Hari K, Kumar S, Rangarajan A, Jolly MK. Multi-Stability and Consequent Phenotypic Plasticity in AMPK-Akt Double Negative Feedback Loop in Cancer Cells. J Clin Med 2021; 10:jcm10030472. [PMID: 33530625 PMCID: PMC7865639 DOI: 10.3390/jcm10030472] [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: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/21/2021] [Indexed: 12/23/2022] Open
Abstract
Adaptation and survival of cancer cells to various stress and growth factor conditions is crucial for successful metastasis. A double-negative feedback loop between two serine/threonine kinases AMPK (AMP-activated protein kinase) and Akt can regulate the adaptation of breast cancer cells to matrix-deprivation stress. This feedback loop can significantly generate two phenotypes or cell states: matrix detachment-triggered pAMPKhigh/ pAktlow state, and matrix (re)attachment-triggered pAkthigh/ pAMPKlow state. However, whether these two cell states can exhibit phenotypic plasticity and heterogeneity in a given cell population, i.e., whether they can co-exist and undergo spontaneous switching to generate the other subpopulation, remains unclear. Here, we develop a mechanism-based mathematical model that captures the set of experimentally reported interactions among AMPK and Akt. Our simulations suggest that the AMPK-Akt feedback loop can give rise to two co-existing phenotypes (pAkthigh/ pAMPKlow and pAMPKhigh/pAktlow) in specific parameter regimes. Next, to test the model predictions, we segregated these two subpopulations in MDA-MB-231 cells and observed that each of them was capable of switching to another in adherent conditions. Finally, the predicted trends are supported by clinical data analysis of The Cancer Genome Atlas (TCGA) breast cancer and pan-cancer cohorts that revealed negatively correlated pAMPK and pAkt protein levels. Overall, our integrated computational-experimental approach unravels that AMPK-Akt feedback loop can generate multi-stability and drive phenotypic switching and heterogeneity in a cancer cell population.
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Affiliation(s)
- Adithya Chedere
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India; (A.C.); (S.K.)
| | - Kishore Hari
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
| | - Saurav Kumar
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India; (A.C.); (S.K.)
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Annapoorni Rangarajan
- Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India; (A.C.); (S.K.)
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
- Correspondence: (A.R.); (M.K.J.)
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
- Correspondence: (A.R.); (M.K.J.)
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25
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Zheng M, Niu Y, Bu J, Liang S, Zhang Z, Liu J, Guo L, Zhang Z, Wang Q. ESRP1 regulates alternative splicing of CARM1 to sensitize small cell lung cancer cells to chemotherapy by inhibiting TGF-β/Smad signaling. Aging (Albany NY) 2021; 13:3554-3572. [PMID: 33495408 PMCID: PMC7906186 DOI: 10.18632/aging.202295] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/08/2020] [Indexed: 12/23/2022]
Abstract
Epithelial splicing regulatory protein 1 (ESRP1) is an RNA-binding protein that regulates alternative splicing of mRNA. ESRP1 plays an important role in chemoresistance of various cancers, including breast cancer, colon cancer and non-small cell lung cancer. However, the role of ESRP1 and its mechanism in small cell lung cancer (SCLC) chemoresistance remains unclear. In this study, we found that ESRP1 is significantly downregulated in SCLC chemo-resistant cells compared with chemo-sensitive cells. Moreover, the expression of ESRP1 was significantly lower in SCLC tissues than that in normal adjacent tissues and positively correlated with overall survival. Overexpression of ESRP1 increased SCLC chemosensitivity, and induced cell apoptosis and cell cycle arrest, whereas knockdown of ESRP1 induced the opposite effects. ESRP1 could inhibit the growth of SCLC in vivo. Through mRNA transcriptome sequencing, we found that ESRP1 regulates coactivator-associated arginine methyltransferase 1 (CARM1) to produce two different transcripts CARM1FL and CARM1ΔE15 by alternative splicing. ESRP1 affects the chemoresistance of SCLC by changing the content of different transcripts of CARM1. Furthermore, CARM1 regulates arginine methylation of Smad7, activates the TGF-β/Smad pathway and induces epithelial-to-mesenchymal transition (EMT), thereby promoting SCLC chemoresistance. Collectively, our study firstly demonstrates that ESRP1 inhibits the TGF-β/Smad signaling pathway by regulating alternative splicing of CARM1, thereby reversing chemoresistance of SCLC. The splicing factor ESRP1 may serve as a new drug resistance marker molecule and a potential therapeutic target in SCLC patients.
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Affiliation(s)
- Meng Zheng
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuchun Niu
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Junguo Bu
- Department of Radiotherapy, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shumei Liang
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhilin Zhang
- Department of Radiotherapy, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Jianhua Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhihua Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Qiongyao Wang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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26
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Kulkarni P. Intrinsically Disordered Proteins: Insights from Poincaré, Waddington, and Lamarck. Biomolecules 2020; 10:E1490. [PMID: 33126482 PMCID: PMC7692701 DOI: 10.3390/biom10111490] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 10/12/2020] [Indexed: 12/28/2022] Open
Abstract
The past quarter-century may justly be referred to as a period analogous to the "Cambrian explosion" in the history of proteins. This period is marked by the appearance of the intrinsically disordered proteins (IDPs) on the scene since their discovery in the mid-1990s. Here, I first reflect on how we accidentally stumbled on these fascinating molecules. Next, I describe our research on the IDPs over the past decade and identify six areas as important for future research in this field. In addition, I draw on discoveries others in the field have made to present a more comprehensive essay. More specifically, I discuss the role of IDPs in two fundamental aspects of life: in phenotypic switching, and in multicellularity that marks one of the major evolutionary transitions. I highlight how serendipity, imagination, and an interdisciplinary approach embodying empirical evidence and theoretical insights from the works of Poincaré, Waddington, and Lamarck, shaped our thinking, and how this led us to propose the MRK hypothesis, a conceptual framework addressing phenotypic switching, the emergence of new traits, and adaptive evolution via nongenetic and IDP conformation-based mechanisms. Finally, I present a perspective on the evolutionary link between phenotypic switching and the origin of multicellularity.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Experimental Therapeutics, City of Hope, National Medical Center, Duarte, CA 91010, USA
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Subbalakshmi AR, Kundnani D, Biswas K, Ghosh A, Hanash SM, Tripathi SC, Jolly MK. NFATc Acts as a Non-Canonical Phenotypic Stability Factor for a Hybrid Epithelial/Mesenchymal Phenotype. Front Oncol 2020; 10:553342. [PMID: 33014880 PMCID: PMC7506140 DOI: 10.3389/fonc.2020.553342] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/13/2020] [Indexed: 12/23/2022] Open
Abstract
Metastasis remains the cause of over 90% of cancer-related deaths. Cells undergoing metastasis use phenotypic plasticity to adapt to their changing environmental conditions and avoid therapy and immune response. Reversible transitions between epithelial and mesenchymal phenotypes – epithelial–mesenchymal transition (EMT) and its reverse mesenchymal–epithelial transition (MET) – form a key axis of phenotypic plasticity during metastasis and therapy resistance. Recent studies have shown that the cells undergoing EMT/MET can attain one or more hybrid epithelial/mesenchymal (E/M) phenotypes, the process of which is termed as partial EMT/MET. Cells in hybrid E/M phenotype(s) can be more aggressive than those in either epithelial or mesenchymal state. Thus, it is crucial to identify the factors and regulatory networks enabling such hybrid E/M phenotypes. Here, employing an integrated computational-experimental approach, we show that the transcription factor nuclear factor of activated T-cell (NFATc) can inhibit the process of complete EMT, thus stabilizing the hybrid E/M phenotype. It increases the range of parameters enabling the existence of a hybrid E/M phenotype, thus behaving as a phenotypic stability factor (PSF). However, unlike previously identified PSFs, it does not increase the mean residence time of the cells in hybrid E/M phenotypes, as shown by stochastic simulations; rather it enables the co-existence of epithelial, mesenchymal and hybrid E/M phenotypes and transitions among them. Clinical data suggests the effect of NFATc on patient survival in a tissue-specific or context-dependent manner. Together, our results indicate that NFATc behaves as a non-canonical PSF for a hybrid E/M phenotype.
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Affiliation(s)
| | - Deepali Kundnani
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Kuheli Biswas
- Department of Physical Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Anandamohan Ghosh
- Department of Physical Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, United States.,Department of Biochemistry, All India Institute of Medical Sciences, Nagpur, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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Jiang L, Griffin CH, Wu R. SEGN: Inferring real-time gene networks mediating phenotypic plasticity. Comput Struct Biotechnol J 2020; 18:2510-2521. [PMID: 33005313 PMCID: PMC7516210 DOI: 10.1016/j.csbj.2020.08.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 12/13/2022] Open
Abstract
The capacity of an organism to alter its phenotype in response to environmental perturbations changes over developmental time and is a process determined by multiple genes that are co-expressed in intricate but organized networks. Characterizing the spatiotemporal change of such gene networks can offer insight into the genomic signatures underlying organismic adaptation, but it represents a major methodological challenge. Here, we integrate the holistic view of systems biology and the interactive notion of evolutionary game theory to reconstruct so-called systems evolutionary game networks (SEGN) that can autonomously detect, track, and visualize environment-induced gene networks along the time axis. The SEGN overcomes the limitations of traditional approaches by inferring context-specific networks, encapsulating bidirectional, signed, and weighted gene-gene interactions into fully informative networks, and monitoring the process of how networks topologically alter across environmental and developmental cues. Based on the design principle of SEGN, we perform a transcriptional plasticity study by culturing Euphrates poplar, a tree that can grow in the saline desert, in saline-free and saline-stress conditions. SEGN characterize previously unknown gene co-regulation that modulates the time trajectories of the trees' response to salt stress. As a marriage of multiple disciplines, SEGN shows its potential to interpret gene interdependence, predict how transcriptional co-regulation responds to various regimes, and provides a hint for exploring the mass, energetic, or signal basis that drives various types of gene interactions.
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Affiliation(s)
- Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Christopher H. Griffin
- Applied Research Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA 17033, USA
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29
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Vernot JP. Senescence-Associated Pro-inflammatory Cytokines and Tumor Cell Plasticity. Front Mol Biosci 2020; 7:63. [PMID: 32478091 PMCID: PMC7237636 DOI: 10.3389/fmolb.2020.00063] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
The well-recognized cell phenotypic heterogeneity in tumors is a great challenge for cancer treatment. Dynamic interconversion and movement within a spectrum of different cell phenotypes (cellular plasticity) with the acquisition of specific cell functions is a fascinating biological puzzle, that represent an additional difficulty for cancer treatment and novel therapies development. The understanding of the molecular mechanisms responsible for moving or stabilizing tumor cells within this spectrum of variable states constitutes a valuable tool to overcome these challenges. In particular, cell transitions between epithelial and mesenchymal phenotypes (EMT-MET) and de-and trans-differentiation processes are relevant, since it has been shown that they confer invasiveness, drug resistance, and metastatic ability, due to the simultaneous acquisition of stem-like cell properties. Multiple drivers participate in these cell conversions events. In particular, cellular senescence and senescence-associated soluble factors have been shown to unveil stem-like cell properties and cell plasticity. By modulating gradually the composition of their secretome and the time of exposure, senescent cells may have differential effect not only on tumor cells but also on surrounding cells. Intriguingly, tumor cells that scape from senescence acquire stem-like cell properties and aggressiveness. The reinforcement of senescence and inflammation by soluble factors and the participation of immune cells may provide a dynamic milieu having varied effects on cell transitions, reprogramming, plasticity, stemness and therefore heterogeneity. This will confer different epithelial/mesenchymal traits (hybrid phenotype) and stem-like cell properties, combinations of which, in a particular cell context, could be responsible for different cellular functions during cancer progression (survival, migration, invasion, colonization or proliferation). Additionally, cooperative behavior between cell subpopulations with different phenotypes/stemness functions could also modulate their cellular plasticity. Here, we will discuss the role of senescence and senescence-associated pro-inflammatory cytokines on the induction of cellular plasticity, their effect role in establishing particular states within this spectrum of cell phenotypes and how this is accompanied by stem-like cell properties that, as the epithelial transitions, may also have a continuum of characteristics providing tumor cells with functional adaptability specifically useful in the different stages of carcinogenesis.
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Affiliation(s)
- Jean Paul Vernot
- Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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30
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Wu C, Ding H, Wang S, Li Y, Liu SB, Wang X, Zheng J, Xue T, Amin HM, Song YH, Zhou J. DAXX inhibits cancer stemness and epithelial-mesenchymal transition in gastric cancer. Br J Cancer 2020; 122:1477-1485. [PMID: 32203224 PMCID: PMC7217831 DOI: 10.1038/s41416-020-0800-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND DAXX is a transcription repressor that has been implicated in several types of cancers, but its role in the development of gastric cancer remains unknown. METHODS We analysed the expression of DAXX in 83 pairs of gastric cancer samples, including neoplastic and adjacent tissues, and correlated the expression levels with clinical stages. We also investigated the molecular mechanisms by which DAXX downregulation promotes cancer growth using both in vitro and in vivo models. RESULTS DAXX was downregulated in advanced gastric cancer samples. The expression of DAXX inversely correlates with that of cancer stem cell markers CD44 and Oct4 in gastric cancer lines. DAXX overexpression in gastric cancer cells inhibited migration, invasion and epithelial- mesenchymal transition (EMT). The inhibition of EMT was achieved through the repression of SNAI3, a key inducer of EMT, by recruiting HDAC-1 into the nucleus. Using a xenograft mouse model, we demonstrated that the MKN45 cells formed smaller tumours when DAXX was overexpressed. Wild-type AGS cells were not able to form tumours in nude mice, but in contrast, formed visible tumours when DAXX was silenced in the cells. CONCLUSION We for the first time demonstrated that DAXX functions as a tumour suppressor in gastric cancer by inhibiting stem cell growth and EMT.
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Affiliation(s)
- Chaofan Wu
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Hui Ding
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Shuochen Wang
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Yangxin Li
- Department of Cardiovascular Surgery & Institute of Cardiovascular Science, First Affiliated Hospital of Soochow University, 215123, Suzhou, Jiangsu, P. R. China
| | - Song-Bai Liu
- Suzhou Vocational Health College, Suzhou Key Laboratory of Biotechnology for Laboratory Medicine, Suzhou, 215009, Jiangsu Province, China
| | - Xiaoxiao Wang
- Suzhou Vocational Health College, Suzhou Key Laboratory of Biotechnology for Laboratory Medicine, Suzhou, 215009, Jiangsu Province, China
| | - Jiqing Zheng
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Ting Xue
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China
| | - Hesham M Amin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, USA
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, P. R. China.
| | - Jin Zhou
- Department of General Surgery, the First Affiliated Hospital of Soochow University, Suzhou, P. R. China.
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31
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Sahoo S, Singh D, Chakraborty P, Jolly MK. Emergent Properties of the HNF4α-PPARγ Network May Drive Consequent Phenotypic Plasticity in NAFLD. J Clin Med 2020; 9:E870. [PMID: 32235813 PMCID: PMC7141525 DOI: 10.3390/jcm9030870] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/15/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common form of chronic liver disease in adults and children. It is characterized by excessive accumulation of lipids in the hepatocytes of patients without any excess alcohol intake. With a global presence of 24% and limited therapeutic options, the disease burden of NAFLD is increasing. Thus, it becomes imperative to attempt to understand the dynamics of disease progression at a systems-level. Here, we decoded the emergent dynamics of underlying gene regulatory networks that were identified to drive the initiation and the progression of NAFLD. We developed a mathematical model to elucidate the dynamics of the HNF4α-PPARγ gene regulatory network. Our simulations reveal that this network can enable multiple co-existing phenotypes under certain biological conditions: an adipocyte, a hepatocyte, and a "hybrid" adipocyte-like state of the hepatocyte. These phenotypes may also switch among each other, thus enabling phenotypic plasticity and consequently leading to simultaneous deregulation of the levels of molecules that maintain a hepatic identity and/or facilitate a partial or complete acquisition of adipocytic traits. These predicted trends are supported by the analysis of clinical data, further substantiating the putative role of phenotypic plasticity in driving NAFLD. Our results unravel how the emergent dynamics of underlying regulatory networks can promote phenotypic plasticity, thereby propelling the clinically observed changes in gene expression often associated with NAFLD.
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Affiliation(s)
- Sarthak Sahoo
- Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Divyoj Singh
- Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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32
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Jolly MK, Celià-Terrassa T. Dynamics of Phenotypic Heterogeneity Associated with EMT and Stemness during Cancer Progression. J Clin Med 2019; 8:E1542. [PMID: 31557977 PMCID: PMC6832750 DOI: 10.3390/jcm8101542] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic and phenotypic heterogeneity contribute to the generation of diverse tumor cell populations, thus enhancing cancer aggressiveness and therapy resistance. Compared to genetic heterogeneity, a consequence of mutational events, phenotypic heterogeneity arises from dynamic, reversible cell state transitions in response to varying intracellular/extracellular signals. Such phenotypic plasticity enables rapid adaptive responses to various stressful conditions and can have a strong impact on cancer progression. Herein, we have reviewed relevant literature on mechanisms associated with dynamic phenotypic changes and cellular plasticity, such as epithelial-mesenchymal transition (EMT) and cancer stemness, which have been reported to facilitate cancer metastasis. We also discuss how non-cell-autonomous mechanisms such as cell-cell communication can lead to an emergent population-level response in tumors. The molecular mechanisms underlying the complexity of tumor systems are crucial for comprehending cancer progression, and may provide new avenues for designing therapeutic strategies.
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Affiliation(s)
- Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.
| | - Toni Celià-Terrassa
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.
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33
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Bhatia S, Monkman J, Blick T, Pinto C, Waltham M, Nagaraj SH, Thompson EW. Interrogation of Phenotypic Plasticity between Epithelial and Mesenchymal States in Breast Cancer. J Clin Med 2019; 8:E893. [PMID: 31234417 PMCID: PMC6617164 DOI: 10.3390/jcm8060893] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/21/2022] Open
Abstract
Dynamic interconversions between transitional epithelial and mesenchymal states underpin the epithelial mesenchymal plasticity (EMP) seen in some carcinoma cell systems. We have delineated epithelial and mesenchymal subpopulations existing within the PMC42-LA breast cancer cell line by their EpCAM expression. These purified but phenotypically plastic states, EpCAMHigh (epithelial) and EpCAMLow (mesenchymal), have the ability to regain the phenotypic equilibrium of the parental population (i.e., 80% epithelial and 20% mesenchymal) over time, although the rate of reversion in the mesenchymal direction (epithelial-mesenchymal transition; EMT) is higher than that in the epithelial direction (mesenchymal-epithelial transition; MET). Single-cell clonal propagation was implemented to delineate the molecular and cellular features of this intrinsic heterogeneity with respect to EMP flux. The dynamics of the phenotypic proportions of epithelial and mesenchymal states in single-cell generated clones revealed clonal diversity and intrinsic plasticity. Single cell-derived clonal progenies displayed differences in their functional attributes of proliferation, stemness marker (CD44/CD24), migration, invasion and chemo-sensitivity. Interrogation of genomic copy number variations (CNV) with whole exome sequencing (WES) in the context of chromosome count from metaphase spread indicated that chromosomal instability was not influential in driving intrinsic phenotypic plasticity. Overall, these findings reveal the stochastic nature of both the epithelial and mesenchymal subpopulations, and the single cell-derived clones for differential functional attributes.
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Affiliation(s)
- Sugandha Bhatia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia.
- School of Biological/Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - James Monkman
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia.
- School of Biological/Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Tony Blick
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia.
- School of Biological/Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Cletus Pinto
- Invasion and Metastasis Unit, St. Vincent's Institute, Melbourne, VIC 3065, Australia.
- University of Melbourne Department of Surgery, St. Vincent's Hospital, Melbourne, VIC 3065, Australia.
| | - Mark Waltham
- Invasion and Metastasis Unit, St. Vincent's Institute, Melbourne, VIC 3065, Australia.
- University of Melbourne Department of Surgery, St. Vincent's Hospital, Melbourne, VIC 3065, Australia.
| | - Shivashankar H Nagaraj
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia.
- School of Biological/Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Erik W Thompson
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia.
- School of Biological/Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
- Invasion and Metastasis Unit, St. Vincent's Institute, Melbourne, VIC 3065, Australia.
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Bocci F, Tripathi SC, Vilchez Mercedes SA, George JT, Casabar JP, Wong PK, Hanash SM, Levine H, Onuchic JN, Jolly MK. NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype. Integr Biol (Camb) 2019; 11:251-263. [PMID: 31329868 PMCID: PMC6686740 DOI: 10.1093/intbio/zyz021] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/10/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022]
Abstract
The epithelial-mesenchymal transition (EMT) is a key process implicated in cancer metastasis and therapy resistance. Recent studies have emphasized that cells can undergo partial EMT to attain a hybrid epithelial/mesenchymal (E/M) phenotype - a cornerstone of tumour aggressiveness and poor prognosis. These cells can have enhanced tumour-initiation potential as compared to purely epithelial or mesenchymal ones and can integrate the properties of cell-cell adhesion and motility that facilitates collective cell migration leading to clusters of circulating tumour cells (CTCs) - the prevalent mode of metastasis. Thus, identifying the molecular players that can enable cells to maintain a hybrid E/M phenotype is crucial to curb the metastatic load. Using an integrated computational-experimental approach, we show that the transcription factor NRF2 can prevent a complete EMT and instead stabilize a hybrid E/M phenotype. Knockdown of NRF2 in hybrid E/M non-small cell lung cancer cells H1975 and bladder cancer cells RT4 destabilized a hybrid E/M phenotype and compromised the ability to collectively migrate to close a wound in vitro. Notably, while NRF2 knockout simultaneously downregulated E-cadherin and ZEB-1, overexpression of NRF2 enriched for a hybrid E/M phenotype by simultaneously upregulating both E-cadherin and ZEB-1 in individual RT4 cells. Further, we predict that NRF2 is maximally expressed in hybrid E/M phenotype(s) and demonstrate that this biphasic dynamic arises from the interconnections among NRF2 and the EMT regulatory circuit. Finally, clinical records from multiple datasets suggest a correlation between a hybrid E/M phenotype, high levels of NRF2 and its targets and poor survival, further strengthening the emerging notion that hybrid E/M phenotype(s) may occupy the 'metastatic sweet spot'.
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Affiliation(s)
- Federico Bocci
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, USA
- Current address: Department of Biochemistry, All India Institute of Medical Sciences, Nagpur, India
| | | | - Jason T George
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Julian P Casabar
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Pak Kin Wong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, USA
- Department of Mechanical Engineering and Department of Surgery, The Pennsylvania State University, University Park, PA, USA
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Physics and Astronomy, Rice University, Houston, TX, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
- Department of Physics and Astronomy, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Current address: Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
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Kulkarni V, Kulkarni P. Intrinsically disordered proteins and phenotypic switching: Implications in cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:63-84. [PMID: 31521237 DOI: 10.1016/bs.pmbts.2019.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It is now well established that intrinsically disordered proteins (IDPs) that constitute a large part of the proteome across the three kingdoms, play critical roles in several biological processes including phenotypic switching. However, dysregulated expression of IDPs that engage in promiscuous interactions can lead to pathological states. In this chapter, using cancer as a paradigm, we discuss how IDP conformational dynamics and the resultant conformational noise can modulate phenotypic switching. Thus, contrary to the prevailing wisdom that phenotypic switching is highly deterministic (has a genetic underpinning) in cancer, emerging evidence suggests that non-genetic mechanisms, at least in part due to the conformational noise, may also be a confounding factor in phenotypic switching.
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Affiliation(s)
- Vivek Kulkarni
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, United States.
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36
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Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level. Biomolecules 2019; 9:biom9020077. [PMID: 30813315 PMCID: PMC6406393 DOI: 10.3390/biom9020077] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/10/2019] [Accepted: 02/10/2019] [Indexed: 01/10/2023] Open
Abstract
Folded proteins show a high degree of structural order and undergo (fairly constrained) collective motions related to their functions. On the other hand, intrinsically disordered proteins (IDPs), while lacking a well-defined three-dimensional structure, do exhibit some structural and dynamical ordering, but are less constrained in their motions than folded proteins. The larger structural plasticity of IDPs emphasizes the importance of entropically driven motions. Many IDPs undergo function-related disorder-to-order transitions driven by their interaction with specific binding partners. As experimental techniques become more sensitive and become better integrated with computational simulations, we are beginning to see how the modest structural ordering and large amplitude collective motions of IDPs endow them with an ability to mediate multiple interactions with different partners in the cell. To illustrate these points, here, we use Prostate-associated gene 4 (PAGE4), an IDP implicated in prostate cancer (PCa) as an example. We first review our previous efforts using molecular dynamics simulations based on atomistic AWSEM to study the conformational dynamics of PAGE4 and how its motions change in its different physiologically relevant phosphorylated forms. Our simulations quantitatively reproduced experimental observations and revealed how structural and dynamical ordering are encoded in the sequence of PAGE4 and can be modulated by different extents of phosphorylation by the kinases HIPK1 and CLK2. This ordering is reflected in changing populations of certain secondary structural elements as well as in the regularity of its collective motions. These ordered features are directly correlated with the functional interactions of WT-PAGE4, HIPK1-PAGE4 and CLK2-PAGE4 with the AP-1 signaling axis. These interactions give rise to repeated transitions between (high HIPK1-PAGE4, low CLK2-PAGE4) and (low HIPK1-PAGE4, high CLK2-PAGE4) cell phenotypes, which possess differing sensitivities to the standard PCa therapies, such as androgen deprivation therapy (ADT). We argue that, although the structural plasticity of an IDP is important in promoting promiscuous interactions, the modulation of the structural ordering is important for sculpting its interactions so as to rewire with agility biomolecular interaction networks with significant functional consequences.
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Kulkarni P, Uversky VN. Intrinsically Disordered Proteins: The Dark Horse of the Dark Proteome. Proteomics 2018; 18:e1800061. [DOI: 10.1002/pmic.201800061] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/07/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research; City of Hope National Medical Center; Duarte CA 91010 USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa FL 33612 USA
- Laboratory of New methods in Biology; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino Moscow Region 142290 Russia
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38
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Lin X, Roy S, Jolly MK, Bocci F, Schafer NP, Tsai MY, Chen Y, He Y, Grishaev A, Weninger K, Orban J, Kulkarni P, Rangarajan G, Levine H, Onuchic JN. PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer. J Mol Biol 2018; 430:2422-2438. [PMID: 29758263 DOI: 10.1016/j.jmb.2018.05.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/13/2018] [Accepted: 05/07/2018] [Indexed: 11/15/2022]
Abstract
Prostate-associated gene 4 (PAGE4) is an intrinsically disordered protein implicated in prostate cancer. Thestress-response kinase homeodomain-interacting protein kinase 1 (HIPK1) phosphorylates two residues in PAGE4, serine 9 and threonine 51. Phosphorylation of these two residues facilitates the interaction of PAGE4 with activator protein-1 (AP-1) transcription factor complex to potentiate AP-1's activity. In contrast, hyperphosphorylation of PAGE4 by CDC-like kinase 2 (CLK2) attenuates this interaction with AP-1. Small-angleX-ray scattering and single-molecule fluorescence resonance energy transfer measurements have shown that PAGE4 expands upon hyperphosphorylation and that this expansion is localized to its N-terminal half. To understand the interactions underlying this structural transition, we performed molecular dynamics simulations using Atomistic AWSEM, a multi-scale molecular model that combines atomistic and coarse-grained simulation approaches. Our simulations show that electrostatic interactions drive transient formation of an N-terminal loop, the destabilization of which accounts for the dramatic change in size upon hyperphosphorylation. Phosphorylation also changes the preference of secondary structure formation of the PAGE4 ensemble, which leads to a transition between states that display different degrees of disorder. Finally, we construct a mechanism-based mathematical model that allows us to capture the interactions ofdifferent phosphoforms of PAGE4 with AP-1 and its downstream target, the androgen receptor (AR)-a key therapeutic target in prostate cancer. Our model predicts intracellular oscillatory dynamics of HIPK1-PAGE4, CLK2-PAGE4, and AR activity, indicating phenotypic heterogeneity in an isogenic cell population. Thus, conformational switching of PAGE4 may potentially affect the efficiency of therapeutically targeting AR activity.
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Affiliation(s)
- Xingcheng Lin
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States; Department of Physics and Astronomy, Rice University, Houston, TX 77005, United States
| | - Susmita Roy
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States
| | - Federico Bocci
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States; Department of Chemistry, Rice University, Houston, TX 77005, United States
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States; Department of Chemistry, Rice University, Houston, TX 77005, United States
| | - Min-Yeh Tsai
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States; Department of Chemistry, Rice University, Houston, TX 77005, United States
| | - Yihong Chen
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, United States
| | - Yanan He
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, United States
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, United States; National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, United States
| | - John Orban
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, United States; Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - Prakash Kulkarni
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, United States; Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, United States
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India; Center for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States; Department of Physics and Astronomy, Rice University, Houston, TX 77005, United States
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States; Department of Physics and Astronomy, Rice University, Houston, TX 77005, United States; Department of Chemistry, Rice University, Houston, TX 77005, United States; Department of BioSciences, Rice University, Houston, TX 77005, United States.
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Jolly MK, Kulkarni P, Weninger K, Orban J, Levine H. Phenotypic Plasticity, Bet-Hedging, and Androgen Independence in Prostate Cancer: Role of Non-Genetic Heterogeneity. Front Oncol 2018; 8:50. [PMID: 29560343 PMCID: PMC5845637 DOI: 10.3389/fonc.2018.00050] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 02/19/2018] [Indexed: 12/21/2022] Open
Abstract
It is well known that genetic mutations can drive drug resistance and lead to tumor relapse. Here, we focus on alternate mechanisms-those without mutations, such as phenotypic plasticity and stochastic cell-to-cell variability that can also evade drug attacks by giving rise to drug-tolerant persisters. The phenomenon of persistence has been well-studied in bacteria and has also recently garnered attention in cancer. We draw a parallel between bacterial persistence and resistance against androgen deprivation therapy in prostate cancer (PCa), the primary standard care for metastatic disease. We illustrate how phenotypic plasticity and consequent mutation-independent or non-genetic heterogeneity possibly driven by protein conformational dynamics can stochastically give rise to androgen independence in PCa, and suggest that dynamic phenotypic plasticity should be considered in devising therapeutic dosing strategies designed to treat and manage PCa.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Prakash Kulkarni
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, United States
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, United States
| | - John Orban
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, United States
- Department of Chemistry and Biochemistry, University of Maryland, College Park, College Park, United States
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
- Department of Bioengineering, Rice University, Houston, TX, United States
- Department of Physics and Astronomy, Rice University, Houston, TX, United States
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Ferrari N, Granata I, Capaia M, Piccirillo M, Guarracino MR, Venè R, Brizzolara A, Petretto A, Inglese E, Morini M, Astigiano S, Amaro AA, Boccardo F, Balbi C, Barboro P. Adaptive phenotype drives resistance to androgen deprivation therapy in prostate cancer. Cell Commun Signal 2017; 15:51. [PMID: 29216878 PMCID: PMC5721601 DOI: 10.1186/s12964-017-0206-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/28/2017] [Indexed: 12/21/2022] Open
Abstract
Background Prostate cancer (PCa), the second most common cancer affecting men worldwide, shows a broad spectrum of biological and clinical behaviour representing the epiphenomenon of an extreme heterogeneity. Androgen deprivation therapy is the mainstay of treatment for advanced forms but after few years the majority of patients progress to castration-resistant prostate cancer (CRPC), a lethal form that poses considerable therapeutic challenges. Methods Western blotting, immunocytochemistry, invasion and reporter assays, and in vivo studies were performed to characterize androgen resistant sublines phenotype in comparison to the parental cell line LNCaP. RNA microarray, mass spectrometry, integrative transcriptomic and proteomic differential analysis coupled with GeneOntology and multivariate analyses were applied to identify deregulated genes and proteins involved in CRPC evolution. Results Treating the androgen-responsive LNCaP cell line for over a year with 10 μM bicalutamide both in the presence and absence of 0.1 nM 5-α-dihydrotestosterone (DHT) we obtained two cell sublines, designated PDB and MDB respectively, presenting several analogies with CRPC. Molecular and functional analyses of PDB and MDB, compared to the parental cell line, showed that both resistant cell lines were PSA low/negative with comparable levels of nuclear androgen receptor devoid of activity due to altered phosphorylation; cell growth and survival were dependent on AKT and p38MAPK activation and PARP-1 overexpression; their malignant phenotype increased both in vitro and in vivo. Performing bioinformatic analyses we highlighted biological processes related to environmental and stress adaptation supporting cell survival and growth. We identified 15 proteins that could direct androgen-resistance acquisition. Eleven out of these 15 proteins were closely related to biological processes involved in PCa progression. Conclusions Our models suggest that environmental factors and epigenetic modulation can activate processes of phenotypic adaptation driving drug-resistance. The identified key proteins of these adaptive phenotypes could be eligible targets for innovative therapies as well as molecules of prognostic and predictive value. Electronic supplementary material The online version of this article (10.1186/s12964-017-0206-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicoletta Ferrari
- Molecular Oncology and Angiogenesis, Ospedale Policlinico San Martino, L.go R. Benzi 10, 16132, Genoa, Italy
| | - Ilaria Granata
- Institute for High Performance Computing and Networking (ICAR), National Research Council (CNR), Via Pietro Castellino 111, 80131, Naples, Italy
| | - Matteo Capaia
- Academic Unit of Medical Oncology, Ospedale Policlinico San Martino, L.go R. Benzi 10, 16132, Genoa, Italy
| | - Marina Piccirillo
- Institute for High Performance Computing and Networking (ICAR), National Research Council (CNR), Via Pietro Castellino 111, 80131, Naples, Italy
| | - Mario Rosario Guarracino
- Institute for High Performance Computing and Networking (ICAR), National Research Council (CNR), Via Pietro Castellino 111, 80131, Naples, Italy
| | - Roberta Venè
- Molecular Oncology and Angiogenesis, Ospedale Policlinico San Martino, L.go R. Benzi 10, 16132, Genoa, Italy
| | - Antonella Brizzolara
- Molecular Oncology and Angiogenesis, Ospedale Policlinico San Martino, L.go R. Benzi 10, 16132, Genoa, Italy
| | - Andrea Petretto
- Core Facilities-Proteomics Laboratory, Giannina Gaslini Institute, L.go G. Gaslini 5, 16147, Genoa, Italy
| | - Elvira Inglese
- Core Facilities-Proteomics Laboratory, Giannina Gaslini Institute, L.go G. Gaslini 5, 16147, Genoa, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, Giannina Gaslini Institute, L.go G. Gaslini 5, 16147, Genoa, Italy
| | - Simonetta Astigiano
- Immunology, Ospedale Policlinico San Martino, L.go R. Benzi 10, 16132, Genoa, Italy
| | - Adriana Agnese Amaro
- Molecular Pathology, Ospedale Policlinico San Martino, L.go R. Benzi 10, 16132, Genoa, Italy
| | - Francesco Boccardo
- Academic Unit of Medical Oncology, Ospedale Policlinico San Martino, L.go R. Benzi 10, 16132, Genoa, Italy.,Department of Internal Medicine and Medical Specialties, School of Medicine, University of Genova, L.go R. Benzi 10, 16132, Genoa, Italy
| | - Cecilia Balbi
- Academic Unit of Medical Oncology, Ospedale Policlinico San Martino, L.go R. Benzi 10, 16132, Genoa, Italy
| | - Paola Barboro
- Academic Unit of Medical Oncology, Ospedale Policlinico San Martino, L.go R. Benzi 10, 16132, Genoa, Italy.
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Jędroszka D, Orzechowska M, Hamouz R, Górniak K, Bednarek AK. Markers of epithelial-to-mesenchymal transition reflect tumor biology according to patient age and Gleason score in prostate cancer. PLoS One 2017; 12:e0188842. [PMID: 29206234 PMCID: PMC5714348 DOI: 10.1371/journal.pone.0188842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/14/2017] [Indexed: 11/19/2022] Open
Abstract
Introduction Prostate carcinoma (PRAD) is one of the most frequently diagnosed malignancies amongst men worldwide. It is well-known that androgen receptor (AR) plays a pivotal role in a vast majority of prostate tumors. However, recent evidence emerged stating that estrogen receptors (ERs) may also contribute to prostate tumor development. Moreover, progression and aggressiveness of prostate cancer may be associated with differential expression genes of epithelial-to-mesenchymal transition (EMT). Therefore we aimed to assess the significance of receptors status as well as EMT marker genes expression among PRAD patients in accordance to their age and Gleason score. Materials and methods We analyzed TCGA gene expression profiles of 497 prostate tumor samples according to 43 genes involved in EMT and 3 hormone receptor genes (AR, ESR1, ESR2) as well as clinical characteristic of cancer patients. Then patients were divided into four groups according to their age and 5 groups according to Gleason score. Next, we evaluated PRAD samples according to relationship between the set of variables in different combinations and compared differential expression in subsequent groups of patients. The analysis was applied using R packages: FactoMineR, gplots, RColorBrewer and NMF. Results MFA analysis resulted in distinct grouping of PRAD patients into four age categories according to expression level of AR, ESR1 and ESR2 with the most distinct group of age less than 50 years old. Further investigations indicated opposite expression profiles of EMT markers between different age groups as well as strong association of EMT gene expression with Gleason score. We found that depending on age of prostate cancer patients and Gleason score EMT genes with distinctly altered expression are: KRT18, KRT19, MUC1 and COL4A1, CTNNB1, SNAI2, ZEB1 and MMP3. Conclusions Our major observation is that prostate cancer from patients under 50 years old compared to older ones has entirely different EMT gene expression profiles showing potentially more aggressive invasive phenotype, despite Gleason score classification.
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Affiliation(s)
- Dorota Jędroszka
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
| | | | - Raneem Hamouz
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
| | - Karolina Górniak
- Department of Pathology, Medical University of Lodz, Lodz, Poland
| | - Andrzej K. Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
- * E-mail:
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Jolly MK, Ward C, Eapen MS, Myers S, Hallgren O, Levine H, Sohal SS. Epithelial-mesenchymal transition, a spectrum of states: Role in lung development, homeostasis, and disease. Dev Dyn 2017. [DOI: 10.1002/dvdy.24541] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics; Rice University; Houston Texas
| | - Chris Ward
- Institute of Cellular Medicine; Newcastle University; Newcastle upon Tyne United Kingdom
| | - Mathew Suji Eapen
- School of Health Sciences; Faculty of Health, University of Tasmania, Launceston, University of Tasmania; Hobart Tasmania Australia
- NHMRC Centre of Research Excellence for Chronic Respiratory Disease; University of Tasmania; Hobart Tasmania Australia
| | - Stephen Myers
- School of Health Sciences; Faculty of Health, University of Tasmania, Launceston, University of Tasmania; Hobart Tasmania Australia
| | - Oskar Hallgren
- Department of Experimental Medical Sciences; Department of Respiratory Medicine and Allergology, Lund University; Sweden
| | - Herbert Levine
- Center for Theoretical Biological Physics; Rice University; Houston Texas
| | - Sukhwinder Singh Sohal
- School of Health Sciences; Faculty of Health, University of Tasmania, Launceston, University of Tasmania; Hobart Tasmania Australia
- NHMRC Centre of Research Excellence for Chronic Respiratory Disease; University of Tasmania; Hobart Tasmania Australia
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43
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Jia D, Jolly MK, Kulkarni P, Levine H. Phenotypic Plasticity and Cell Fate Decisions in Cancer: Insights from Dynamical Systems Theory. Cancers (Basel) 2017; 9:E70. [PMID: 28640191 PMCID: PMC5532606 DOI: 10.3390/cancers9070070] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/13/2017] [Accepted: 06/13/2017] [Indexed: 01/11/2023] Open
Abstract
Waddington's epigenetic landscape, a famous metaphor in developmental biology, depicts how a stem cell progresses from an undifferentiated phenotype to a differentiated one. The concept of "landscape" in the context of dynamical systems theory represents a high-dimensional space, in which each cell phenotype is considered as an "attractor" that is determined by interactions between multiple molecular players, and is buffered against environmental fluctuations. In addition, biological noise is thought to play an important role during these cell-fate decisions and in fact controls transitions between different phenotypes. Here, we discuss the phenotypic transitions in cancer from a dynamical systems perspective and invoke the concept of "cancer attractors"-hidden stable states of the underlying regulatory network that are not occupied by normal cells. Phenotypic transitions in cancer occur at varying levels depending on the context. Using epithelial-to-mesenchymal transition (EMT), cancer stem-like properties, metabolic reprogramming and the emergence of therapy resistance as examples, we illustrate how phenotypic plasticity in cancer cells enables them to acquire hybrid phenotypes (such as hybrid epithelial/mesenchymal and hybrid metabolic phenotypes) that tend to be more aggressive and notoriously resilient to therapies such as chemotherapy and androgen-deprivation therapy. Furthermore, we highlight multiple factors that may give rise to phenotypic plasticity in cancer cells, such as (a) multi-stability or oscillatory behaviors governed by underlying regulatory networks involved in cell-fate decisions in cancer cells, and (b) network rewiring due to conformational dynamics of intrinsically disordered proteins (IDPs) that are highly enriched in cancer cells. We conclude by discussing why a therapeutic approach that promotes "recanalization", i.e., the exit from "cancer attractors" and re-entry into "normal attractors", is more likely to succeed rather than a conventional approach that targets individual molecules/pathways.
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Affiliation(s)
- Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
- Graduate Program in Systems, Synthetic and Physical Biology, Rice University, Houston, TX 77005, USA.
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
| | - Prakash Kulkarni
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA.
- Department of Biosciences, Rice University, Houston, TX 77005, USA.
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Jolly MK, Tripathi SC, Somarelli JA, Hanash SM, Levine H. Epithelial/mesenchymal plasticity: how have quantitative mathematical models helped improve our understanding? Mol Oncol 2017; 11:739-754. [PMID: 28548388 PMCID: PMC5496493 DOI: 10.1002/1878-0261.12084] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/11/2017] [Accepted: 05/18/2017] [Indexed: 12/17/2022] Open
Abstract
Phenotypic plasticity, the ability of cells to reversibly alter their phenotypes in response to signals, presents a significant clinical challenge to treating solid tumors. Tumor cells utilize phenotypic plasticity to evade therapies, metastasize, and colonize distant organs. As a result, phenotypic plasticity can accelerate tumor progression. A well‐studied example of phenotypic plasticity is the bidirectional conversions among epithelial, mesenchymal, and hybrid epithelial/mesenchymal (E/M) phenotype(s). These conversions can alter a repertoire of cellular traits associated with multiple hallmarks of cancer, such as metabolism, immune evasion, invasion, and metastasis. To tackle the complexity and heterogeneity of these transitions, mathematical models have been developed that seek to capture the experimentally verified molecular mechanisms and act as ‘hypothesis‐generating machines’. Here, we discuss how these quantitative mathematical models have helped us explain existing experimental data, guided further experiments, and provided an improved conceptual framework for understanding how multiple intracellular and extracellular signals can drive E/M plasticity at both the single‐cell and population levels. We also discuss the implications of this plasticity in driving multiple aggressive facets of tumor progression.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jason A Somarelli
- Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
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45
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Mooney SM, Talebian V, Jolly MK, Jia D, Gromala M, Levine H, McConkey BJ. The GRHL2/ZEB Feedback Loop-A Key Axis in the Regulation of EMT in Breast Cancer. J Cell Biochem 2017; 118:2559-2570. [PMID: 28266048 DOI: 10.1002/jcb.25974] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/03/2017] [Indexed: 12/17/2022]
Abstract
More than 90% of cancer-related deaths are caused by metastasis. Epithelial-to-Mesenchymal Transition (EMT) causes tumor cell dissemination while the reverse process, Mesenchymal-to-Epithelial Transition (MET) allows cancer cells to grow and establish a potentially deadly metastatic lesion. Recent evidence indicates that in addition to E and M, cells can adopt a stable hybrid Epithelial/Mesenchymal (E/M) state where they can move collectively leading to clusters of Circulating Tumor Cells-the "bad actors" of metastasis. EMT is postulated to occur in all four major histological breast cancer subtypes. Here, we identify a set of genes strongly correlated with CDH1 in 877 cancer cell lines, and differentially expressed genes in cell lines overexpressing ZEB1, SNAIL, and TWIST. GRHL2 and ESRP1 appear in both these sets and also correlate with CDH1 at the protein level in 40 breast cancer specimens. Next, we find that GRHL2 and CD24 expression coincide with an epithelial character in human mammary epithelial cells. Further, we show that high GRHL2 expression is highly correlated with worse relapse-free survival in all four subtypes of breast cancer. Finally, we integrate CD24, GRHL2, and ESRP1 into a mathematical model of EMT regulation to validate the role of these players in EMT. Our data analysis and modeling results highlight the relationships among multiple crucial EMT/MET drivers including ZEB1, GRHL2, CD24, and ESRP1, particularly in basal-like breast cancers, which are most similar to triple-negative breast cancer (TNBC) and are considered the most dangerous subtype. J. Cell. Biochem. 118: 2559-2570, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Steven M Mooney
- Department of Biology, University of Waterloo, Waterloo N2L3G1, ON, Canada
| | - Vida Talebian
- Department of Biology, University of Waterloo, Waterloo N2L3G1, ON, Canada
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston 77005, Texas.,Department of Bioengineering, Rice University, Houston 77005, Texas
| | - Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston 77005, Texas.,Program in Systems/Synthetic/Physical Biology, Rice University, Houston 77005, Texas
| | - Monica Gromala
- Department of Biology, University of Waterloo, Waterloo N2L3G1, ON, Canada
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston 77005, Texas.,Program in Systems/Synthetic/Physical Biology, Rice University, Houston 77005, Texas.,Department of Physics and Astronomy, Rice University, Houston 77005, Texas
| | - Brendan J McConkey
- Department of Biology, University of Waterloo, Waterloo N2L3G1, ON, Canada
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Kulkarni P. Intrinsically disordered proteins and prostate cancer: pouring new wine in an old bottle. Asian J Androl 2017; 18:659-61. [PMID: 27427556 PMCID: PMC5000785 DOI: 10.4103/1008-682x.184272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Prakash Kulkarni
- Protein Biophysics & Structural Biology Laboratory, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
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Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity. Proc Natl Acad Sci U S A 2017; 114:E2644-E2653. [PMID: 28289210 DOI: 10.1073/pnas.1700082114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) that lack a unique 3D structure and comprise a large fraction of the human proteome play important roles in numerous cellular functions. Prostate-Associated Gene 4 (PAGE4) is an IDP that acts as a potentiator of the Activator Protein-1 (AP-1) transcription factor. Homeodomain-Interacting Protein Kinase 1 (HIPK1) phosphorylates PAGE4 at S9 and T51, but only T51 is critical for its activity. Here, we identify a second kinase, CDC-Like Kinase 2 (CLK2), which acts on PAGE4 and hyperphosphorylates it at multiple S/T residues, including S9 and T51. We demonstrate that HIPK1 is expressed in both androgen-dependent and androgen-independent prostate cancer (PCa) cells, whereas CLK2 and PAGE4 are expressed only in androgen-dependent cells. Cell-based studies indicate that PAGE4 interaction with the two kinases leads to opposing functions. HIPK1-phosphorylated PAGE4 (HIPK1-PAGE4) potentiates c-Jun, whereas CLK2-phosphorylated PAGE4 (CLK2-PAGE4) attenuates c-Jun activity. Consistent with the cellular data, biophysical measurements (small-angle X-ray scattering, single-molecule fluorescence resonance energy transfer, and NMR) indicate that HIPK1-PAGE4 exhibits a relatively compact conformational ensemble that binds AP-1, whereas CLK2-PAGE4 is more expanded and resembles a random coil with diminished affinity for AP-1. Taken together, the results suggest that the phosphorylation-induced conformational dynamics of PAGE4 may play a role in modulating changes between PCa cell phenotypes. A mathematical model based on our experimental data demonstrates how differential phosphorylation of PAGE4 can lead to transitions between androgen-dependent and androgen-independent phenotypes by altering the AP-1/androgen receptor regulatory circuit in PCa cells.
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49
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Zambelli B, Uversky VN, Ciurli S. Nickel impact on human health: An intrinsic disorder perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1714-1731. [DOI: 10.1016/j.bbapap.2016.09.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/31/2016] [Accepted: 09/14/2016] [Indexed: 01/26/2023]
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