1
|
Padget RL, Zeitz MJ, Blair GA, Wu X, North MD, Tanenbaum MT, Stanley KE, Phillips CM, King DR, Lamouille S, Gourdie RG, Hoeker GS, Swanger SA, Poelzing S, Smyth JW. Acute Adenoviral Infection Elicits an Arrhythmogenic Substrate Prior to Myocarditis. Circ Res 2024; 134:892-912. [PMID: 38415360 PMCID: PMC11003857 DOI: 10.1161/circresaha.122.322437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Viral cardiac infection represents a significant clinical challenge encompassing several etiological agents, disease stages, complex presentation, and a resulting lack of mechanistic understanding. Myocarditis is a major cause of sudden cardiac death in young adults, where current knowledge in the field is dominated by later disease phases and pathological immune responses. However, little is known regarding how infection can acutely induce an arrhythmogenic substrate before significant immune responses. Adenovirus is a leading cause of myocarditis, but due to species specificity, models of infection are lacking, and it is not understood how adenoviral infection may underlie sudden cardiac arrest. Mouse adenovirus type-3 was previously reported as cardiotropic, yet it has not been utilized to understand the mechanisms of cardiac infection and pathology. METHODS We have developed mouse adenovirus type-3 infection as a model to investigate acute cardiac infection and molecular alterations to the infected heart before an appreciable immune response or gross cardiomyopathy. RESULTS Optical mapping of infected hearts exposes decreases in conduction velocity concomitant with increased Cx43Ser368 phosphorylation, a residue known to regulate gap junction function. Hearts from animals harboring a phospho-null mutation at Cx43Ser368 are protected against mouse adenovirus type-3-induced conduction velocity slowing. Additional to gap junction alterations, patch clamping of mouse adenovirus type-3-infected adult mouse ventricular cardiomyocytes reveals prolonged action potential duration as a result of decreased IK1 and IKs current density. Turning to human systems, we find human adenovirus type-5 increases phosphorylation of Cx43Ser368 and disrupts synchrony in human induced pluripotent stem cell-derived cardiomyocytes, indicating common mechanisms with our mouse whole heart and adult cardiomyocyte data. CONCLUSIONS Together, these findings demonstrate that adenoviral infection creates an arrhythmogenic substrate through direct targeting of gap junction and ion channel function in the heart. Such alterations are known to precipitate arrhythmias and likely contribute to sudden cardiac death in acutely infected patients.
Collapse
Affiliation(s)
- Rachel L. Padget
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
| | - Michael J. Zeitz
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
| | - Grace A. Blair
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
| | - Xiaobo Wu
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
| | - Michael D. North
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
| | | | - Kari E. Stanley
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
| | - Chelsea M. Phillips
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
| | - D. Ryan King
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
| | - Samy Lamouille
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Robert G. Gourdie
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
- Department of Biomedical Engineering and Mechanics, College of Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Gregory S. Hoeker
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
| | - Sharon A. Swanger
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Steven Poelzing
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
- Department of Biomedical Engineering and Mechanics, College of Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - James W. Smyth
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA 24016, USA
- Center for Vascular and Heart Research, FBRI at VTC, Roanoke, VA 24016, USA
- Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, USA
- Department of Biomedical Engineering and Mechanics, College of Engineering, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| |
Collapse
|
2
|
Lamouille S, Wheeler CE, Deaver SE, Zeitz MJ, Sheng Z, Gourdie RG, Smyth JW. Abstract 459: Targeting the non-junctional tumorigenic function of connexin43 in cancer cell plasticity. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Tumors are highly heterogeneous and dynamic, with both cancer cells and cancer stem cells (CSCs) displaying a high degree of plasticity contributing to metastasis and tumor recurrence following treatment. Epithelial-mesenchymal transition (EMT) enables cancer cells to acquire migratory and invasive characteristics, access the circulatory system, and metastasize. Moreover, EMT is associated with therapeutic resistance and CSC generation. Our previous research demonstrated a redistribution of the gap junction protein connexin43 (Cx43) from the plasma membrane to the cytosol during EMT. Using super-resolution STochastic Optical Reconstruction Microscopy (STORM), we have recently identified increased interaction of such intracellular Cx43 with microtubules during EMT and in primary glioblastoma (GBM) CSCs (GSCs). We further report a tumorigenic function for cytosolic Cx43/microtubule complexing in cancer cell and CSC proliferation, migration, and survival. Cx43 localization and activity is regulated by multiple sites for protein-protein interaction within the Cx43 carboxy-terminus (CT), including a tubulin binding domain. We employed a Cx43 mimetic peptide named JM2 (juxtamembrane 2) encompassing the microtubule binding sequence of the Cx43 CT. Following administration, JM2 efficiently and specifically disrupts the interaction of Cx43 with microtubules, inhibits GSC-derived neurosphere formation in vitro, and patient GBM-derived organoid growth ex vivo. Using an orthotopic GBM patient derived xenograft mouse model, we demonstrate in vivo that JM2 significantly decreases the number of GSCs within brain tumors, inhibits the formation of highly invasive GBM tumors, and increases mouse survival in combination with the chemotherapy alkylating agent temozolomide. Further examining the role of Cx43/microtubule complexing in the context of metastatic disease, we observed JM2 also decreases mesenchymal marker expression and inhibits cell migration and invasion in EMT models. Using an in vivo orthotopic breast cancer mouse model we find that intratumoral administration of JM2 prevents metastasis, significantly decreasing cancer cell lung colonization. Our findings validate targeting Cx43 complexing with microtubules, with JM2, as a novel therapeutic approach for cancer treatment through inhibition of EMT-associated increases in invasion and metastasis, and elimination of CSCs. Modulation of non-junctional Cx43 functions therefore represents a viable therapeutic approach to target cellular plasticity with broad therapeutic implications for many cancers.
Citation Format: Samy Lamouille, Christina E. Wheeler, Stacie E. Deaver, Michael J. Zeitz, Zhi Sheng, Robert G. Gourdie, James W. Smyth. Targeting the non-junctional tumorigenic function of connexin43 in cancer cell plasticity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 459.
Collapse
|
3
|
Zeitz MJ, Smyth JW. Gap Junctions and Ageing. Subcell Biochem 2023; 102:113-137. [PMID: 36600132 DOI: 10.1007/978-3-031-21410-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Gap junctions, comprising connexin proteins, create conduits directly coupling the cytoplasms of adjacent cells. Expressed in essentially all tissues, dynamic gap junction structures enable the exchange of small molecules including ions and second messengers, and are central to maintenance of homeostasis and synchronized excitability. With such diverse and critical roles throughout the body, it is unsurprising that alterations to gap junction and/or connexin expression and function underlie a broad array of age-related pathologies. From neurological dysfunction to cardiac arrhythmia and bone loss, it is hard to identify a human disease state that does not involve reduced, or in some cases inappropriate, intercellular communication to affect organ function. With a complex life cycle encompassing several key regulatory steps, pathological gap junction remodeling during ageing can arise from alterations in gene expression, translation, intracellular trafficking, and posttranslational modification of connexins. Connexin proteins are now known to "moonlight" and perform a variety of non-junctional functions in the cell, independent of gap junctions. Furthermore, connexin "hemichannels" on the cell surface can communicate with the extracellular space without ever coupling to an adjacent cell to form a gap junction channel. This chapter will focus primarily on gap junctions in ageing, but such non-junctional connexin functions will be referred to where appropriate and the full spectrum of connexin biology should be noted as potentially causative/contributing to some findings in connexin knockout animals, for example.
Collapse
Affiliation(s)
- Michael J Zeitz
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, USA.,FBRI Center for Vascular and Heart Research, Roanoke, VA, USA
| | - James W Smyth
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, USA. .,FBRI Center for Vascular and Heart Research, Roanoke, VA, USA. .,Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA, USA. .,Department of Basic Science Education, Virginia Tech Carilion School of Medicine, Roanoke, VA, USA.
| |
Collapse
|
4
|
Padget RL, Blair GA, North MD, King DR, Zeitz MJ, Tanenbaum MN, Hoeker GS, Swanger SA, Poelzing S, Smyth JW. Adenovirus increases arrhythmia susceptibility during acute cardiac infection. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r6175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rachel L. Padget
- Translational Biology, Medicine, and Health Graduate ProgramVirginia TechBlacksburgVA
- Virginia TechBlacksburgVA
| | - Grace A. Blair
- Fralin Biomedical Research InstituteRoanokeVA
- Translational Biology, Medicine, and Health Graduate ProgramFralin Biomedical Research InstituteRoanokeVA
| | | | - D. Ryan King
- Translational Biology, Medicine, and Health Graduate ProgramVirginia TechBlacksburgVA
- Virginia TechBlacksburgVA
| | | | | | | | - Sharon A. Swanger
- Fralin Biomedical Research InstituteRoanokeVA
- Department of Biomedical Sciences and PathobiologyFralin Biomedical Research InstituteRoanokeVA
| | - Steven Poelzing
- Fralin Biomedical Research InstituteRoanokeVA
- Department of Biomedical Engineering and MechanicsFralin Biomedical Research InstituteRoanokeVA
| | - James W. Smyth
- Fralin Biomedical Research InstituteRoanokeVA
- Department of BiologyFralin Biomedical Research InstituteRoanokeVA
| |
Collapse
|
5
|
Calhoun PJ, Phan AV, Taylor JD, James CC, Padget RL, Zeitz MJ, Smyth JW. Adenovirus targets transcriptional and posttranslational mechanisms to limit gap junction function. FASEB J 2020; 34:9694-9712. [PMID: 32485054 DOI: 10.1096/fj.202000667r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/05/2020] [Accepted: 05/12/2020] [Indexed: 01/19/2023]
Abstract
Adenoviruses are responsible for a spectrum of pathogenesis including viral myocarditis. The gap junction protein connexin43 (Cx43, gene name GJA1) facilitates rapid propagation of action potentials necessary for each heartbeat. Gap junctions also propagate innate and adaptive antiviral immune responses, but how viruses may target these structures is not understood. Given this immunological role of Cx43, we hypothesized that gap junctions would be targeted during adenovirus type 5 (Ad5) infection. We find reduced Cx43 protein levels due to decreased GJA1 mRNA transcripts dependent upon β-catenin transcriptional activity during Ad5 infection, with early viral protein E4orf1 sufficient to induce β-catenin phosphorylation. Loss of gap junction function occurs prior to reduced Cx43 protein levels with Ad5 infection rapidly inducing Cx43 phosphorylation events consistent with altered gap junction conductance. Direct Cx43 interaction with ZO-1 plays a critical role in gap junction regulation. We find loss of Cx43/ZO-1 complexing during Ad5 infection by co-immunoprecipitation and complementary studies in human induced pluripotent stem cell derived-cardiomyocytes reveal Cx43 gap junction remodeling by reduced ZO-1 complexing. These findings reveal specific targeting of gap junction function by Ad5 leading to loss of intercellular communication which would contribute to dangerous pathological states including arrhythmias in infected hearts.
Collapse
Affiliation(s)
- Patrick J Calhoun
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Allen V Phan
- Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | | | - Carissa C James
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA.,Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA, USA
| | - Rachel L Padget
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA.,Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA, USA
| | - Michael J Zeitz
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA
| | - James W Smyth
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| |
Collapse
|
6
|
James CC, Zeitz MJ, Calhoun PJ, Lamouille S, Smyth JW. Altered translation initiation of Gja1 limits gap junction formation during epithelial-mesenchymal transition. Mol Biol Cell 2018; 29:797-808. [PMID: 29467255 PMCID: PMC5905293 DOI: 10.1091/mbc.e17-06-0406] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is activated during development, wound healing, and pathologies including fibrosis and cancer metastasis. Hallmarks of EMT are remodeling of intercellular junctions and adhesion proteins, including gap junctions. The GJA1 mRNA transcript encoding the gap junction protein connexin43 (Cx43) has been demonstrated to undergo internal translation initiation, yielding truncated isoforms that modulate gap junctions. The PI3K/Akt/mTOR pathway is central to translation regulation and is activated during EMT, leading us to hypothesize that altered translation initiation would contribute to gap junction loss. Using TGF-β-induced EMT as a model, we find reductions in Cx43 gap junctions despite increased transcription and stabilization of Cx43 protein. Biochemical experiments reveal suppression of the internally translated Cx43 isoform, GJA1-20k in a Smad3 and ERK-dependent manner. Ectopic expression of GJA1-20k does not halt EMT, but is sufficient to rescue gap junction formation. GJA1-20k localizes to the Golgi apparatus, and using superresolution localization microscopy we find retention of GJA1-43k at the Golgi in mesenchymal cells lacking GJA1-20k. NativePAGE demonstrates that levels of GJA1-20k regulate GJA1-43k hexamer oligomerization, a limiting step in Cx43 trafficking. These findings reveal alterations in translation initiation as an unexplored mechanism by which the cell regulates Cx43 gap junction formation during EMT.
Collapse
Affiliation(s)
- Carissa C James
- Virginia Tech Carilion Research Institute and School of Medicine, Roanoke, VA 24016.,Graduate Program in Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Michael J Zeitz
- Virginia Tech Carilion Research Institute and School of Medicine, Roanoke, VA 24016
| | - Patrick J Calhoun
- Virginia Tech Carilion Research Institute and School of Medicine, Roanoke, VA 24016.,Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Samy Lamouille
- Virginia Tech Carilion Research Institute and School of Medicine, Roanoke, VA 24016
| | - James W Smyth
- Virginia Tech Carilion Research Institute and School of Medicine, Roanoke, VA 24016.,Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| |
Collapse
|
7
|
Entz M, George SA, Zeitz MJ, Raisch T, Smyth JW, Poelzing S. Heart Rate and Extracellular Sodium and Potassium Modulation of Gap Junction Mediated Conduction in Guinea Pigs. Front Physiol 2016; 7:16. [PMID: 26869934 PMCID: PMC4735342 DOI: 10.3389/fphys.2016.00016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/12/2016] [Indexed: 11/29/2022] Open
Abstract
Background: Recent studies suggested that cardiac conduction in murine hearts with narrow perinexi and 50% reduced connexin43 (Cx43) expression is more sensitive to relatively physiological changes of extracellular potassium ([K+]o) and sodium ([Na+]o). Purpose: Determine whether similar [K+]o and [Na+]o changes alter conduction velocity (CV) sensitivity to pharmacologic gap junction (GJ) uncoupling in guinea pigs. Methods: [K+]o and [Na+]o were varied in Langendorff perfused guinea pig ventricles (Solution A: [K+]o = 4.56 and [Na+]o = 153.3 mM. Solution B: [K+]o = 6.95 and [Na+]o = 145.5 mM). Gap junctions were inhibited with carbenoxolone (CBX) (15 and 30 μM). Epicardial CV was quantified by optical mapping. Perinexal width was measured with transmission electron microscopy. Total and phosphorylated Cx43 were evaluated by western blotting. Results: Solution composition did not alter CV under control conditions or with 15μM CBX. Decreasing the basic cycle length (BCL) of pacing from 300 to 160 ms decreased CV uniformly with both solutions. At 30 μM CBX, a change in solution did not alter CV either longitudinally or transversely at BCL = 300 ms. However, reducing BCL to 160 ms caused CV to decrease more in hearts perfused with Solution B than A. Solution composition did not alter perinexal width, nor did it change total or phosphorylated serine 368 Cx43 expression. These data suggest that the solution dependent CV changes were independent of altered perinexal width or GJ coupling. Action potential duration was always shorter in hearts perfused with Solution B than A, independent of pacing rate and/or CBX concentration. Conclusions: Increased heart rate and GJ uncoupling can unmask small CV differences caused by changing [K+]o and [Na+]o. These data suggest that modulating extracellular ionic composition may be a novel anti-arrhythmic target in diseases with abnormal GJ coupling, particularly when heart rate cannot be controlled.
Collapse
Affiliation(s)
- Michael Entz
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA; Virginia Tech Carilion Research Institute and Center for Heart and Regenerative Medicine, Virginia Polytechnic Institute and State UniversityRoanoke, VA, USA
| | - Sharon A George
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA; Virginia Tech Carilion Research Institute and Center for Heart and Regenerative Medicine, Virginia Polytechnic Institute and State UniversityRoanoke, VA, USA
| | - Michael J Zeitz
- Virginia Tech Carilion Research Institute and Center for Heart and Regenerative Medicine, Virginia Polytechnic Institute and State University Roanoke, VA, USA
| | - Tristan Raisch
- Virginia Tech Carilion Research Institute and Center for Heart and Regenerative Medicine, Virginia Polytechnic Institute and State UniversityRoanoke, VA, USA; Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - James W Smyth
- Virginia Tech Carilion Research Institute and Center for Heart and Regenerative Medicine, Virginia Polytechnic Institute and State UniversityRoanoke, VA, USA; Department of Biological Sciences, College of Science, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Steven Poelzing
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA; Virginia Tech Carilion Research Institute and Center for Heart and Regenerative Medicine, Virginia Polytechnic Institute and State UniversityRoanoke, VA, USA; Department of Biological Sciences, College of Science, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| |
Collapse
|
8
|
Ay F, Vu TH, Zeitz MJ, Varoquaux N, Carette JE, Vert JP, Hoffman AR, Noble WS. Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C. BMC Genomics 2015; 16:121. [PMID: 25887659 PMCID: PMC4369351 DOI: 10.1186/s12864-015-1236-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/12/2015] [Indexed: 12/02/2022] Open
Abstract
Background Several recently developed experimental methods, each an extension of the chromatin conformation capture (3C) assay, have enabled the genome-wide profiling of chromatin contacts between pairs of genomic loci in 3D. Especially in complex eukaryotes, data generated by these methods, coupled with other genome-wide datasets, demonstrated that non-random chromatin folding correlates strongly with cellular processes such as gene expression and DNA replication. Results We describe a genome architecture assay, tethered multiple 3C (TM3C), that maps genome-wide chromatin contacts via a simple protocol of restriction enzyme digestion and religation of fragments upon agarose gel beads followed by paired-end sequencing. In addition to identifying contacts between pairs of loci, TM3C enables identification of contacts among more than two loci simultaneously. We use TM3C to assay the genome architectures of two human cell lines: KBM7, a near-haploid chronic leukemia cell line, and NHEK, a normal diploid human epidermal keratinocyte cell line. We confirm that the contact frequency maps produced by TM3C exhibit features characteristic of existing genome architecture datasets, including the expected scaling of contact probabilities with genomic distance, megabase scale chromosomal compartments and sub-megabase scale topological domains. We also confirm that TM3C captures several known cell type-specific contacts, ploidy shifts and translocations, such as Philadelphia chromosome formation (Ph+) in KBM7. We confirm a subset of the triple contacts involving the IGF2-H19 imprinting control region (ICR) using PCR analysis for KBM7 cells. Our genome-wide analysis of pairwise and triple contacts demonstrates their preference for linking open chromatin regions to each other and for linking regions with higher numbers of DNase hypersensitive sites (DHSs) to each other. For near-haploid KBM7 cells, we infer whole genome 3D models that exhibit clustering of small chromosomes with each other and large chromosomes with each other, consistent with previous studies of the genome architectures of other human cell lines. Conclusion TM3C is a simple protocol for ascertaining genome architecture and can be used to identify simultaneous contacts among three or four loci. Application of TM3C to a near-haploid human cell line revealed large-scale features of chromosomal organization and multi-way chromatin contacts that preferentially link regions of open chromatin. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1236-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, 98195, WA, USA.
| | - Thanh H Vu
- Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, 94304, CA, USA.
| | - Michael J Zeitz
- Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, 94304, CA, USA.
| | - Nelle Varoquaux
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 35 rue St Honoré, Fontainebleau, 77300, France. .,Institut Curie, Paris, F-75248, France. .,U900, INSERM, ParisF-75248, France.
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, 94305, CA, USA.
| | - Jean-Philippe Vert
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 35 rue St Honoré, Fontainebleau, 77300, France. .,Institut Curie, Paris, F-75248, France. .,U900, INSERM, ParisF-75248, France.
| | - Andrew R Hoffman
- Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, 94304, CA, USA.
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, 98195, WA, USA. .,Department of Computer Science and Engineering, University of Washington, Seattle, 98195, WA, USA.
| |
Collapse
|
9
|
Zhang H, Zeitz MJ, Wang H, Niu B, Ge S, Li W, Cui J, Wang G, Qian G, Higgins MJ, Fan X, Hoffman AR, Hu JF. Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus. ACTA ACUST UNITED AC 2014; 204:61-75. [PMID: 24395636 PMCID: PMC3882787 DOI: 10.1083/jcb.201304152] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A long noncoding RNA directly builds an intrachromosomal interaction complex to establish allele-specific transcriptional gene silencing over a large chromosomal domain. Kcnq1ot1 is a long noncoding ribonucleic acid (RNA; lncRNA) that participates in the regulation of genes within the Kcnq1 imprinting domain. Using a novel RNA-guided chromatin conformation capture method, we demonstrate that the 5′ region of Kcnq1ot1 RNA orchestrates a long-range intrachromosomal loop between KvDMR1 and the Kcnq1 promoter that is required for maintenance of imprinting. PRC2 (polycomb repressive complex 2), which participates in the allelic repression of Kcnq1, is also recruited by Kcnq1ot1 RNA via EZH2. Targeted suppression of Kcnq1ot1 lncRNA prevents the creation of this long-range intrachromosomal loop and causes loss of Kcnq1 imprinting. These observations delineate a novel mechanism by which an lncRNA directly builds an intrachromosomal interaction complex to establish allele-specific transcriptional gene silencing over a large chromosomal domain.
Collapse
Affiliation(s)
- He Zhang
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun 130061, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Zeitz MJ, Lerner PP, Ay F, Van Nostrand E, Heidmann JD, Noble WS, Hoffman AR. Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome. Nucleus 2013; 4:487-93. [PMID: 24448439 DOI: 10.4161/nucl.27364] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
22q11.2 deletion syndrome (22q11DS) results from a hemizygous microdeletion on chromosome 22 and is characterized by extensive phenotypic variability. Penetrance of signs, including congenital heart, craniofacial, and neurobehavioral abnormalities, varies widely and is not well correlated with genotype. The three-dimensional structure of the genome may help explain some of this variability. The physical interaction profile of a given gene locus with other genetic elements, such as enhancers and co-regulated genes, contributes to its regulation. Thus, it is possible that regulatory interactions with elements outside the deletion region are disrupted in the disease state and modulate the resulting spectrum of symptoms. COMT, a gene within the commonly deleted ~3 Mb region has been implicated as a contributor to the neurological features frequently found in 22q11DS patients. We used this locus as bait in a 4C-seq experiment to investigate genome-wide interaction profiles in B lymphocyte and fibroblast cell lines derived from both 22q11DS and unaffected individuals. All normal B lymphocyte lines displayed local, conserved chromatin looping interactions with regions that are lost in atypical and distal deletions, which may mediate similarities between typical, atypical, and distal 22q11 deletion phenotypes. There are also distinct clusterings of cis interactions based on disease state. We identified regions of differential trans interactions present in normal, and lost in deletion-carrying, B lymphocyte cell lines. This data suggests that hemizygous chromosomal deletions such as 22q11DS can have widespread effects on chromatin organization, and may contribute to the inherent phenotypic variability.
Collapse
Affiliation(s)
- Michael J Zeitz
- Veterans Affairs Palo Alto Health Care System; Stanford University Medical School; Palo Alto, CA USA; Department of Genome Sciences; University of Washington; Seattle, WA USA; Department of Genetics and Department of Developmental Biology; Stanford University Medical Center; Stanford, CA USA; Department of Computer Science and Engineering; University of Washington; Seattle, WA USA
| | - Paula P Lerner
- Veterans Affairs Palo Alto Health Care System; Stanford University Medical School; Palo Alto, CA USA
| | - Ferhat Ay
- Department of Genome Sciences; University of Washington; Seattle, WA USA
| | - Eric Van Nostrand
- Department of Genetics and Department of Developmental Biology; Stanford University Medical Center; Stanford, CA USA
| | - Julia D Heidmann
- Veterans Affairs Palo Alto Health Care System; Stanford University Medical School; Palo Alto, CA USA
| | - William S Noble
- Department of Genome Sciences; University of Washington; Seattle, WA USA; Department of Computer Science and Engineering; University of Washington; Seattle, WA USA
| | - Andrew R Hoffman
- Veterans Affairs Palo Alto Health Care System; Stanford University Medical School; Palo Alto, CA USA
| |
Collapse
|
11
|
Zeitz MJ, Ay F, Heidmann JD, Lerner PL, Noble WS, Steelman BN, Hoffman AR. Genomic interaction profiles in breast cancer reveal altered chromatin architecture. PLoS One 2013; 8:e73974. [PMID: 24019942 PMCID: PMC3760796 DOI: 10.1371/journal.pone.0073974] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 07/24/2013] [Indexed: 11/18/2022] Open
Abstract
Gene transcription can be regulated by remote enhancer regions through chromosome looping either in cis or in trans. Cancer cells are characterized by wholesale changes in long-range gene interactions, but the role that these long-range interactions play in cancer progression and metastasis is not well understood. In this study, we used IGFBP3, a gene involved in breast cancer pathogenesis, as bait in a 4C-seq experiment comparing normal breast cells (HMEC) with two breast cancer cell lines (MCF7, an ER positive cell line, and MDA-MB-231, a triple negative cell line). The IGFBP3 long-range interaction profile was substantially altered in breast cancer. Many interactions seen in normal breast cells are lost and novel interactions appear in cancer lines. We found that in HMEC, the breast carcinoma amplified sequence gene family (BCAS) 1–4 were among the top 10 most significantly enriched regions of interaction with IGFBP3. 3D-FISH analysis indicated that the translocation-prone BCAS genes, which are located on chromosomes 1, 17, and 20, are in close physical proximity with IGFBP3 and each other in normal breast cells. We also found that epidermal growth factor receptor (EGFR), a gene implicated in tumorigenesis, interacts significantly with IGFBP3 and that this interaction may play a role in their regulation. Breakpoint analysis suggests that when an IGFBP3 interacting region undergoes a translocation an additional interaction detectable by 4C is gained. Overall, our data from multiple lines of evidence suggest an important role for long-range chromosomal interactions in the pathogenesis of cancer.
Collapse
Affiliation(s)
- Michael J. Zeitz
- Department of Medicine, Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, California, United States of America
- * E-mail:
| | - Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Julia D. Heidmann
- Department of Medicine, Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, California, United States of America
| | - Paula L. Lerner
- Department of Medicine, Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, California, United States of America
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
| | - Brandon N. Steelman
- Department of Medicine, Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, California, United States of America
| | - Andrew R. Hoffman
- Department of Medicine, Veterans Affairs Palo Alto Health Care System, Stanford University Medical School, Palo Alto, California, United States of America
| |
Collapse
|
12
|
Zeitz MJ, Mukherjee L, Bhattacharya S, Xu J, Berezney R. A probabilistic model for the arrangement of a subset of human chromosome territories in WI38 human fibroblasts. J Cell Physiol 2009; 221:120-9. [PMID: 19507193 DOI: 10.1002/jcp.21842] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
There is growing evidence that chromosome territories have a probabilistic non-random arrangement within the cell nucleus of mammalian cells. Other than their radial positioning, however, our knowledge of the degree and specificity of chromosome territory associations is predominantly limited to studies of pair-wise associations. In this study we have investigated the association profiles of eight human chromosome pairs (numbers 1, 2, 3, 4, 6, 7, 8, 9) in the cell nuclei of G(0)-arrested WI38 diploid lung fibroblasts. Associations between heterologous chromosome combinations ranged from 52% to 78% while the homologous chromosome pairs had much lower levels of association (3-25%). A geometric computational method termed the Generalized Median Graph enabled identification of the most probable arrangement of these eight chromosome pairs. Approximately 41% of the predicted associations are present in any given nucleus. The association levels of several chromosome pairs were very similar in a series of lung fibroblast cell lines but strikingly different in skin and colon derived fibroblast cells. We conclude that a large subset of human chromosomes has a preferred probabilistic arrangement in WI38 cells and that the resulting chromosomal associations show tissue origin specificity.
Collapse
Affiliation(s)
- Michael J Zeitz
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | | | | | | | | |
Collapse
|
13
|
Zeitz MJ, Marella NV, Malyavantham KS, Goetze S, Bode J, Raska I, Berezney R. Organization of the amplified type I interferon gene cluster and associated chromosome regions in the interphase nucleus of human osteosarcoma cells. Chromosome Res 2009; 17:305-19. [PMID: 19283497 DOI: 10.1007/s10577-009-9023-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Revised: 12/01/2008] [Accepted: 12/01/2008] [Indexed: 12/13/2022]
Abstract
The organization of the amplified type I interferon (IFN) gene cluster and surrounding chromosomal regions was studied in the interphase cell nucleus of the human osteosarcoma cell line MG63. Rather than being arranged in a linear ladder-like array as in mitotic chromosomes, a cluster of approximately 15 foci was detected that was preferentially associated along the periphery of both the cell nucleus and a chromosome territory containing components of chromosomes 4, 8, and 9. Interspersed within the IFN gene foci were corresponding foci derived from amplified centromere 4 and 9 sequences. Other copies of chromosomes 4 and 8 were frequently detected in pairs or higher-order arrays lacking discrete borders between the chromosomes. In contrast, while chromosomes 4 and 8 in normal WI38 human fibroblast and osteoblast cells were occasionally found to associate closely, discrete boundaries were always detected between the two. DNA replication timing of the IFN gene cluster in early- to mid-S phase of WI38 cells was conserved in the amplified IFN gene cluster of MG63. Quantitative RT-PCR demonstrated a approximately 3-fold increase in IFN beta transcripts in MG63 compared with WI38 and RNA/DNA FISH experiments revealed 1-5 foci of IFN beta transcripts per cell with only approximately 5% of the cells showing foci within the highly amplified IFN gene cluster.
Collapse
Affiliation(s)
- Michael J Zeitz
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | | | | | | | | | | | | |
Collapse
|