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Shukla V, Rao M, Zhang H, Beers J, Wangsa D, Wangsa D, Buishand FO, Wang Y, Yu Z, Stevenson HS, Reardon ES, McLoughlin KC, Kaufman AS, Payabyab EC, Hong JA, Zhang M, Davis S, Edelman D, Chen G, Miettinen MM, Restifo NP, Ried T, Meltzer PA, Schrump DS. ASXL3 Is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer. Cancer Res 2017; 77:6267-6281. [PMID: 28935813 DOI: 10.1158/0008-5472.can-17-0570] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/28/2017] [Accepted: 09/07/2017] [Indexed: 01/16/2023]
Abstract
In this study, we generated induced pluripotent stem cells (iPSC) from normal human small airway epithelial cells (SAEC) to investigate epigenetic mechanisms of stemness and pluripotency in lung cancers. We documented key hallmarks of reprogramming in lung iPSCs (Lu-iPSC) that coincided with modulation of more than 15,000 genes relative to parental SAECs. Of particular novelty, we identified the PRC2-associated protein, ASXL3, which was markedly upregulated in Lu-iPSCs and small cell lung cancer (SCLC) lines and clinical specimens. ASXL3 overexpression correlated with increased genomic copy number in SCLC lines. ASXL3 silencing inhibited proliferation, clonogenicity, and teratoma formation by Lu-iPSCs, and diminished clonogenicity and malignant growth of SCLC cells in vivo Collectively, our studies validate the utility of the Lu-iPSC model for elucidating epigenetic mechanisms contributing to pulmonary carcinogenesis and highlight ASXL3 as a novel candidate target for SCLC therapy. Cancer Res; 77(22); 6267-81. ©2017 AACR.
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Affiliation(s)
- Vivek Shukla
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Mahadev Rao
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Hongen Zhang
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | | | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Danny Wangsa
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | | | - Yonghong Wang
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Zhiya Yu
- Laboratory of Pathology, Center for Cancer Research, NCI, Rockville, Maryland
| | - Holly S Stevenson
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Emily S Reardon
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Kaitlin C McLoughlin
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Andrew S Kaufman
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Eden C Payabyab
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Julie A Hong
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Mary Zhang
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Sean Davis
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Daniel Edelman
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | | | - Markku M Miettinen
- Laboratory of Pathology, Center for Cancer Research, NCI, Rockville, Maryland
| | | | - Thomas Ried
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - Paul A Meltzer
- Genetics Branch, Center for Cancer Research, NCI, Rockville, Maryland
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, NCI, Rockville, Maryland.
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Notwell JH, Chung T, Heavner W, Bejerano G. A family of transposable elements co-opted into developmental enhancers in the mouse neocortex. Nat Commun 2015; 6:6644. [PMID: 25806706 PMCID: PMC4438107 DOI: 10.1038/ncomms7644] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/13/2015] [Indexed: 12/27/2022] Open
Abstract
The neocortex is a mammalian-specific structure that is responsible for higher functions such as cognition, emotion and perception. To gain insight into its evolution and the gene regulatory codes that pattern it, we studied the overlap of its active developmental enhancers with transposable element (TE) families and compared this overlap to uniformly shuffled enhancers. Here we show a striking enrichment of the MER130 repeat family among active enhancers in the mouse dorsal cerebral wall, which gives rise to the neocortex, at embryonic day 14.5. We show that MER130 instances preserve a common code of transcriptional regulatory logic, function as enhancers and are adjacent to critical neocortical genes. MER130, a nonautonomous interspersed TE, originates in the tetrapod or possibly Sarcopterygii ancestor, which far predates the appearance of the neocortex. Our results show that MER130 elements were recruited, likely through their common regulatory logic, as neocortical enhancers.
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Affiliation(s)
- James H Notwell
- Department of Computer Science, Stanford University, 279 Campus Drive West (MC 5329), Beckman Center B-300, Stanford, California 94305-5329, USA
| | - Tisha Chung
- Department of Developmental Biology, Stanford University, 279 Campus Drive West (MC 5329), Beckman Center B-300, Stanford, California 94305-5329, USA
| | - Whitney Heavner
- 1] Department of Developmental Biology, Stanford University, 279 Campus Drive West (MC 5329), Beckman Center B-300, Stanford, California 94305-5329, USA [2] Department of Biology, Stanford University, 279 Campus Drive West (MC 5329), Beckman Center B-300, Stanford, California 94305-5329, USA
| | - Gill Bejerano
- 1] Department of Computer Science, Stanford University, 279 Campus Drive West (MC 5329), Beckman Center B-300, Stanford, California 94305-5329, USA [2] Department of Developmental Biology, Stanford University, 279 Campus Drive West (MC 5329), Beckman Center B-300, Stanford, California 94305-5329, USA [3] Department of Pediatrics, Division of Medical Genetics, Stanford University, 279 Campus Drive West (MC 5329), Beckman Center B-300, Stanford, California 94305-5329, USA
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Lowe CB, Haussler D. 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS One 2012; 7:e43128. [PMID: 22952639 PMCID: PMC3428314 DOI: 10.1371/journal.pone.0043128] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 07/17/2012] [Indexed: 11/18/2022] Open
Abstract
Recent research supports the view that changes in gene regulation, as opposed to changes in the genes themselves, play a significant role in morphological evolution. Gene regulation is largely dependent on transcription factor binding sites. Researchers are now able to use the available 29 mammalian genomes to measure selective constraint at the level of binding sites. This detailed map of constraint suggests that mammalian genomes co-opt fragments of mobile elements to act as gene regulatory sequence on a large scale. In the human genome we detect over 280,000 putative regulatory elements, totaling approximately 7 Mb of sequence, that originated as mobile element insertions. These putative regulatory regions are conserved non-exonic elements (CNEEs), which show considerable cross-species constraint and signatures of continued negative selection in humans, yet do not appear in a known mature transcript. These putative regulatory elements were co-opted from SINE, LINE, LTR and DNA transposon insertions. We demonstrate that at least 11%, and an estimated 20%, of gene regulatory sequence in the human genome showing cross-species conservation was co-opted from mobile elements. The location in the genome of CNEEs co-opted from mobile elements closely resembles that of CNEEs in general, except in the centers of the largest gene deserts where recognizable co-option events are relatively rare. We find that regions of certain mobile element insertions are more likely to be held under purifying selection than others. In particular, we show 6 examples where paralogous instances of an often co-opted mobile element region define a sequence motif that closely matches a transcription factor's binding profile.
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Affiliation(s)
- Craig B. Lowe
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - David Haussler
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
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Smith JJ, Sumiyama K, Amemiya CT. A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. Mol Biol Evol 2011; 29:985-93. [PMID: 22045999 DOI: 10.1093/molbev/msr267] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Emerging data from the coelacanth genome are beginning to shed light on the origin and evolution of tetrapod genes and noncoding elements. Of particular relevance is the realization that coelacanth retains active copies of transposable elements that once served as raw material for the evolution of new functional sequences in the vertebrate lineage. Recognizing the evolutionary significance of coelacanth genome in this regard, we employed an ab initio search strategy to further classify its repetitive complement. This analysis uncovered a class of interspersed elements (Latimeria Harbinger 1-LatiHarb1) that is a major contributor to coelacanth genome structure and gene content (∼1% to 4% or the genome). Sequence analyses indicate that 1) each ∼8.7 kb LatiHarb1 element contains two coding regions, a transposase gene and a gene whose function is as yet unknown (MYB-like) and 2) copies of LatiHarb1 retain biological activity in the coelacanth genome. Functional analyses verify transcriptional and enhancer activities of LatiHarb1 in vivo and reveal transcriptional decoupling that could permit MYB-like genes to play functional roles not directly linked to transposition. Thus, LatiHarb1 represents the first known instance of a harbinger-superfamily transposon with contemporary activity in a vertebrate genome. Analyses of LatiHarb1 further corroborate the notion that exaptation of anciently active harbinger elements gave rise to at least two vertebrate genes (harbi1 and naif1) and indicate that the vertebrate gene tsnare1 also traces its ancestry to this transposon superfamily. Based on our analyses of LatiHarb1, we speculate that several functional features of harbinger elements may predispose the transposon superfamily toward recurrent exaptive evolution of cellular coding genes. In addition, these analyses further reinforce the broad utility of the coelacanth genome and other "outgroup" genomes in understanding the ancestry and evolution of vertebrate genes and genomes.
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Affiliation(s)
- Jeramiah J Smith
- Benaroya Research Institute at Virginia Mason Medical Center, Seattle, WA, USA.
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The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 2011; 477:587-91. [PMID: 21881562 PMCID: PMC3184186 DOI: 10.1038/nature10390] [Citation(s) in RCA: 473] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 07/27/2011] [Indexed: 01/10/2023]
Abstract
The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments1. Among amniotes, genome sequences are available for mammals2 and birds3–5, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes3. Also, A. carolinensis mobile elements are very young and diverse – more so than in any other sequenced amniote genome. This lizard genome’s GC content is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds6. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
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