Submitted Successfully!
Thank you for your contribution! You can also upload a video entry related to this topic through the link below:
https://encyclopedia.pub/user/video_add?id=14963
Check Note
2000/2000
Ver. Summary Created by Modification Content Size Created at Operation
1 + 1318 word(s) 1318 2021-10-09 07:57:37 |
2 Done Meta information modification 1318 2021-10-12 04:05:47 |
Gene Amplification
Edit
Upload a video

Oncogene amplification is closely linked to the pathogenesis of a broad spectrum of human malignant tumors. The amplified genes localize either to the extrachromosomal circular DNA, which has been referred to as cytogenetically visible double minutes (DMs), or submicroscopic episome, or to the chromosomal homogeneously staining region (HSR). The extrachromosomal circle from a chromosome arm can initiate gene amplification, resulting in the formation of DMs or HSR, if it had a sequence element required for replication initiation (the replication initiation region/matrix attachment region; the IR/MAR), under a genetic background that permits gene amplification.

  • gene amplification
  • extrachromosomal DNA
  • double minutes
  • micronucleus
  • cancer
  • genome plasticity
  • chromothripsis
  • gene expression
  • repeat-induced gene silencing
Information
Contributor :
View Times: 64
Revisions: 2 times (View History)
Update Time: 12 Oct 2021

1. Gene Amplification and the Extrachromosomal Circles in Human Cancer

The amplification of oncogenes or drug-resistant genes plays a pivotal role in human cell malignant transformation by conferring growth advantage to the cells through the overproduction of the amplified gene product. A classical cytogenetic study located the amplified genes at the extrachromosomal double minutes (DMs) or the chromosomal homogeneously staining region (HSR) [1]. DMs and HSR mutually interconvert [2][3], and share the same sequence [4]. DMs are stable extrachromosomal elements that contain circular DNA. Circularity has been suggested based on electron microscopy [5], sensitivity to radiation-mediated breakage [6], and the absence of telomeric structures [7]; this was recently re-enforced by integrating ultrastructural imaging, long-range optical mapping, and computational analysis of whole-genome sequencing [8]. In contrast, cytogenetically undetectable circular DNA has been identified in many normal and cancer cell lines and normal tissues more than three decades ago [9]. Recently, many reports have described circular extrachromosomal DNA in normal or cancer cells [10]. In general, the circles in normal cells [11][12] were smaller in size (less than 1 kbp) than those in cancer cells (1–2 Mbp) [13]. The former is referred to as extrachromosomal closed circular DNA (eccDNA), and the latter are referred to as extrachromosomal DNA (ecDNA). EcDNAs are equivalent to conventional DMs; however, the term ecDNA was recently used instead of DMs because it does not always appear as a doublet among the chromosome spread specimens. Several extensive studies that used a large number of clinical samples together with the most advanced techniques, unambiguously, reinforced the tight relationship between malignancy and the appearance of ecDNA/DMs [13][14].

It is important to note that gene expression from the same amplicon sequence is higher in the extrachromosomal context than in the chromosomal context [15] because the chromatin of extrachromosomal DNA is more favorable for gene expression [8][16]. Consistently, DMs were replicated early in the S phase, while the HSRs of the same amplicon were replicated at the end of the S phase [4]. The higher gene expression may reflect the circular nature that poses a topological constraint that favors DNA helix unwinding [8]. Alternatively, I now propose that it may reflect the plausible localization of extrachromosomal elements in the interchromosome domain (ICD)compartment, where gene expression is favored [17].

2. Gene Amplification and the Extrachromosomal Circles in Human Cancer

The amplification of oncogenes or drug-resistant genes plays a pivotal role in human cell malignant transformation by conferring growth advantage to the cells through the overproduction of the amplified gene product. A classical cytogenetic study located the amplified genes at the extrachromosomal double minutes (DMs) or the chromosomal homogeneously staining region (HSR) [1]. DMs and HSR mutually interconvert [2][3], and share the same sequence [4]. DMs are stable extrachromosomal elements that contain circular DNA. Circularity has been suggested based on electron microscopy [5], sensitivity to radiation-mediated breakage [6], and the absence of telomeric structures [7]; this was recently re-enforced by integrating ultrastructural imaging, long-range optical mapping, and computational analysis of whole-genome sequencing [8]. In contrast, cytogenetically undetectable circular DNA has been identified in many normal and cancer cell lines and normal tissues more than three decades ago [9]. Recently, many reports have described circular extrachromosomal DNA in normal or cancer cells [10]. In general, the circles in normal cells [11][12] were smaller in size (less than 1 kbp) than those in cancer cells (1–2 Mbp) [13]. The former is referred to as extrachromosomal closed circular DNA (eccDNA), and the latter are referred to as extrachromosomal DNA (ecDNA). EcDNAs are equivalent to conventional DMs; however, the term ecDNA was recently used instead of DMs because it does not always appear as a doublet among the chromosome spread specimens. Several extensive studies that used a large number of clinical samples together with the most advanced techniques, unambiguously, reinforced the tight relationship between malignancy and the appearance of ecDNA/DMs [13][14].

It is important to note that gene expression from the same amplicon sequence is higher in the extrachromosomal context than in the chromosomal context [15] because the chromatin of extrachromosomal DNA is more favorable for gene expression [8][16]. Consistently, DMs were replicated early in the S phase, while the HSRs of the same amplicon were replicated at the end of the S phase [4]. The higher gene expression may reflect the circular nature that poses a topological constraint that favors DNA helix unwinding [8]. Alternatively, I now propose that it may reflect the plausible localization of extrachromosomal elements in the interchromosome domain (ICD)compartment, where gene expression is favored [17].

3. From Chromosome Arm to Gene Amplification

The episome/eccDNA bearing the IR/MAR sequence was multimerized to generate larger and complex DMs/ecDNAs. The mechanism that generates an initial small circle from the chromosome arm was discussed as follows: The most plausible mechanism is chromothripsis, which is mediated by micronuclei. Chromothripsis has been suggested by cancer genomics, and it involves the abrupt fragmentation of a specific chromosome followed by re-ligation and extensive rearrangement of many fragments [18][19]. The fragmentation of a specific chromosome might occur in micronuclei [20][21] if the nuclear membrane of the micronuclei ruptures [22][23]. It has been reported that replication [24] and transcription [25] are defective in lamina-negative micronuclei. The re-ligation of the fragment produces a large number of circular molecules [26]. Among such circles, the circles with IR/MAR would be amplified as described above. A model system reproduces this process in culture [27]. It is known that human chromosomes are specifically eliminated in human-rodent hybrid cells. In such hybrids, the human chromosome was selectively incorporated into micronuclei because of the malfunctioning of the human centromere in such hybrids. Then, the micronuclear content was broken, and the human chromosome was eliminated. Importantly, there remained numerous acentric stable DMs with a mark of the human genome, that is, Alu, among stable rodent chromosomes. Such DMs are composed of a patchwork of sequences derived from multiple human chromosome regions, consistent with the structure of natural DMs/ecDNA in human cancer [28].

4. Applications of the Extrachromosomal Element-Mediated Gene Amplification

The circular plasmid DNA bearing the IR/MAR mimics gene amplification, thus providing an excellent model to study genetic plasticity associated with human malignancy. Furthermore, the system provides a novel platform for recombinant protein production, whose efficiency needs to be increased, especially in the case of biopharmaceutical production. However, this application has two major limitations. One is the cell-type dependency of the amplification efficiency ([29] our unpublished results). The problem was technically solved by amplifying the target genes on the artificial chromosome [30][31] in the amplification-prone cells, followed by its transfer to the amplification-difficult cells by micronuclei-mediated chromosome transfer [31]. Another problem was that the amplification produced an ordered tandem repeat, which was subjected to repeat-induced gene silencing (RIGS; [32][33]). RIGS is an important cellular mechanism that heterochromatinizes the pericentric region to increase mechanical strength [34], prevent transposon spreading [35], or silence transgenes [36][37]. The problem was, at least in part, overcome by the finding that RIGS is sequence-dependent [38]. Some sequences, which included the core IR [39], the MAR, or the human genomic B-3-31 sequence, resulted in a reverse phenomenon, that is, repeat-induced gene activation (RIGA), while other sequences, which included bacterial plasmid, phage, or human transposon sequences, resulted in RIGS. Furthermore, knock-out of a histone deacetylase SIRT1 might alleviate RIGS, in combination with butyrate treatment, which inhibits another type of histone deacetylase [40]. Therefore, we are now able to amplify sequences of interest that are not subject to RIGS. We anticipate an increase in recombinant production in a gene number-dependent manner from the amplified recombinant genes.

References

  1. Cowell, J.K. Double minutes and homogenously staining regions: Gene amplification in mammalian cells. Annu. Rev. Genet. 1982, 16, 21–59.
  2. Wahl, G.M. The importance of circular DNA in mammalian gene amplification. Cancer Res. 1989, 49, 1333–1340.
  3. Von Hoff, D.D.; Forseth, B.; Clare, C.N.; Hansen, K.L.; VanDevanter, D. Double minutes arise from circular extrachromosomal DNA intermediates which integrate into chromosomal sites in human HL-60 leukemia cells. J. Clin. Investig. 1990, 85, 1887–1895.
  4. Shimizu, N.; Ochi, T.; Itonaga, K. Replication timing of amplified genetic regions relates to intranuclear localization but not to genetic activity or G/R band. Exp. Cell Res. 2001, 268, 201–210.
  5. Hamkalo, B.A.; Farnham, P.J.; Johnston, R.; Schimke, R.T. Ultrastructural features of minute chromosomes in a methotrexate-resistant mouse 3T3 cell line. Proc. Natl. Acad. Sci. USA 1985, 82, 1026–1030.
  6. VanDevanter, D.R.; Piaskowski, V.D.; Casper, J.T.; Douglass, E.C.; Von Hoff, D.D. Ability of circular extrachromosomal DNA molecules to carry amplified MYCN proto-oncogenes in human neuroblastomas in vivo. J. Natl. Cancer Inst. 1990, 82, 1815–1821.
  7. Lin, C.C.; Meyne, J.; Sasi, R.; Moyzis, R.K. Apparent lack of telomere sequences on double minute chromosomes. Cancer Genet. Cytogenet. 1990, 48, 271–274.
  8. Wu, S.; Turner, K.M.; Nguyen, N.; Raviram, R.; Erb, M.; Santini, J.; Luebeck, J.; Rajkumar, U.; Diao, Y.; Li, B.; et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 2019, 575, 699–703.
  9. Gaubatz, J.W. Extrachromosomal circular DNAs and genomic sequence plasticity in eukaryotic cells. Mutat. Res. 1990, 237, 271–292.
  10. Paulsen, T.; Kumar, P.; Koseoglu, M.M.; Dutta, A. Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells. Trends Genet. 2018, 34, 270–278.
  11. Shibata, Y.; Kumar, P.; Layer, R.; Willcox, S.; Gagan, J.R.; Griffith, J.D.; Dutta, A. Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science 2012, 336, 82–86.
  12. Moller, H.D.; Mohiyuddin, M.; Prada-Luengo, I.; Sailani, M.R.; Halling, J.F.; Plomgaard, P.; Maretty, L.; Hansen, A.J.; Snyder, M.P.; Pilegaard, H.; et al. Circular DNA elements of chromosomal origin are common in healthy human somatic tissue. Nat. Commun. 2018, 9, 1069.
  13. Turner, K.M.; Deshpande, V.; Beyter, D.; Koga, T.; Rusert, J.; Lee, C.; Li, B.; Arden, K.; Ren, B.; Nathanson, D.A.; et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 2017, 543, 122–125.
  14. Verhaak, R.G.W.; Bafna, V.; Mischel, P.S. Extrachromosomal oncogene amplification in tum.our pathogenesis and evolution. Nat. Rev. Cancer 2019, 19, 283–288.
  15. Shimizu, N.; Hanada, N.; Utani, K.; Sekiguchi, N. Interconversion of intra- and extra-chromosomal sites of gene amplification by modulation of gene expression and DNA methylation. J. Cell Biochem. 2007, 102, 515–529.
  16. Mitsuda, S.H.; Shimizu, N. Epigenetic Repeat-Induced Gene Silencing in the Chromosomal and Extrachromosomal Contexts in Human Cells. PLoS ONE 2016, 11, e0161288.
  17. Cremer, T.; Cremer, C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2001, 2, 292–301.
  18. Stephens, P.J.; Greenman, C.D.; Fu, B.; Yang, F.; Bignell, G.R.; Mudie, L.J.; Pleasance, E.D.; Lau, K.W.; Beare, D.; Stebbings, L.A.; et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 2011, 144, 27–40.
  19. Meyerson, M.; Pellman, D. Cancer genomes evolve by pulverizing single chromosomes. Cell 2011, 144, 9–10.
  20. Crasta, K.; Ganem, N.J.; Dagher, R.; Lantermann, A.B.; Ivanova, E.V.; Pan, Y.; Nezi, L.; Protopopov, A.; Chowdhury, D.; Pellman, D. DNA breaks and chromosome pulverization from errors in mitosis. Nature 2012, 482, 53–58.
  21. Zhang, C.Z.; Spektor, A.; Cornils, H.; Francis, J.M.; Jackson, E.K.; Liu, S.; Meyerson, M.; Pellman, D. Chromothripsis from DNA damage in micronuclei. Nature 2015, 522, 179–184.
  22. Hatch, E.M.; Fischer, A.H.; Deerinck, T.J.; Hetzer, M.W. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell 2013, 154, 47–60.
  23. Lusk, C.P.; King, M.C. Rotten to the Core: Why Micronuclei Rupture. Dev. Cell 2018, 47, 265–266.
  24. Okamoto, A.; Utani, K.I.; Shimizu, N. DNA replication occurs in all lamina positive micronuclei, but never in lamina negative micronuclei. Mutagenesis 2012, 27, 323–327.
  25. Utani, K.; Kawamoto, J.K.; Shimizu, N. Micronuclei bearing acentric extrachromosomal chromatin are transcriptionally competent and may perturb the cancer cell phenotype. Mol. Cancer Res. 2007, 5, 695–704.
  26. Ly, P.; Cleveland, D.W. Rebuilding Chromosomes After Catastrophe: Emerging Mechanisms of Chromothripsis. Trends Cell Biol. 2017, 27, 917–930.
  27. Taniguchi, R.; Utani, K.; Thakur, B.; Ishine, K.; Aladjem, M.I.; Shimizu, N. SIRT1 stabilizes extrachromosomal gene amplification and contributes to repeat-induced gene silencing. J. Biol. Chem. 2021, 296, 100356.
  28. Morton, A.R.; Dogan-Artun, N.; Faber, Z.J.; MacLeod, G.; Bartels, C.F.; Piazza, M.S.; Allan, K.C.; Mack, S.C.; Wang, X.; Gimple, R.C.; et al. Functional Enhancers Shape Extrachromosomal Oncogene Amplifications. Cell 2019, 179, 1330–1341.e13.
  29. Hamlin, J.L. Initiation of replication in mammalian chromosomes. Crit. Rev. Eukaryot. Gene Expr. 1992, 2, 359–381.
  30. Asoshina, M.; Myo, G.; Tada, N.; Tajino, K.; Shimizu, N. Targeted amplification of a sequence of interest in artificial chromosome in mammalian cells. Nucleic Acids Res. 2019, 47, 5998–6006.
  31. Ohira, T.; Miyauchi, K.; Uno, N.; Shimizu, N.; Kazuki, Y.; Oshimura, M.; Kugoh, H. An efficient protein production system via gene amplification on a human artificial chromosome and the chromosome transfer to CHO cells. Sci. Rep. 2019, 9, 16954.
  32. Garrick, D.; Fiering, S.; Martin, D.I.; Whitelaw, E. Repeat-induced gene silencing in mammals. Nat. Genet. 1998, 18, 56–59.
  33. Hsieh, J.; Fire, A. Recognition and silencing of repeated DNA. Annu. Rev. Genet. 2000, 34, 187–204.
  34. Reddy, B.D.; Wang, Y.; Niu, L.; Higuchi, E.C.; Marguerat, S.B.; Bahler, J.; Smith, G.R.; Jia, S. Elimination of a specific histone H3K14 acetyltransferase complex bypasses the RNAi pathway to regulate pericentric heterochromatin functions. Genes Dev. 2011, 25, 214–219.
  35. Kondo, Y.; Issa, J.P. Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. J. Biol. Chem. 2003, 278, 27658–27662.
  36. McBurney, M.W.; Mai, T.; Yang, X.; Jardine, K. Evidence for repeat-induced gene silencing in cultured Mammalian cells: Inactivation of tandem repeats of transfected genes. Expr. Cell Res. 2002, 274, 1–8.
  37. Henikoff, S. Conspiracy of silence among repeated transgenes. Bioessays 1998, 20, 532–535.
  38. Ogaki, Y.; Fukuma, M.; Shimizu, N. Repeat induces not only gene silencing, but also gene activation in mammalian cells. PLoS ONE 2020, 15, e0235127.
  39. Ohsaki, K.; Ohgaki, Y.; Shimizu, N. Amplification of a transgene within a long array of replication origins favors higher gene expression in animal cells. PLoS ONE 2017, 12, e0175585.
  40. L’Abbate, A.; Macchia, G.; D’Addabbo, P.; Lonoce, A.; Tolomeo, D.; Trombetta, D.; Kok, K.; Bartenhagen, C.; Whelan, C.; Palumbo, O.; et al. Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer. Nucleic Acids Res. 2014, 42, 9131–9145.
More
Information
Contributor :
View Times: 64
Revisions: 2 times (View History)
Update Time: 12 Oct 2021
Table of Contents

    Confirm

    Are you sure to Delete?

    Video Upload Options

    Do you have a full video?
    Cite
    If you have any further questions, please contact Encyclopedia Editorial Office.
    Shimizu, N. Gene Amplification. Encyclopedia. Available online: https://encyclopedia.pub/entry/14963 (accessed on 04 July 2022).
    Shimizu N. Gene Amplification. Encyclopedia. Available at: https://encyclopedia.pub/entry/14963. Accessed July 04, 2022.
    Shimizu, Noriaki. "Gene Amplification," Encyclopedia, https://encyclopedia.pub/entry/14963 (accessed July 04, 2022).
    Shimizu, N. (2021, October 12). Gene Amplification. In Encyclopedia. https://encyclopedia.pub/entry/14963
    Shimizu, Noriaki. ''Gene Amplification.'' Encyclopedia. Web. 12 October, 2021.
    Share
    Download
    Cite
    Top