1
|
Yan X, Mischel P, Chang H. Extrachromosomal DNA in cancer. Nat Rev Cancer 2024; 24:261-273. [PMID: 38409389 DOI: 10.1038/s41568-024-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Extrachromosomal DNA (ecDNA) has recently been recognized as a major contributor to cancer pathogenesis that is identified in most cancer types and is associated with poor outcomes. When it was discovered over 60 years ago, ecDNA was considered to be rare, and its impact on tumour biology was not well understood. The application of modern imaging and computational techniques has yielded powerful new insights into the importance of ecDNA in cancer. The non-chromosomal inheritance of ecDNA during cell division results in high oncogene copy number, intra-tumoural genetic heterogeneity and rapid tumour evolution that contributes to treatment resistance and shorter patient survival. In addition, the circular architecture of ecDNA results in altered patterns of gene regulation that drive elevated oncogene expression, potentially enabling the remodelling of tumour genomes. The generation of clusters of ecDNAs, termed ecDNA hubs, results in interactions between enhancers and promoters in trans, yielding a new paradigm in oncogenic transcription. In this Review, we highlight the rapid advancements in ecDNA research, providing new insights into ecDNA biogenesis, maintenance and transcription and its role in promoting tumour heterogeneity. To conclude, we delve into a set of unanswered questions whose answers will pave the way for the development of ecDNA targeted therapeutic approaches.
Collapse
Affiliation(s)
- Xiaowei Yan
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Howard Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
2
|
Herrera-Moreno JF, Prada D, Baccarelli AA. Early Environment and Telomeres: a Long-Term Toxic Relationship. Curr Environ Health Rep 2023; 10:112-124. [PMID: 36944821 PMCID: PMC10849088 DOI: 10.1007/s40572-023-00395-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 03/23/2023]
Abstract
PURPOSE OF REVIEW Telomere length (TL) shortening is a hallmark of biological aging. While studies have extensively focused on the impact of environmental exposures on TL in older populations, consistent evidence indicates that prenatal environmental exposures to air pollutants, polycyclic aromatic hydrocarbons, metals, and endocrine-disrupting chemicals influence TL shortening. Here, we summarize evidence linking prenatal environmental exposures with children's TL and discuss potential long-term effects. RECENT FINDINGS Current evidence shows that prenatal environmental exposures alter TL and identify pregnancy as a critical window of susceptibility for telomere damage in children. However, results vary across studies, possibly depending on the source, exposure time window, and stage evaluated. Additional research is needed to investigate whether early TL alterations mediate long-term health effects of offspring. Prenatal environmental exposures induce early childhood changes in TL. Based on known links between TL and biological aging, these alterations may have long-term impact on individuals' health throughout life.
Collapse
Affiliation(s)
- José Francisco Herrera-Moreno
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168Th Street, Suite 1105E, New York, NY, 10032, USA
| | - Diddier Prada
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168Th Street, Suite 1105E, New York, NY, 10032, USA
- Instituto Nacional de Cancerología - México, 14080, Mexico City, Mexico
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168Th Street, Suite 1105E, New York, NY, 10032, USA.
| |
Collapse
|
3
|
Lysak MA. Celebrating Mendel, McClintock, and Darlington: On end-to-end chromosome fusions and nested chromosome fusions. THE PLANT CELL 2022; 34:2475-2491. [PMID: 35441689 PMCID: PMC9252491 DOI: 10.1093/plcell/koac116] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/13/2022] [Indexed: 05/04/2023]
Abstract
The evolution of eukaryotic genomes is accompanied by fluctuations in chromosome number, reflecting cycles of chromosome number increase (polyploidy and centric fissions) and decrease (chromosome fusions). Although all chromosome fusions result from DNA recombination between two or more nonhomologous chromosomes, several mechanisms of descending dysploidy are exploited by eukaryotes to reduce their chromosome number. Genome sequencing and comparative genomics have accelerated the identification of inter-genome chromosome collinearity and gross chromosomal rearrangements and have shown that end-to-end chromosome fusions (EEFs) and nested chromosome fusions (NCFs) may have played a more important role in the evolution of eukaryotic karyotypes than previously thought. The present review aims to summarize the limited knowledge on the origin, frequency, and evolutionary implications of EEF and NCF events in eukaryotes and especially in land plants. The interactions between nonhomologous chromosomes in interphase nuclei and chromosome (mis)pairing during meiosis are examined for their potential importance in the origin of EEFs and NCFs. The remaining open questions that need to be addressed are discussed.
Collapse
Affiliation(s)
- Martin A Lysak
- CEITEC—Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| |
Collapse
|
4
|
Jespersen N, Monrroy L, Barandun J. Impact of Genome Reduction in Microsporidia. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 114:1-42. [PMID: 35543997 DOI: 10.1007/978-3-030-93306-7_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microsporidia represent an evolutionary outlier in the tree of life and occupy the extreme edge of the eukaryotic domain with some of their biological features. Many of these unicellular fungi-like organisms have reduced their genomic content to potentially the lowest limit. With some of the most compacted eukaryotic genomes, microsporidia are excellent model organisms to study reductive evolution and its functional consequences. While the growing number of sequenced microsporidian genomes have elucidated genome composition and organization, a recent increase in complementary post-genomic studies has started to shed light on the impacts of genome reduction in these unique pathogens. This chapter will discuss the biological framework enabling genome minimization and will use one of the most ancient and essential macromolecular complexes, the ribosome, to illustrate the effects of extreme genome reduction on a structural, molecular, and cellular level. We outline how reductive evolution in microsporidia has shaped DNA organization, the composition and function of the ribosome, and the complexity of the ribosome biogenesis process. Studying compacted mechanisms, processes, or macromolecular machines in microsporidia illuminates their unique lifestyle and provides valuable insights for comparative eukaryotic structural biology.
Collapse
Affiliation(s)
- Nathan Jespersen
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden.
| | - Leonardo Monrroy
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden.
| |
Collapse
|
5
|
Liu Y, Wang J, Huang Z, Liang J, Xia Q, Xia Q, Liu X. Environmental pollutants exposure: A potential contributor for aging and age-related diseases. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 83:103575. [PMID: 33385577 DOI: 10.1016/j.etap.2020.103575] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/13/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Telomeres are "protective messengers" at the ends of eukaryotic chromosomes that protect them from degradation, end to end fusion and recombination. Admittedly, telomeres progressively shorten with age that can also be significantly accelerated by pathological conditions, which are often considered as potential contributors for cellular senescence. It is commonly believed that constant accumulation of senescent cells may lead to dysfunctional tissues and organs, thereby accelerating aging process and subsequent occurrence of age-related diseases. In particular, epidemiological data has indicated a significant association between environmental pollutants exposure and a high incidence of age-related diseases. Moreover, there is growing evidence that environmental toxicity has a detrimental impact on telomere length. Overall, a consensus is emerging that environmental pollutants exposure could lead to accelerated telomere erosion and further induce premature senescence, which may be responsible for the acceleration of aging and the high morbidity and mortality rates of age-related diseases.
Collapse
Affiliation(s)
- Yaru Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui, 230022, China
| | - Jiequan Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui, 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui, 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui, 230000, China
| | - Zhaogang Huang
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui, 230022, China
| | - Jun Liang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui, 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui, 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui, 230000, China
| | - Qingrong Xia
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui, 230000, China; Department of Pharmacy, Anhui Mental Health Center, Hefei, Anhui, 230000, China; Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, Anhui, 230000, China
| | - Quan Xia
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui, 230022, China.
| | - Xinhua Liu
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China.
| |
Collapse
|
6
|
Engin AB, Engin A. The Connection Between Cell Fate and Telomere. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1275:71-100. [PMID: 33539012 DOI: 10.1007/978-3-030-49844-3_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abolition of telomerase activity results in telomere shortening, a process that eventually destabilizes the ends of chromosomes, leading to genomic instability and cell growth arrest or death. Telomere shortening leads to the attainment of the "Hayflick limit", and the transition of cells to state of senescence. If senescence is bypassed, cells undergo crisis through loss of checkpoints. This process causes massive cell death concomitant with further telomere shortening and spontaneous telomere fusions. In functional telomere of mammalian cells, DNA contains double-stranded tandem repeats of TTAGGG. The Shelterin complex, which is composed of six different proteins, is required for the regulation of telomere length and stability in cells. Telomere protection by telomeric repeat binding protein 2 (TRF2) is dependent on DNA damage response (DDR) inhibition via formation of T-loop structures. Many protein kinases contribute to the DDR activated cell cycle checkpoint pathways, and prevent DNA replication until damaged DNA is repaired. Thereby, the connection between cell fate and telomere length-associated telomerase activity is regulated by multiple protein kinase activities. Contrarily, inactivation of DNA damage checkpoint protein kinases in senescent cells can restore cell-cycle progression into S phase. Therefore, telomere-initiated senescence is a DNA damage checkpoint response that is activated with a direct contribution from dysfunctional telomeres. In this review, in addition to the above mentioned, the choice of main repair pathways, which comprise non-homologous end joining and homologous recombination in telomere uncapping telomere dysfunctions, are discussed.
Collapse
Affiliation(s)
- Ayse Basak Engin
- Department of Toxicology, Faculty of Pharmacy, Gazi University, Ankara, Turkey.
| | - Atilla Engin
- Department of General Surgery, Faculty of Medicine, Gazi University, Ankara, Turkey
| |
Collapse
|
7
|
Shumate A, Zimin AV, Sherman RM, Puiu D, Wagner JM, Olson ND, Pertea M, Salit ML, Zook JM, Salzberg SL. Assembly and annotation of an Ashkenazi human reference genome. Genome Biol 2020; 21:129. [PMID: 32487205 PMCID: PMC7265644 DOI: 10.1186/s13059-020-02047-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/15/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population. There is a need for reference genomes from multiple human populations to avoid potential biases. RESULTS Here, we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more complete than GRCh38, the latest version of the human reference genome, and is annotated with highly similar gene content. The Ashkenazi reference genome, Ash1, contains 2,973,118,650 nucleotides as compared to 2,937,639,212 in GRCh38. Annotation identified 20,157 protein-coding genes, of which 19,563 are > 99% identical to their counterparts on GRCh38. Most of the remaining genes have small differences. Forty of the protein-coding genes in GRCh38 are missing from Ash1; however, all of these genes are members of multi-gene families for which Ash1 contains other copies. Eleven genes appear on different chromosomes from their homologs in GRCh38. Alignment of DNA sequences from an unrelated Ashkenazi individual to Ash1 identified ~ 1 million fewer homozygous SNPs than alignment of those same sequences to the more-distant GRCh38 genome, illustrating one of the benefits of population-specific reference genomes. CONCLUSIONS The Ash1 genome is presented as a reference for any genetic studies involving Ashkenazi Jewish individuals.
Collapse
Affiliation(s)
- Alaina Shumate
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Aleksey V Zimin
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Rachel M Sherman
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Daniela Puiu
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Justin M Wagner
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nathan D Olson
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Marc L Salit
- Joint Initiative for Metrology in Biology, Stanford University, Stanford, CA, USA
| | - Justin M Zook
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
8
|
Stroik S, Kurtz K, Hendrickson EA. CtIP is essential for telomere replication. Nucleic Acids Res 2019; 47:8927-8940. [PMID: 31378812 PMCID: PMC6755089 DOI: 10.1093/nar/gkz652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/08/2019] [Accepted: 07/16/2019] [Indexed: 01/10/2023] Open
Abstract
The maintenance of telomere length is critical to longevity and survival. Specifically, the failure to properly replicate, resect, and/or form appropriate telomeric structures drives telomere shortening and, in turn, genomic instability. The endonuclease CtIP is a DNA repair protein that is well-known to promote genome stability through the resection of endogenous DNA double-stranded breaks. Here, we describe a novel role for CtIP. We show that in the absence of CtIP, human telomeres shorten rapidly to non-viable lengths. This telomere dysfunction results in an accumulation of fusions, breaks, and frank telomere loss. Additionally, CtIP suppresses the generation of circular, extrachromosomal telomeric DNA. These latter structures appear to arise from arrested DNA replication forks that accumulate in the absence of CtIP. Hence, CtIP is required for faithful replication through telomeres via its roles at stalled replication tracts. Our findings demonstrate a new role for CtIP as a protector of human telomere integrity.
Collapse
Affiliation(s)
- Susanna Stroik
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Kevin Kurtz
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| |
Collapse
|
9
|
Günes C, Wezel F, Southgate J, Bolenz C. Implications of TERT promoter mutations and telomerase activity in urothelial carcinogenesis. Nat Rev Urol 2019; 15:386-393. [PMID: 29599449 DOI: 10.1038/s41585-018-0001-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Telomerase activity imparts eukaryotic cells with unlimited proliferation capacity, one of the cancer hallmarks. Over 90% of human urothelial carcinoma of the bladder (UCB) tumours are positive for telomerase activity. Telomerase activation can occur through several mechanisms. Mutations in the core promoter region of the human telomerase reverse transcriptase gene (TERT) cause telomerase reactivation in 60-80% of UCBs, whereas the prevalence of these mutations is lower in urothelial cancers of other origins. TERT promoter mutations are the most frequent genetic alteration across all stages of UCB, indicating a strong selection pressure during neoplastic transformation. TERT promoter mutations could arise during regeneration of normal urothelium and, owing to consequential telomerase reactivation, might be the basis of UCB initiation, which represents a new model of urothelial cancer origination. In the future, TERT promoter mutations and telomerase activity might have diagnostic and therapeutic applications in UCB.
Collapse
Affiliation(s)
- Cagatay Günes
- Department of Urology, University of Ulm, Ulm, Germany.
| | - Felix Wezel
- Department of Urology, University of Ulm, Ulm, Germany
| | - Jennifer Southgate
- Department of Biology, Jack Birch Unit of Molecular Carcinogenesis, University of York, York, UK
| | | |
Collapse
|